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Primate MHC class I from Genomes

D.N. Olivieri 1 , F. Gambón-Deza 2
1 Department of Computer Science, University of Vigo, Ourense 32004, Spain
2 Department of Immunology, Hospital of Meixoiero, Vigo, SPAIN
olivieri@uvigo.es; fgambon@gmail.com

Abstract
The major histocompatibility complex (MHC) molecule plays a central role in the adaptive im-
munity of jawed vertebrates. Allelic variations have been studied extensively in some primate
species, however a comprehensive description of the number of genes remains incomplete. Here,
a bioinformatics program was developed to identify three MHC Class I exons (EX2, EX3 and
EX4) from Whole Genome Sequencing (WGS) datasets. With this algorithm, MHC Class I exons
sequences were extracted from 30 WGS datasets of primates, representatives of Apes, Old World
and New World monkeys and prosimians. There is a high variability in the number of genes be-
tween species. From human WGS, six viable genes (HLA-A, -B, -C, -E, -F, and -G) and four
pseudogene sequences (HLA-H, -J, -L, -V) are obtained. These genes serve to identify the phy-
logenetic clades of MHC-I in primates. The results indicate that human clades of HLA-A -B and
-C were generated shortly after the separation of Old World monkeys. The clades pertaining to
HLA-E, -H and -F are found in all primate families, except in Prosimians. In the clades defined by
HLA-G, -L and -J, there are sequences from Old world monkeys. Specific clades are found in the
four primate families. The evolution of these genes is consistent with birth and death processes
having a high turnover rates.
Keywords: Major Histocompatibility Complex, MHC Evolution, Immunologic Repertoire,
Mammalian Evolution, Gene Discovery

1. Introduction originally studied as the cause of transplant

The Major Histocompatibility Complex
(MHC) molecules are amongst the most in-
tensely studied of the adaptive immune sys-
tem, especially in primates and the mouse
since they are responsible for transplant re-
jection and antigen presentation. These
molecules were first discovered in humans on
the surface of leukocyte membranes and were
given the name HLA (Human Leukocyte Anti-
gen). Although the molecules of MHC were
Preprint submitted to Elsevier
rejection, their primary function is in the de-
fense of the organism against pathogens. The
molecule of MHC class I presents endogenous
antigen to the CD8+ T lymphocytes and the
MHC class II presents exogenous antigens to
the CD4+ T lymphocytes. Other molecules
related to these pathways are present in the
same chromosome MHC regions, sometimes
referred to collectively as the MHC class III
genes (i.e., complement proteins, cytokines,
February 15, 2018
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etc.), although this is a nomenclature that is
simply used to make a distinction from the
MHCI and MHCII genes.
MHC class I (MHC-I) are encoded by genes
with at least 6 exons. The exons of particular
interest are exons-2 and -3 (EX2 and EX3, re-
spectively) encoding the protein domains α1
and α2, that are responsible for presenting
peptides to TCR. These domains also repre-
sent regions of the highest allelic variation.
These genes are essential for the innate and
adaptive immune responses and are subject to
environmental and evolutionary pressures to-
gether with likely coevolution effects through
their interaction with TCR and KIR (de Groot
et al., 2015; Garcia et al., 2009).
In humans, the MHC-I region consists of
six genes. The HLA-A, -B and -C genes are
highly polymorphic and are expressed by all
cells. These molecules are considered the clas-
sical MHC-I molecules and their role is to
present peptides to cytotoxic T lymphocytes.
Unlike the classical MHC genes, the non-
classical genes, HLA-E, -F and -G, exhibit
limited polymorphism. In particular, HLA-E
is a CD94/NKG2A ligand, HLA-G cells are
found only in the trophoblast (Castro et al.,
1996; Djurisic & Hviid, 2014; Lynge-Nilsson
et al., 2014) and HLA-F is involved in NK cell
signaling (Lee et al., 2010). Both HLA-F and
HLA-G are expressed by a restricted set of cell
populations.
Apart from these MHC-I genes in humans,
complete genes have been identified that are
not expressed because of different causes:
some are pseudogenes (e.g., the known pseu-
dogenes HLA-H, -K, -J and -L) (Moscoso
et al., 2006; Heinrichs & Orr, 1990) as well as
individual MHC-like exons that are not found
in tandem with other valid structural exons
(e.g., those possessing stop-codons) needed
to form functional MHC-I molecule (Horton
et al., 2004).
2
All humans possess the haplotype with six
MHC-I expressed genes. Orthologs to these
haplotypes have been sought in Apes, Old
World, and New World monkeys. Previous
studies have described MHC-I genes ortholo-
gous to those in humans, and the human pseu-
dogene, HLA-H, is actually a viable MHC-
I gene in chimpanzees and gorillas (Wilming
et al., 2013). At present, there are detailed de-
scriptions of the MHC loci in Apes, but few
such descriptions in evolutionarily more dis-
tant primates. For these more distant primate
species, several RNA studies have attempted
to characterize allelic variability (de Groot
et al., 2012). Nonetheless, these sequences
have not been studied within the context of the
germline MHC genes from all these species.
In recent years, genome sequences of pri-
mates have become publicly available in the
form of assembled WGS datasets. These
assemblies consist of relatively large con-
tigs containing most of the genomic se-
quences. In this paper, we describe the anal-
ysis of MHC-I exon sequences EX2, EX3
and EX4 from primates that were identified
from WGS data using a new bioinformat-
ics tool, called MHCfinder, freely availble
at http://vgenerepertoire.org/. The primate
datasets we utilized in this study are indi-
cated in the phylogenetic ordering of 1, ob-
tained from molecular studies Perelman et al.
(2011); Rogers & Gibbs (2014) and diver-
gence times further confirmed with sets of
published works summarized by TimeTree
(Hedges et al., 2006). From the sequences
found by MHCfinder, this wealth of de-
tailed genomic information may help to clar-
ify evolutionary processes that have shaped the
MHC-I genes in primates.
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Eulemur flavifrons (LGHW01)

Lemuriformes Lemuroidea Eulemur macaco (LGHX01)
Propithecus coquereli (JZKE01)
Microcebus murinus (ABDC02)
Lorisiformes
Lorisoidea Otolemur garnettii (AAQR03)

Tarsiformes Tarsiidae Tarsius syrichta (ABRT02 )

s )
m ian rhini
i
os sir
Cebus capucinus (LVWQ01)
Ceboidea
Pr trep
Aotus nancymaae (JYKP01)
Callithrix jacchus (ACFV01, BBXK01)
(S Saimiri boliviensis (AGCE01)

A Nasalis larvatus (JMHX01)

(H nthr New World primates Colobus angolensis (JYKR01)
es

ap op Rhinopithecus roxellana (JABR01)

in

lor oid Mandrillus leucophaeus (JYKQ01)

rrh

hin s Chlorocebus sabaeus (AQIB01)

es) Cercopithecoidea
aty

Macaca fascicularis (AQIA01)

Pl

mo Macaca mulatta (JSUE03, AANU01)

nk 43.1 Mya
Macaca nemestrina (JZLF01)
ey Ca Cercocebus atys (JZLG01)
s an tar
da rhi Papio anubis (AHZZ01)
pe ne
s s 27.3-35 Mya Homo sapiens (ABBA01)
Pan troglodytes (AADA01, AACZ04)
Hominoidea Pan paniscus (AJFE02)
Old World primates Gorilla gorilla (CABD03, CYUI03)
Pongo abelii (ABGA01)
60 40 20 0 Mya Nomascus leucogenys (ADFV01)

Eocene Oligocene Milocene

Holocene

Figure 1: The phylogenetic tree of the primates indicating the species studied in this work. The tree is based upon
divergence times obtained from (Hedges et al., 2006), and previous molecular phylogenetic studies Perelman et al.
(2011); Rogers & Gibbs (2014).

2. Methods genes varies considerably across other mam-

2.1. Datasets
The WGS assembly datasets of 30 primate
species were obtained from the NCBI in the
form of FASTA files consisting of assembled
contigs, or for more mature projects, scaffolds
and/or fully constructed chromosomes. The
average genome coverage in these datasets is
> 15−20× with contig assembly N50 > 15kbs.
A detailed summary of the accession num-
bers and relevant assembly parameters can be
found in Table 1.
2.2. Software
While there are six viable MHC-I genes
in Homo sapiens, the number of MHC-I
3
mal species. Nonetheless, the MHC-I exon ar-
chitecture is nearly universal across all mam-
mal species (Birch et al., 2006). A diagram of
the Homo sapiens MHC-I (HLA) exon struc-
ture and corresponding protein domains was
described (Lefranc et al., 2005) (see also se-
quence repositories of the by the IMGT) and
the a large collection of MHC-I alleles at the
IPD-MHC database (Robinson et al., 2011).
The relevant genomic signals (i.e., the exons,
introns, 50 -URT and 30 -URT) can be identi-
fied to a high degree of accuracy without re-
sorting to general gene finding software tools.
Therefore, viable exons (i.e., those exons that
could form a functionally expressed MHC-I
molecule) can be accurately determined using
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All rights reserved. No reuse allowed without permission.
homology criteria with a supervised machine
learning classifier.
The MHCfinder program extracts exons
EX2 and EX3 that encode the α1 and α2
domains, respectively, together with exon
EX4 that encodes the constant domain. Al-
though other exons constitute the full MHC-
I gene, these three exons are of particular in-
terest for characterizing and comparing MHC-
I genes within and amongst species. Thus,
MHCfinder ignores the peptide leader (L)
(given by EX1), as well as all peptides cor-
responding to the transmembrane and cyto-
plasmic (T m , indicated by EX5 through EX8).
While the exon/intron structure of MHC Class
I is thought to be universal across jawed ver-
tebrates, the specific intron spacing between
the exon sequences EX2, EX3, and EX4 varies
considerably. As such, the algorithm only
imposes a simple structural requirement that
EX2, EX3 and EX4 are found in a tandem
arrangement along the DNA sequence, but
places no hard restrictions on the intron sep-
aration.
Figure 2 summarizes the principal steps of
the MHCfinder algorithm. This program was
implemented as a multi-threaded application
in the python programming language, with the
biopython library (Cock et al., 2009) for low-
level sequence analysis, and the scikits library
(Pedregosa et al., 2011) for machine learning
tasks. First, a Tblastn query from a consensus
protein sequences from known MHC-I exons
(EX2, EX3, and EX4 from humans) is made
against all available primate WGS datasets.
The search result is a listing of candidate WGS
contigs likely to contain valid exons, together
with the position of the matching nucleotide
sequence and similarity scores; this listing is
referred to as a hit table. The algorithm pro-
cesses each line of the hit table, analyzing a
nucleotide region larger than the nucleotide
positions in the hit, so as to determine the pre-
4
cise start/stop positions of the exon reading-
frame (defined by AG and GT motifs, respec-
tively). Once the exons are identified, they are
translated into amino acid sequences by check-
ing all valid reading frames. Those sequences
containing stop-codons in the reading frame
are discarded, while valid exons are saved and
converted into numerical feature vectors (i.e.,
a unique array of numbers, that uniquely char-
acterizes the string of amino acids). A sim-
ple transformation of AA to feature vector was
used (based upon the frequency of each AA
and pairs of AA), because it was found to
discriminate sequences better than other more
sophisticated transformation procedures (e.g.,
those based upon positional physicochemical
properties of each AA within the sequence).
From the feature vector representation, a
machine learning procedure with a Random
Forest (Breiman, 2001) was used to classify
the sequence into one of the exon types: EX2,
EX3, and EX4. Supervised training is per-
formed by defining these classes with sets of
annotated exons from H. sapiens and defin-
ing a null set from a random background se-
quences. Binary classification is carried out
for each exon type with a background/signal
ratio of 3:1, determined empirically. The
prediction precision is improved by multiple
training/prediction iterations; positively iden-
tified sequences are included in the training
set for subsequent training/predictions. This
process is referred to as iterative supervised
learning, and is a common machine learning
technique whereby new information is con-
tinually accrued to the knowledge base for
improving prediction accuracy (e.g., modern
speech recognition has benefited from such
techniques).
In our gene finding algorithm, MHCfinder,
a probable functionally expressed MHC-I gene
that must contain a tandem arrangement of
the three viable exons (i.e. those that do not
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2. tblastn WGS Datasets

1. HLA class I query
query sequence restricted search for
Primates
g e
nti me ion alu or
e
co fra reg ev sc
1 AANU01104903.1 54.2 65.25 0/-3...979 668 4.69e-29 115
2 AANU01018014.1 52.5 64.41 0/-1...577 269 5.87e-29 112
tblastn Hit table 3 AANU01104950.1 52.5 65.25 0/2 3635 3943 6.24e-29 115

.....

N ABSL01193118.1 60.4 72.92 0/2 2 145 2.08e-05 56.6

3. Loop over tblastn hit table results
tblastn hit table results

Exon defined between AG and GT

3.A Find exon in larger contig region R AAAGCTTCCTCA...TTTCAATCGTAGA
specified by hit coordinates
exon

3.B a)Translate NN sequence to AA; NNseq= TCCTCA ... TTTCAAT

b) Translate AA sequence to feature AAseq= SHSLRYFHT ...LPEPLTLRW

vector

FeatVec= 0,1,5,9,2,8,15,0,0,1...

3.C Use Random Forest to classify

valid exons EX2, EX3, and EX4
4
2

yes valid MHC-I gene

EX
EX

EX

(if valid, add to list) (tandem EX arrangement)

EX2 EX4 pseudogene

(e.g., here missing EX3)
no
EX2 EX3
end

EX3 EX2
4. From positive exons, determine structure "indeterminate" examples
(valid gene, pseudogene, or undertermined) (at end or start of contig)
EX4 EX3
end

Figure 2: The steps in the MHC-I prediction algorithm. The selection of valid MHC-I exons is based upon a Tblastn
pre-selection, an exon reading-frame identification procedure, and classification with a random forest method.

contain stop codons in the reading frame),
EX2-EX3-EX4 along the germline sequence.
Nonetheless, viable exons, which are homolo-
gous to MHC-I constituent exons, exist in the
genome that do not form tandem arrangements
(i.e., they are isolated or an exon is missing),
and thus, do not express MHC-I molecules. In
5
humans, we found 31 exons, 18 of which are
constituents of six functional MHC-I genes;
the other exons while viable, must be pseudo-
genes. Similar results are seen in all the other
species studied.
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Tree construction. To study the phylogenetic
relationships from the MHC-I exons, we con-
structed a large phylogenetic tree by align-
ing sequences with ClustalO and then used
phyML with the WAG matrix (part of the Fast-
tree software (Price et al., 2010)). In all cases,
500 bootstrapped samples were made. While
trees were studied using the three exon se-
quences (EX2-EX3-EX4), the final analysis
was made only with EX2, since this exon pro-
vides the most discriminatory information.
3. Results
Exon sequences EX2, EX3 and EX4 of
MHC-I were obtained from 30 WGS primate
datasets using our software tool, MHCfinder,
described in the Methods section. These se-
quences are homologous to the human MHC-
I and were found by an iterative supervised
learning procedure (Methods). As described,
these sequences are flanked by splicing sig-
nals AG/GT and have an ORF starting two nu-
cleotides after the AG and terminating one nu-
cleotide before the last GT. Exons are consid-
ered correct if these conditions are met, while
exons possessing stop codons within the read-
ing frame are discarded. Those exons found
in a tandem arrangement (i.e. with EX2-EX3-
EX4 and with nominal intron spacing) are con-
sidered candidate MHC-I genes (referred to as
probably viable genes throughout the rest of
the paper, since they have the necessary con-
ditions to be expressed). Valid exons that do
not participate in a tandem arrangement are
considered probable pseudogenes (referred as
pseudogenes throughout) or indeterminate if
they are found at the extreme ends of the con-
tigs (referred to throughout the text as indeter-
minate). Figure 3 shows graphical maps of the
MHC-I exons found in contigs of G. gorilla.
The exons found in tandem configurations,
EX2-EX3-EX4, are indicated as probably vi-
6
able MHC-I genes. Table 1 lists the number of
exons and candidate viable genes per species
found from different WGS datasets. Differ-
ences in the number of exons between WGS
datasets from the same species is indicative of
the variability between individuals of the same
species, as well as maturity/completeness and
sequencing methods used in constructing the
assemblies.
At present, there are 42 WGS of Homo
sapiens in the NCBI repository. From these
datasets, MHCfinder was used to find all
MHC-I exon sequences and the phylogenetic
tree of Figure 4 was constructed using the de-
duced amino acid sequences of EX2. The pro-
gram tags the EX2 sequence as belonging to
one of the following categories: (1) a proba-
ble expressed MHC-1 gene (since it is part of
a tandem arrangement EX2-EX3-EX4), (2) a
pseudogene (because it lacks either EX3, EX4
or both), or (3) an indeterminate gene (because
it is found at the extreme edge the contig, but
could form a viable gene; see graphic of Fig-
ure 2). In the resulting tree, six viable genes
(HLA-A, -B, -C, -E, -F and -G) and four pseu-
dogenes (HLA-H, -J, -L and -V) can be dis-
cerned. Also, the tree demonstrates that con-
siderable variability exists amongst the clas-
sic genes (A, B, and C), forming several lin-
eages. However, with respect to the nonclas-
sical genes (E, F, and G), the sequences are
invariable. Also, the known pseudogene se-
quences, L, J and V are conserved, while the H
pseudogene form separate lineages; this may
be related to its proximity to the HLA-A locus
(Grimsley et al., 1998).
Hominidae diversified approximately 20
(Million years ago) Mya. Eight WGS datasets
were used to study the MHC-I exons from the
Ape family; the number of exons identified
from the WGS of Ape species is provided in
Table 1. The number of probable viable genes
per species is between two and eight. The
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Table 1: MHC classI Exons and genes of Primates. All values for the contig N50 were > 15kbp, except N. larvatus
(for which no exons were found). For some assemblies, a reliable number for the coverage could not be ascertained,
and are indicated by N/A (not available).
Species WGS N50(kbp) Cov. EX2 EX3 EX4 Genes
Lemuriformes
E. flavifrons LGHW01 27.3 52x 1 1 1 1
E. macaco LGHX01 20.0 21x 1 0 1 0
P. coquereli JZKE01 28.1 104.7x 6 6 7 6
M. murinus ABDC02 182.9 221.6x 9 10 9 6
Lorisiformes
O. garnettii AAQR03 27.1 137x 13 11 13 8
Tarsiformes
T. syrichta ABRT02 38.2 48x 7 8 10 5
Platyrrhini
C. capucinus LVWQ01 41.2 81x 23 20 24 15
A. nancymaae JYKP01 28.5 113.4x 28 32 28 12
C. jacchus ACFV01 29.3 6.6x 22 20 20 13
C. jacchus BBXK01 61 N/A 5 6 8 3
S. boliviensis AGCE01 38.8 80x 15 17 22 8
Cercopithecoidea
N. larvatus JMHX01 13.3 290 - - - -
C. angolensis JYKR01 38.4 86.8x 8 8 10 4
R. roxellana JABR01 77.2 53.7x 20 14 22 8
M. leucophaeus JYKQ01 31.3 117.2x 6 7 16 3
C. sabaeus AQIB01 90.4 95x 9 10 10 6
M. fascicularis AQIA01 86 68x 17 19 21 12
M. mulatta JSUE03 107 47.4x 31 28 32 17
M. mulatta AANU01 25.7 N/A 26 34 32 17
M. nemestrina JZLF01 107 113.1x 24 20 28 12
C. atys JZLG01 113 192.0x 24 19 22 12
P. anubis AHZZ01 40.3 92x 30 21 20 16
Apes
H. sapiens ABBA01 100 13 8 10 6
P. troglodytes AADA01 108.4 N/A 9 8 6 3
P. troglodytes AACZ04 384.8 70x 12 10 10 8
P. paniscus AJFE02 67 26x 10 8 8 6
G. gorilla CABD03 53 N/A 10 9 8 5
G. gorilla CYUI03 ¿1000 NA/ 7 11 8 5
P. abelii ABGA01 15.6 6x 13 10 9 3
N. leucogenys ADFV01 35 5.6x 6 6 5 2

7
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All rights reserved. No reuse allowed without permission.

EX2 EX4
HLA-V

2
EX
HLA-J

EX2
HLA-H

4
EX

4
2

EX
EX

3
EX
HLA-H

2
EX
HLA-F

3
EX
EX 2

4
EX3
EX

HLA-G

4
EX 2
3
EX
EX
HLA-E
3
4

2
EX
EX

EX

HLA-C
3
EX
4
3

EX
EX

2
3
EX

EX
EX

HLA-B

3
2

EX
EX

HLA-H

Figure 3: Graphical representation of the MHC-I exons obtained in G. gorilla (CABD03) with the MHCfinder pro-
gram. Each contig is represented by a line and exons by boxes. Tandem exon arrangements (EX2-EX3-EX4) are
colored blue, indicating the high possibility of being a viable and functionally expressed MHC-I gene (explained in
text). Exons not part of tandem arrangements, thus indicative of pseudogenes, are marked in red. Exons that are found
at the extreme ends of the contigs may be considered indeterminate if they could form tandem arrangements with
exons in other contigs (colored in light blue).

presence of pseudogenes is demonstrated by study (Daza-Vamenta et al., 2004)) (Table 1).

the existence of more exons than needed for
the viable genes.
The Cercopithecus family consists of mon-
keys closest to hominids and are also referred
to as Old World monkeys. The divergence
time between Cercopithecidae and Hominidae
is approximately 29Mya. The number of
MHC-I genes in these animals varies consid-
erably; between four in C. angolensis and 18
in M. Mulatta (22 were found in a detailed
8
In general, the Cercopithecus species possess
more MHC-I genes than found in Hominidae
species.
The Platyrrhines are monkeys of South and
Central America. These species diverged
from hominids approximately 43 Mya. Five
WGS datasets of Platyrrhines were analyzed
to identify MHC-I genes and pseudogenes us-
ing MHCfinder. The number of viable MHC-I
genes found is between nine (in S. bolivien-
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All rights reserved. No reuse allowed without permission.

Homo_sapiens-LRUM01-EX2-198|Pseu/1-89

s-LO QL0 1-EX -246| Pseu/ 1-89

Homo_ sapien s-LOQ

-EX2-22 0|Pseu/ 1-89

-89

Ho mo ap ien s-A BB A0 1-E X2 -27 Pse u/1 -89

Homo_sapien s-JSAF02-EX2 -206|Pseu/1-8 9
Homo_sapiens-LRUL0 1-EX2-188|Pseu/1-89
Homo_sap iens-LIQK 02-EX2-18 |Pseu/ 1-89
Hom o_sa piens
Hom o_s apie

ap ien s-AAA DD 01- EX 2-2 71| seu /1-8 9

-89
Ho mo _sa ien s-L BL P0 1-E

-8 9
C o n se n supi en s- A D D F0 2- E 2- 30 6| Ps u/ 1- 89
se u/1 -89
Ho m o_

Hom o_s api

Ho mo _s pi en s- LD OC 01 -E X2 88 |P se u/
Ho mo _s ien s-L BH Z0 -E X2 -1 12 Ps eu /1 -889

3 /1 -8 30 8| P se t/ 1- 89
7| In de /1 -8 9
2-24 8|Ps eu/1

1- 89
H om o_ sa pi en s-

2|P se u/1
H om

01 -E X2 30 4| In de t/1
H om _ sa p ie n L K H W 0 1 -E X 22 -3 8 |P s e u /1 -8 9
H o m _ sa p ie n ie n s -L J C 0 1 -E XX 2 -2 8 |P s e uu /1 -88 9
H o m m o _ s a n s -L M B D 0 1 -E

9
u/
eu

H oo m o _ s a p ie n s -L B H Z 0 2 3 -1 1 4 H C /1 s e u /1 -8
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Figure 4: The phylogenetic tree of 333 EX2 sequences of MHC-I found with our |MHCfinder— algorithm from the
42 WGS datasets of Homo sapiens. The probable viable genes are colored in blue, pseudogenes are colored red, and
those genes that are indeterminate are colored light blue. The sequences in brown correspond to consensus sequences
that are used to identify clades. The nodes of the principal clades have been labeled. The tree was constructed after
aligning sequences with ClustalO and using the phyML (part of the Fasttree software (Price et al., 2010)) with the
gamma parameter, WGS matrix, and 500 bootstrapped samples.

sis) and 15 (in C. capucinus). Lemuriformes cause these sequenced assemblies are still in a
and Tarsiiformes represent the oldest extant nascent stage.
primates that diverged from other primates
approximately 76 Mya. Compared to other Using MHCfinder, 20 WGS datasets from
taxa of this study, few exons were found from the Simians family (not including humans)
the datasets of Eulemur species, perhaps be- were studied, from which 210 viable genes
were found. Of the 3 MHC-I exons stud-
9
bioRxiv preprint first posted online Feb. 15, 2018; doi: http://dx.doi.org/10.1101/266064. The copyright holder for this preprint
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
All rights reserved. No reuse allowed without permission.

t/1- 89

|M HC /1Ind et/ 1-8 9

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Callithrix_jacchus-ACFV01-EX2-21|MHC /1-88
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eu /1 -8 9
MH

p it r c io x e t t - A U 3 - H C 2 2 | H M a ca ca s e _a ta- SU -A 1 - 1 X2 X - 8 9
h e o c e _ a ll a a - Q 0 1 E X - - 1 | M C / 1 - 8 9 P a c a e n _ n s a t a - J r is G 0 X 2 - E 1 - E /1 8 9
c n n J I I- H 9
C h M a c a u s _ r b u s _ u b is a - J AS U EB 0 1 - E X 2 - 1 cerI n d e C / 1/ 1 - 8- 8 9
C-

M a n s c a b u u l t t la Z L - E 0 1 R 0 H C /1 -
lo r - 0 c M o c a c e _ m u la ic u s - J 0 1 K R A B |M H C - 8 9 9
o c e c a _ n o x e ll a ty s - A H B R 00 3 - EE X 22 - 1 | | M Ho-1 t / 1 - - 8 99
I-

C a r c o c a m s c t y Z Z - J Y - J - 1 7 |M t/ 1 8
b e an -J Z - In /1 8 M e c a a _ f a _ a A H is a n a X 2 2 - 6 d e C /1 -

HLA-F
1
M a P a p u s _ s m e s tr a - J AZ L G Z 0 1 - - E XX 2 - 73 | M d e tC / 1 - -89 9 C a a c a _ u s is - n s e ll - E - E X 7 |I n 9
ce

H
cac io a in 0 E 2 |I H / 8 M a c a c c e b u b o le r o x Z 0 1 0 1 2 - 2 2 5 |M e u /1 -8
a _ n _ a n b a e u a - J ZB R 0 11 - E X X 2 - - 6 |I nn d eC / 11 - 8 99

HLA-J
M a c c o a n a n g s _ H Z L G E X X 2 - |P s 9
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C e rc e m u b
is s - A L F - E X 2 - 1 5 |I n d e t / 1 - 8 9 M e r io _ s _ c u - A - J Z 0 1 - 1 - E -1 4 e t/ 1 -89
P a p o c e b ue s tr in - A H ZQ IB 00 1 - E 2 - 1 48 |M Hd e t /t / 1 - 8- 8 9 C a p b u it h e b is ty s Z Z U 0 X 2 |I n d
o-

C io s a Z 1 X |M C /11 - 8 9 P o lo o p a n u s _ a A H A N 0 3 -E 2 -5 H C /1 -89
M a c e rc o c e _ a n u _ a ty s-J Z L F 0 1 - E- E X 22 - 9 |M -
C h in io _ b u b is a - A U E -E X |M /1 -8
2

HC - 9 R a p o c e n u la tt -J S D 0 3 X 2 -5 H C
a b -J 0 X - 8
M a c c a _ n e b u s _ a is -A H Z L G 1 -E X 2 - 2 26 |M HH C /1/1 - 8 99 3 P e r c _ a m u la tt a A B 3 -E 2 -6 |M -8 9
o- C a p io c a _ m u a -C U I0 -E X
aca m e s ty s -J Z Z 0 0 1 -E 2 -1 |M H C /1 - 8 9 9 C /1 -8 9

L
M a c _ fa s c ic tr in a -J Z L G 1 -E X X 2 -76 |M H C /1 - 8 9 P a c a c a _ o ri ll a -C Y E 0 2 -H /1 -8 |M H

A-
rc
1
a 0 |P s C /1 - 8 9 MH M a c a a _ g o ri ll -A J F -H L A X 2 -4 |I n d e t/ 9
M a n M a c a c c a _ m u u la ri s -AZ L F 0 11 -E X 22 -2 0 |M e M o ri ll a _ g c u s 3 -E 2 -3 /1 -8
e u /1 -8 9 C- x2 9

HL
G o ri ll a n is s 1 0 -e A B D 00 3 -E X -3 |P s e u H C /1 -8 9
d ri llu a_m la tt a -E -1
u la tt -J S UQ IA 0 1 X 2 -2 0 |I n dH C /1 -8 -c
0, 55

-8
s_ le
3 |I n e t/ 1 99 I- G a n _ p n s u ri ll a -C A B D -E X 2 2 -3 |M u /1 -8
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R hi no ol ob us _au co p h a ea -A A N UE 0 3 -E X X 2 -0 |M
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d e t/ -8 9 ce C-I P o n s e _ g o ll a -C F E 0 2 0 4 -E X -7 |P se H C /1 -8 9 9
0,9 7
pi th ec u s- JY 0 1 -E 2 -1 C o ri ll a _ g o ri s -A J A C Z 1 -E X 2 |M
ng ol
M ac ac us _r ox elen si s- JY K Q 0 1 -EX 2 -1 4 |M
5 |M H C /11-8 -8 9 rc MH G o ri ll a n is c u te s -A D A 0 X 2- 12 |I nd et /1
G n _ p a g lo d y e s- A A JZ LF 01 -E-E X 2- 10 t/1 -8 9
-8
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a_ la KR X 2 -4 H CC /1 -8 99
C er co ne m es trina -J A B R 01 -E X 2- |M H /1 -8 9 1 P a n _ tr o g lo d yt tr in a- Q R 03 In de /1 -8 9
P a n _ tr o ne m es tt ii- A A 2- E X 2- 6|X2 -2 |M H C -8 9
0, 82
Co lo bu ce bu s_ at na -J ZL F001 -E X 2- 5| M H C C /1 -8
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/1 -8 99 P a ac a_ _g ar ne A B R T0 C 02 -E /1
0, 94

s_ ys E X 2- 4| M H C /1 eu
Ce rc oc an go le ns is--J ZL G 011- Ps
87

M acle m ur ric ht a- us -A BD EX 2- 7| t/1 -8 9

0,020,64

JY KR -E X2 -45| M H C /1 -8 9 O tors iu s_ sys_ m ur in -A BD C0 2- EX 2- 8| In de /1- 89

0,76

eb
Ma ca ca us _a tys -J ZL 01 -E X2 |In de -8 9 Ta ro ce bu m ur in us -A BD C0 2- HC
_m
Pa n_ tro ula tta -JS UE G0 1- EX -6 |M HCt/1 -8 9 0,
92 M ic ro ce bu s_ ur in us BD C0 2- EX 2- 3|M/1- 89
76 -H
2- 11 |In /1 -8 9 75
0,7 7

glo dy tes 03 -E de 0, 0, M ic oc eb us _m rin us -A -23 |M HC

HLA
X2 t/1 -8 9
Pa n_t rog -A
lod yte s-A AD A0 1-E X2-22 |In de t/1 Mi cr ce bu s_ mu s-J ZL G0 1-E X22-1 1|M HC /1- 89
0

0,
Pan _pa nis AC Z0 4-E -0| Ps -89 69 Mi cro aty
bu s_ tta -AA NU 01- EX
X2 MHeu /1- 89 76 |MH C/1 -89
Gor illa_ goricus -AJ FE0 2-E X2--7| C/1 -89 0, Ce rco ce ula E03 -EX 2-6 1-89
Ma cac a_m ula tta- JSU-AQ IA0 1-E X2- 3|In det/
0,

lla-C YUI 03-E 8|M HC /1-8

-p3 Ma cac a_m
76

Gori lla_g orilla 9

HLA-MHCI
X2- 3|M HC/ ,4 6 cicu laris p3/1-89
Pong o_abe
-CAB D03 -EX2
-7|M HC/11-89 0 0 ,7 Mac aca _fas -MH C-I- 21|Ind et/1-8 9
Nomas cus_leu cogenylii-AB GA01 -EX2- 9|MH -89 Con sens us10 ina-JZ LF01 -EX2- X2-11|P seu/1-8 9
s-ADFV 01-EX2 -3|MHC C/1-8 9 0, 71 Maca ca_ne mestr BR01-E
/1-89 0,9 5 Rhinop ithecus _roxell ana-JA 9
Consensu s10-ex2-H LA-E/1-89
Tarsius_syrichta-AB RT02-EX2-3|MHC/1- 89 HLA-E 0,76 0,7 2
0,8 8
Cercocebu s_atys-JZL G01-EX2-1 9|Indet/1-8
Papio_anubis-AHZZ 01-EX2-1|MHC/1-89
Callithrix_jacchus-BBXK01-EX2-3|MHC/1-89 0,65 Saimiri_boliviensis-AGCE01-EX2-5|MHC/1-89
Callithrix_jacchus-A CFV01-EX2-8|MHC/ 1-89 Cebus_capucinus-LV WQ01-EX2-14|MHC/ 1-89
Aotus_nan cymaae-JY KP01-EX2 -16|Indet/1
-89 0,76
0,8 6
MHC-I-platy-1 Cebus_cap ucinus-LVW Q01-EX2-1
2|Pseu/1-8 8
Q01-EX 2-6|MHet/1-8 C/1-89 0, 84 Aotus_ nancym aae-JY KP01-E
Cebus_ capucin us-LVW 9 Saim iri_bo X2-19|M HC/1-8
GCE0 1-EX2 -7|Ind 0, 8 0 ,9 Saim iri_b livien sis-A GCE0 1-EX2 -10|In det/1 9
Saim iri_bo livien sis-A 1-EX 2-8|I ndet
/1-89
t/1- 89 0 ,7
7 Aotu s_n olivi ensi s-AG CE0 1-EX 2-11 -89
ensi s-AG CE0 19|I ndeC/1 7
Aot us_ anc yma ae-J YKP 01-E
Saim iri_b olivi hus -AC FV0 1-E X2-2-5 |Inde
76

0 ,7
0, 86

|MH -89
2 ,6 7 0 Sa imi ri_nan cym aae -JY X2- 9|Ps eu/1 t/1-8 9
0,

Cal lithr ix_j acc

0 ,7

s-A CF V01 -EX -1| MH C/1 -89 0 ,6 0 0 ,7 7 Ce bu s_ bol ivie nsi KP 01- EX 2-8 -89
jac chu X2 t/1 -89
0,

s-A GC E0 |Ind
Cal lith rix_ ivie nsi s-A GC E0 1-E -10 |In de Ce bu s_ ca pu cin us -LV 1-E X2 -13 et/1 -89
2

6
MHC-
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HC /1--8 89 0, 99 0 ,8
01 -E X2
0, 79 0,7

Ce bu s_ ca pu WQ |MH
Sa imi ri_ bolcy ma ae -JY KPQ0 1- EX 2- 7|M In de t/1
9
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0,78

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X2 -1 7| HC /1 -8
HLA- Sa buiri ca pu cin us -L VW Q0 1- EX 2-
0,68

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Ao tus _n ca pu cin us -L VW KP 01 -E 2- 2| Mse u/ 1- 899 aty- /1- 89
S aiim _b ol ivci nu s- LV Q0 1- EX 2- 20 |M HC /1- 89
Ce bu s_ nc ym aa e- JY BX K0 1- EX X2 -93||PM H C /11--889
4
0 ,7 1 2 m iri _b ie ns is W Q 01 -E 5| MH C/
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na us -B -E C al lit ol -A 1- 89
9

Ao tu s_ ch 01 iv
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rix _j ac ch us -A C FV -E X 2- P se u/
0,9 2

89
7

A o tuus _n an ch us -A G C E 01 EX 2- 3| HC /1 -8 9
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82

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X 1| P se u /1 -8 9 u/ 1- 9
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0 ,8

C al lit ix _j ac ch es -A A D AZ 04 -E XX2- se u /1 -9 5 C a llll it h ri xa_n cy m aaa e- JY KF V 01 -E X X 2- 4| M H C /1 -8 9

2 -1 |P
0,83

9
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C al lit _t ro gl od ytyt es -A A C |P s e-V /1 -8 C it h ri ja c a e -J P 01 2- 15
|M H C /1 -8 9
E 0 2 -E
0,85 0,14

X 2 -1 -9 59 C a ll it h x _ ja c h u s Y K P -E X 2-
0,9 6
0,7 6

A
P an ro gl od is cu s- A JF D 0 3 -E x 2 -H L s e u /1 /1 -8 9 MHC C a ll it h ri x _ ja c c h u -A C F 0 1 -E X 2| M H C /1 /1 -8 9
|P
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P o en 3 2 -1 n d e /1 -8 9
ll a _ g C o n s -C Y U I00 1 -E XX 2 -4 |I|P s e uu /1 -8 9
-I- S a ll it h ri x _ ja c c h u ss -A C F K 0 1 -E X 2 -1 0 |MH C /1 -8 9
C aa im ir i_ri x _ ja c c h -J R V 0 1 X 2 -1
pla
HLA-

G o ri a A -8 ll u U -E |M H C /1
ll e C it b cc s -A L
g o ri li i- A B GF V 0 1 -E X 2 -1 |P s C /1 -8 9 A a ll it h ri x o li v h u s C F 0 1 -E 2 -2 0 H C /1
X -8 9
ll a _ e C 1 -E 2 -4 |M H C /1 8 5
G o ri g o _ a bh u s -A C F V 00 1 -E XX 2 -9 |M H e t/ 1 - - 8 99
ty- A o tu h ri x _ ja c ie n s -A C V 0 1 -E X 2 -0 |I |M H C -8 9
3 A oo tu ss__ n a _ ja c cc h u sis -A GF V 0 1 -E X 2 -7 n d e /1 -8
P o n _ ja c c h u s -A B X K 0 1 -E X 2 -30 |I n ds e u /11 - 8 9 |M H t/ 1 -8 9 9
G

C tu n n c h -A C
ri x c c s -B B R -E 1
0 1 X 2 - 2 |Pn d /1 - 8 9
- e t/ 8 C e b s _ n a n c y m u s -B C F V E 0 1 X 2 -1 C
it h _ ja hu A C e b u s _ a n y m a a e B X 0 1 -E-E X 2 -28 |M H /1 -8 9
C a ll ll it h ri x _ ja c c ll a n a -J-J Y K R0 1 - E - E X 22 - 9 |I|M H Cu /1 - - 8 99 A oa ll itu s _ cc a p uc y m aa a e - - J Y K K 0 1 -E X2 C
C a ll it h ri x ro x e n s is B G A IB 0 1 - E X 2 - 8 |P s eH C / 1/ 1 - 88 9 C tu h a c a JY P -1 |M H /1 -8
C a e c u s _ n g o lee li i- A s - A Q Q 0 11 - E XX 2 - 1- 2 |M H C / 1 - - 8 99 C e b s _ r ix _ p u in u e - J K P 0 1 - X 2 -0 1 |P C /1 -8 9 9
S e b u s n a ja c in s - L Y K 0 1 E X 2 |P s e u
HC /1 -8 S a im u s _ c n c c c h u s - V W P 0 - E X - 2 s e u /1 -8
p1

h a W 0
p it b u s _ o _ a b b a e u - L V W Q 0 1 - E- E X 22 - 8 |M | M seu /1 -89 A a im ir _ c a p y m u s L V Q 1 - E 2 - 4 |I n /1 -8 9 9
in o s HL C o t ir i_ a p u c a a - A W 0 1 X 2 1 |M d e
R h C o lo P o n g s _ s a c in u s - L VV W QG 0 11 - E XX 2 - 06 | P s e uu / 11 - 8 99
I-

C ea l l iu s _ i_ bb o li u c inin u s e - J YC F VQ 0 1 -- E X 2 - 1 4 |I H C /1 t/ 1 - 8 9
C-I-p2

u
e b a p u in u s - L Z L F 0 - E 2 - 3 | P s e C / 1 - 8 9 A- C t n o v - K 0 -
C-

E n -
r o c u s _ c a p u cc in u t y s - J J Z L T 0 2 1 - E XX 2 -2 6 | PM H e t /t / 1 - 8- 8 99 P e b u h r a li v ie n u s L V P 1 - X 2 0 |P d e 8 9
lo
C h C e b u s _ c a p u s _ a r in a - A B R L F 0 1 - EX 2 - - 1 1 | | I n dd e t / 11 - 8 8 9 AB P a b u s _ i x _ n c ie s - L V W 0 1 E X - 1 s e t/ 1
P o n _ s _ c j a y m n s is - W Q 0 - E 2 - 6 |I u /1 - 8 9
MH

b c u t - Z 0 E 2 5 In e / - 9
C e b u s _ o c e b m e s h t a a - J Z L G 0 3 - E X X 2 - 1 0 | | I n d H CC / 11 - 8 8 9 C C a n g t r c a p c c a is A G Q 1 - X 2 2 |M H n d e t - 8 9
P o n o og ap uc h ae -A C 01 EX -5
A-

/
C e e r c _ n e s y r ics t r iny s - J U E 0 1 - 1 - E X 2 - 2 - 2 6 | MM H C / / 1 - - 8 9 9 P a n _ t _ a l o u i n u s - J G C E 0 - E 2 - |M C / 1 -
G a n s e ro b d cin us -A YK E 1 X 18 HC 1- 89
HLA-MH

Pa o r n _ _ t r o n s g l o e l i i y t e u s - L V C F P 0 0 1 - - E X 2 - 2 2 | M H /1-8 8 9
HL

C ca s_ e t JS Z 0 E X 1 | H C /1 -8 9
c a iu e m s _ a t a - H Z B R 1 - - E 2 - 2 8 | M H C / 1 - 8 7 P - s - 1 2
M a T a r s a _ n e b u u la t i s - A - J A L F 0R 0 1 - E X X 2 - 2 - 6- 0 | M| M Hd e t u / 1 1 - 8- 8 9 9 O o n n _ i l l a t r o g g l ou s 1d y t e A B - A AL V WW QV 0 1 - E XE X 2 - 6 | M| I n d C / 1 - 9
c / t o g pa _ g l o d 0 s G C Q 0 - E 2 - 0 e 8
ca coc _m u b a n a -J Z Y K 0 1 3-E E X X2 -5 | I n se e t /1 -8 le o_ n o d yte - e -A A0 Z 0 1-E X2 -26 |In HC/ t/1-8 9
P on s t r g isc i l l a - a -L YK P0 1- - 8 - E | I n e u
O t o le m u r _ g a r r n e t t t i i - - A A n s u 0 3 - - E XX 2 - 2 - 9 5 | MI n d d e t t / 1 1 - 8 8 9 9

M a C e r a c a _ a nx e l l r i n a i s - J Q I A E 0 0 1 - - E X 22 - 8 2 | P I n d H C u / 1
O t o le m u r _ _ g a r n e t t i i n s e U EF 0 1 3 - E - E X 2 - 1 1 2 | | I n n d e e t / t / 1 - - 8

m a is r i l y t s x 2 A C 1 - 0 4 1 - X - 0 | I n d e 1 -
P o n n _ _ t r oa n g o r r i l l m a u s e - J Y K P 0 X 2 V 0 1 2 - 1 4 | P s
on g e og lo u a C e- V P 1 E | M X

9
C a n _p _ g o cy cin aa -J YK - E F X 1 7
O t o le m u r _ g a r n e t t i i - AA A QQ R s 1 E X 2 - 2 3 0 | | I n H Ce t / 1/ 1 - - 8 9 9

u r b e cu l a e s - A - H Z E X - E E X 2 - | M d t / 1 8 9
O t le m u r g a r n e C o - J S Z L E 0 0 1 E X 2 - - 1 6 6 | I I n d d e e t / 1

c i o o t s A U U 1 -E - | e
g o o _ n s l o d y s - A- C AY U J Y W Q 0 1 - E XX 2 - H C 2 - 5 e t / 1 - 9 0
P a n lla _ an u m ae -J 0 3 AD - E 2-

M a P a p s _ r e s l e n r i s - - J S A N L F 0 0 1 - E X X 2 2 - 2- 4 | M| P s _ g l i s- - C - A A C L 0 4 2 X 2 2 - 3 | M H C e t / - 8
P a ri lla n ap y a ae D s- 01 EX
le u r g a e ii - A R 3 - - 2 2 | I n e / 1 - 8 8 9

_a ab u s d y t e JF B DI 0 3 KP 01 -EX 2- 20| / 1 - | M H - 9 0

a r - A AJ Y U A D Z - A - E - 4 | - 9 | 2 | M H C / 1 1 - 8 9
i A
P o r i s _ c n c y m a A B n y V 1 - 8 9 |M H / 1 - 8 9 - 8 9
M ic t o le mm u r _ g a r r n e t t t ii - AA A QQ R 00 3 - - E XM H C4 | I I n d d e t t / 1 - - 8 9 9

c u n e mn g o u l a t t a - A - J Z L G 0 1 1 - E E X X 2 2 - 9
at a- S I 1 E 2 - -4 |In d

G o tu s_ na nc ym - C ge C F V0 / 1 - 27 C C / 1 9
ul in -J Q 0 1- EX 2 2 6 In

be eli 1 0 t e s s - A E0 0 3 - E 01- -EX 2- 12| Ind 8 9 C / 1

e n e B G FE I 0 A 0 4 / 1 X 2 I n d M H H / 1 - 8 9 9
G o bu _ na nc la co -A F - B 2-
M ic r o c e u r _ g a r n e t t t ii - A A Q R 0 3 - E X 22 - 5 | - I -n d ee t / 11 - 88 9

_ c a a Z B -
m str ta s-A WQ 0 1- EX X -2 5|

ith a _a ci ul t t na J I 0 1 -E X
A
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lii i-A - e x - A A D 2- - E X 2 EX 2- 11| Ind et/1

op ac s s m la ri s- Q ZZ 0 1 E t t i A 02 3 - 0 1 - E X - 8 - 8 e t C C / 1 - 8 8
C eo t ut u s __ n ag o r _ le uc h u s - A H L A0 3 - E 2 - 1 2 - 1 0 |M H C
a_ e lat ri V CE 0 3- -E 2 -2

H / -8 9

-A B 2 A C A EX X - 6 2- 10 Ind et -8

i n ac b u _ f a a_ m u st ty s - A H K 0 1-
1 |

A o u s a _ u s c h u 2 - E E X X 2 - 8 |M
M ic r o c e b u s _ m u r e t t ii - - A A Q R 00 3 - E- E X 22 - 62 | M H CC / 11 - 8 99

E
i - A 0 1 -E X - E 2 9 | I n / 1 - / 1 - - 8
ac em u la -L G U 0 01 EX 2

A o t r i l l s c _ ja c c - E X S U 1 - 4 - E X 2

B GA - H Z 0 1 2- 2 - 9 | M 18 |Ps et /1-8 9

R h M o l o c a c a c a _ e m e s _ a e u s - A A E HQ I B G 0
ac n _m ic us -A N E A - X

A o a r ix _ ja 1 0 a - J A 0 Z 0 - E 8 9
HC /1 -8 9
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A - E X2 2 - 2 X 2 - - 4 | de 89 89 9
G 0 L 0 - 7 | H |M e /1 9
M a_ a c in is AA SU I 01 -E

G o m it h r ix u s la t t B G A C 0 1 /1 - n d e t/ /1 - 8
6
|M HC /1 -8
d

N a ll it h n s u i- A - A D A - G - 6 |I H C 9
_ m r in s - A D 0 3 E X - 0 | M C / 1 - 8 9

C ca a ac n u a bi - A L t/1
A 1 A - 4- E X |M M H C / H u/ -8

Q X -4 | 1 M
s
C a ll s e a _ m e li t e s - A A L A X 2 - 2 |M /1 -8 -8 9 -8 9
ac ac fas uc ns a- -J AQ Z 01

M a u s _ m u r in u s - A B D CC 0 2 -- E X 22 - 9 | | P s eH C / 1/ 1 - 88 9

a M a c a_ eb a b u t t a s- JZ
01 -E C E 2 H C 1 C 1- 9

R 2 - |M M | M H
C n c
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-8
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C oa c ag o _ ag lo dd y te- e x 2 A 0 1 3 - E X -2 |M H |M H n d e t/ 1 -8 9
M a a c a c a c a _ m ri n u s - A B D C 0 22 - E XX 2 - 6 |I n dH C / / 1 - 88 9

- 03 1 H H C
ac ac _ p ie tt ta s- Z Z

M n
M cac coc s _ s _a u l a aeu tys 9
M n r o lo 0
1 9

-E X / 1 X 2 - 6 C/ / 1 - 8 9 /1- 89

- E 1 | I HC C / 1 C / / 1 - 8
M M aca _ca liv ula lat ari -AH HZ

P oa n __t tr o gs u s 1li i- A BC A B D0 2 -E 4 -E X X 2 -1 |I n d e 1 -8 9
a _ fa m u la la tt a -J B D CC 0 2 -- E X 22 - 0 |M H Ce t / 1 - - 8 9
ta J U A - X

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Figure 5: The phylogenetic tree of 417 EX2 sequences of MHC-I found in primate (Prosimians, Platyrrhini, Cercop-
ithecus and Hominidae) WGS datasets with the software MHCfinder. Primate orders are distinguished by color codes,
indicated in the legend. Clades that are suggestive of representing a gene or group of genes have been collapsed. Each
collapsed clade are labeled with the human isoform orthologs, however, those clades not containing human genes are
assigned new names (e.g., MHC I-p1, etc.). The nodes of the principal clades have been labeled. The tree was con-
structed after aligning sequences with ClustalO and using the phyML (part of the Fasttree software (Price et al., 2010))
with the gamma parameter, WGS matrix, and 500 bootstrapped samples. The consensus sequences for identifying
clades are marked in black.

10
bioRxiv preprint first posted online Feb. 15, 2018; doi: http://dx.doi.org/10.1101/266064. The copyright holder for this preprint
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
All rights reserved. No reuse allowed without permission.
ied (i.e., EX2, EX3 and EX4), EX2 contain
the most information to discriminate genes for
classification. A phylogenetic tree (Figure 5)
was constructed from 410 EX2 exons found
from the primate WGS datasets, consisting of
both viable (those having exons in tandem)
and nonviable genes. In the tree, clades were
collapsed to improve the visualization of re-
sults. Human sequences from the HLA iso-
types HLA-A, -B, -C, -E, -F, -G, -H, -J, -V
and -L genes were aligned with the sequences
from non-human primates in order to associate
and identify clades homologous to those in hu-
mans. Apart from these homologous human
clades, other clades were also identified. Three
clades containing only sequences from Cer-
copithecus species are designated with MHC-
I-cerco-1, MHC-I-cerco-2 and MHC-I-cerco-
3. Another three clades with sequences ex-
clusive to Platyrrhini also are identified, indi-
cated by MHC-I-platy-1, MHC-I-platy-2 and
MHC-I-platy-3. Also, there are three other
clades that have sequences from at least two
primate orders and have been labeled MHC-I-
p1, MHC-I-p2 and MHC-I-p3. The MHC-I-
p1 clade contains of the largest number of se-
quences, with representatives from all primate
species except Hominids, perhaps suggesting
a concrete function that was made superfluous
in the differentiation of Hominid species.
Most of the sequences from the HLA-ABC
clade (i.e. consisting of HLA-A, -B and -C se-
quences) are from Hominid species. Also, this
clade contains a single sequence from Cerco-
pithecus and seven sequences from Platyrrhi-
nus. HLA A, -B and -C have a common ori-
gin and must have been generated after the
separation of the Hominids from the Cerco-
pithecus, previously described by other au-
thors (Piontkivska & Nei, 2003). The se-
quences from these clades constitute the clas-
sical HLA-Class I genes. Therefore, it is likely
that Cercopithecus and Prosimian species de-
11
veloped other genes that overtook the basic
functions of these classical HLA-class I found
in Hominids.
From the tree of Figure 5, the HLA-E and -F
clades contain sequences from all the primate
orders except Prosimians. HLA-G, -H, -J and
-L clades have sequences from Apes and Cer-
copithecus. With the analysis of MHCfinder,
most of EX2 sequences of Cercopithecus of
the HLA-G clade are identified as pseudo-
genes, consistent with experimental results
(Castro et al., 1996). All the sequences of the
HLA-V clade are pseudogenes and are only
found in Hominids.
Three clades (indicated by the name cerco)
are found that contain sequences only from
Cercopithecus species. These sequences were
generated after the separation of Old World
monkeys from the Hominidae family. In a sim-
ilar way, three clades contain sequences only
from Platyrrhine species (indicated by name
platy.
Another three clades exist that are com-
posed of sequences from at least two pri-
mate families, but lacking sequences from
Hominids. Of these, the MHC-I-p1 clade
(where p is used to indicate primate) is the
largest. In particular, the MHC-I-p1 and MHC-
I-p2 clades contain sequences from Prosimi-
ans, Platyrrhines and Cercopithecus, while the
third clade of this group lacks sequences from
Cercopithecus.
3.1. Allele assignment to clades
Several studies concerning the gene alleles
of MHC-I have been described in non-human
primates and are available at the IPD-MHC
database (www.ebi.ac.uk/ipd/mhc) (Robinson
et al., 2013; de Groot et al., 2012). These alle-
les were aligned with the germline sequences
to classify alleles as classical MHC-I (with al-
lelic variation) or nonclassical MHC-I (with-
out allelic variation).
bioRxiv preprint first posted online Feb. 15, 2018; doi: http://dx.doi.org/10.1101/266064. The copyright holder for this preprint
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
All rights reserved. No reuse allowed without permission.
M. Mulatta has been extensively studied to
reveal such allelic variation of MHC-I. We ob-
tained allele sequences of M. Mulatta from
the IPD-MHC database and aligned them to
the germline sequences found by MHCfinder.
Figure 6 shows the resulting phylogenetic tree.
To reduce sequence redundancy, only one rep-
resentative allele from each allele lineage was
included in the tree construction. The Mamu-
A alleles belongs to the genes that define the
MHC-I-p2 and MHC-I-cerco-3 clades. In pre-
vious publications, difficulties have been de-
scribed in assigning specific orthology to the
Mamu-B alleles (Liu et al., 2013). The tree
of Figure 6 resolves this difficulty by show-
ing that Mamu-B alleles correspond to genes
belonging to the MHC-I-p1, MHC-I-cerco-1,
-cerco2 and HLA-H clades.
C. jacchus is considered the reference or-
ganism for studies of allelic variation of MHC-
I genes in New World monkeys. Many pub-
lished studies (Cao et al., 2015; van der Wiel
et al., 2013; Kono et al., 2014) have con-
cluded that the MHC-I alleles in C. Jacchus
are orthologous to the HLA-G gene. Fig-
ure 6 shows the phylogenetic tree of germline
EX2 sequences obtained from MHCfinder to-
gether with allele sequences from the IPD-
MHC database. The tree confirms the results
of these studies, since the majority of alleles
are from gene C. jacchus-ACFV01-13—MHC
belonging to the HLA-G clade. However, the
alleles of the lineage Caja-G*18 belong to the
MHC-I-platy-3 clade.
4. Discussion
A bioinformatics program,
MHCfinder (freely available at
http://vgenerepertoire.org/), was devel-
oped that identifies the MHC-I exons (EX2,
EX3 and EX4) from WGS datasets. The algo-
rithm determines the in-frame exon nucleotide
12
sequences, deduces the amino acid sequence,
and transforms it to a 400 element feature
vector. Each element of the feature vector
represents the frequency of occurrence of each
AA and pairs of AA (i.e., one of the 20 × 20
possibilities) within the protein sequence. A
supervised learning procedure is used to train
a machine learning classifier to recognize
exons homologous to those known in humans.
We found that feature vectors based upon the
simple frequency of AA occurrence transform
has a higher classification accuracy (attaining
predictive precision of 98%) than other more
sophisticated transforms based upon posi-
tional physicochemical properties. If the exon
architecture is known, small modifications
could render the algorithm a more general
gene finding method, thereby facilitating rapid
identification of gene/specific exons from any
species whose genome has been sequenced.
With MHCfinder, exon sequences of
MHC-I were obtained from 30 primate
WGS datasets. The sequences have
been made available in the repository
vgenerepertoire.org. The program iden-
tifies individual exons, referred to here as
viable, meaning that they have a valid reading
frame. If the exons are found with the canoni-
cal MHC-I exon/intron structure (i.e., they are
arranged in tandem, EX2-EX3-EX4 within
the same WGS contig and have a valid intron
spacing), then MHCfinder considers this a
viable gene (i.e., that is likely functionally
expressed). Nonetheless, problems associated
with WGS datasets (e.g., incorrect sequence
assembly or low coverage of certain regions)
may result in an underestimate of the total
number of viable MHC-I genes found by
MHCfinder. In WGS datasets with relatively
high coverage and N50¿15k (which is the
case for most datasets we used), the results
of MHCfinder agreed with annotated gene
results, when available. While the use of WGS
bioRxiv preprint first posted online Feb. 15, 2018; doi: http://dx.doi.org/10.1101/266064. The copyright holder for this preprint
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
All rights reserved. No reuse allowed without permission.

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M a m o -1 |1 -8 9
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MHC-I-cerco-1 M a m u -A 1 *0 2 3
M a m u -A *0 0 3 |1 -8 9
a ta -J M a m u -A 1 10 6 C -I- p2
M ac ac m ul at ta -A SU E0 3- EX M am u- B *1 17 62
M a u- A 1* 10 ?? ?M H
a m ul AN u-
at ta -J U0 1- EX 2- 15 |M H B *0 56 M amse ns us 2
SU 2- C |1 -8 C on u- A4 *0 3
Ca llit hri Co ns en E0 3- EX 2- 14 |M HC |1 9
x su 22 |P se -8 M am u- A3 *1
Ca llit hri jac ch us -B BX s1 0- ex 2- HL u| 1- 9 M am u- A4 *0 1 HC |1- 89
x jac ch
us -AC K0 1-E X2 -3| MH A- E| 1-89 X2 -15 |M |1- 89
Ca llith rix 89 M am -A 4* 03 NU 01 -E eu
Cal lith rix
jac chu s-B FV 01 -EX 2-8 C| 1-8 9 Ma muca mu lat ta- AA E0 3-E X2 -2| Ps
BX K0 1-E |M HC |1- Ma ca a mu latt a-J SU
jac X2 89
Cal lithr ix jaccchu s-A CF V01 -EX -2| MH C|1 -89 Ma cac *06 1
Mac aca mula
hus -AC FV0
1-E
2-9 |Ps eu|
1-8 9 Ma mu -A1 *04 9
tta-A EHK 01-E X2- 3|M HC| 1-89 Ma mu -A11*06 0

Caja-B
X2-2 |Pse u|1-8
Mam u-B*0 31 7 HLA-E Mam u-A *121
Mam u-A1 04
Mamu -A1*0
Callithrix jacchus-A CFV01-E 4*01 01|1-8 9 Mamu-A 1*043
X2-5|MH C|1-89
Callithrix jacchus-ACFV0 1-EX2-19|Pseu |1-89 Mamu-A1* 040
Mamu-B*074 Mamu-A1*042
Caja-G*07 02|1-89
Macaca mulatta-AANU01-EX2-20|MHC|1-89 Consensus10-ex2-HL A-A|1-89
Mamu-B*064
Mamu-B* 070
9
HLA-ABC Consensus 10-ex2-HL A-C|1-89
Consen sus10-E X2-HLA
U01-E X2-8|M HC|1-8 Callith rix jacchu s-ACF -B|1-89
Macac a mulatt a-AAN seu|1 -89 Calli thrix V01-E X2-14 |Pseu
UE03 -EX2 -18|P u-B* 013 Call ithri x jacch us-A CFV 01-E X2-1 7|Ps |1-89
Maca ca mulat ta-JS Mam
Mam u-B *09
2 Caj a-B 6*0jacc hus -AC FV0 1-EX eu|1 -89
eu| 1-8 9 Ca llith rix 1 01| 1-8 2-15 |MH C|1-
U01 -EX 2-9 |Ps -B* 053 Ca llith rix jac chu s-B 9 89
Ma cac a mu
latt a-A AN Ma mu
Ma mu -B|1- 89
eu
*07 6 MHC-I-platy-2 Ca ja- B*
Ca llit hr 02
jac chu s-A BX K01 -EX 2-1
01
ix jac ch|1- 89
CF V0 |MH
1-E X2 -10 C|1 -89
03 -E X2 -4| Ps C| 1- 89 Ca llit hr us
|M HC |1-
89
JS UE 1- EX 2- 5| MHu- B* 05 1 Ca ja ix jac ch -A CF V0
mu lat ta-
Ma ca ca lat ta -A AN
mu
U0 M am u- B* 09 5
M am H C |1 -8 9
MHC-I-p1 + MHC-I-cerco-2 C aj a--B *0 1 01 us -J RU L0 1- EX 2- 20 |M
C aj B7 *0 1 |1 -8 9 1- EX 2- HC
0| Ps eu |1- 89
Ma ca ca 13 |Mse u| 1- 89 C al a- B *0 1 01 |1 -8 |1 -8 9

ul at ta -J SUN U 01 -E
EX 2-
E0 3- X 2- 3| P u- B *0 82
M am u -B *1 34 5
7 MHC-I-platy-3 C al lit hr ix ja 02 |1 -8 9 9
C a jalit hr ix ja
C a ja -B 3
cc hu
cc hu s- A C FV
am -A A Mam *0 -B 3 *0 1 0 1 s- A C F 01 -E X 2-
M ac ac a m ul at ta Mam
u -B *0 1 1 C a ja *0
u -B 8 9 C a -B 5 1 0 |1 -8 9 V 01 -E X 18 |M H
M ac ac M a mm u -B *0 51 C a llll it h ri x*0 1 0 12 |1 -8 9 2- 7| C |1 -8
MHC
M a m u -B *1 -8 9 C a it h ri ja c P s |1 |1 -8 9
|1
M a |P s e u |1 -8 99 C a ll it h x ja c c h u s -A -8 9 9
C a ja -B ri x ja c h u s
E 0 3 X
2 -1
9 H C -8
-E X 2 -2 2 |M e rc o 2 |1* 1 0 16
-B 6
HLA-G C ll it h 1 * 0 c c h u -B B X V 0 1 -E
C a ja -B ri x ja1 0 1 s -A C K 0 1
CF
X 2 -1
S U 1 -E C -I -c a m u -B * 00 9 1 C aa ja - G * 0 3 c c h u|1 -8 9 F V 0 1 -E X 2 -0 1 |P s e
tt a -J A N U 00 -M H M mu -B* 37 C ja - * 1 0 1 s -A -E X |P u
u la Ma mu -B*0 28 C aa ja - GG * 1 88 0 4 |1 -8 9 C F V 2 -0 s e u |1 |1 -8 9
a m la tt a -An s u s 1 |M
cac M aa m u - B * 00 9 0 C ja * 1 0 |1 - 0 1 -E H C -8 9
Ma c a m u o n s e M amu -B* 071 C a ja - G * 8 0 1 |1 8 9 X2 |1 -8
Ma
ca C
M a m u - B * 0 4 79 C a ja - G * 1 8 3 |1 - 8 9 -2 |M 9
M a m u - B * -8 9 C a ja - G * 1 8 0 6 |1 - 8 9 HC
|1 -8
M a m u H C |1 - 8 7 C a ja - G 1 8 0 9 |1 - 8
C a ja - G * 1 8 0 2 - 8 9 9
M 9 |M e u |1* 0 24 4 C aa ja - G * * 1 8 0 5 |1|1 - 8 9
-2 s -B *0 4 C ja - G 1 0 9
X 2 2 |P u - B 0 8 0 C a a j a - G * 2 58 0 87 | 1 - - 8 9
-E -1 a m u B * 3 C j -G *1 0 |1 8
E 0 3 - E X 2 M a m u - - B * 01 - 8 99 C aj a-G *1 9 1| -8 9
U 1 M am u | -8 5 C aj a- * 9 01 1- 9
-JS NU0 M a m HC | 1 0 2 9 C a a- G* 10 02 |1- 89
a
la tt - A A M 1|M HC B * 0 6 6 M o ja- G* 10 0 |1 89
mu tta -2 |M u - B * 0 1 6 M a ns G 15 0 1|1 -8
ca X2 19 a m u - B * 1 0 8 M a ca e n * 1 0 2 | - 8 9
ca mu
la
-E 2- M a m u - - B * * 0 0 0 3 4 M a c cac c a s u 5 0 1 | 1 1 - 8 9
Ma aca 03 - EX M am u -B *0 1 5 M a a a m s 2 - 9
M a ca c m u 1 0 | 1 8 9
c UE 01 M a mm u - B * 0 0 0 1 C ac c a ca a m ul l a t - e x - 8 9
Ma - JS NU M a mu -B * *0 a j a ca m u at t a 2
M | u - B |1 8 0

tta AA M a mu u-B A2 a - ca m u l a ta - A - H
C aj ja- -G *0 7 0 01| 01 2|1
26 m u C 1- 6
M a mP s e - B * 1 - 8 9 9

G m u lat t t a -JS A N L A
aj a- G *0 7 6 1 |1 -8
2- M a a m MH C| * 0

C a a G 0

u la - M a m u-
m latta * 2 u la ta - A U U - G
C aj ja- -G* *23 7 0 1 0 1-8 9

a- G *1 7 05 |1 -8 -8 9
M 8| MH u - B

M a m
M a m u - u| * 0 4 8 8

C a ja G *0 0 4| -8 9

1 lat t t a -J A E0 0 1 | 1
G *1 6 03 |1 -8 9 9
a m u B 1- 6

a M a
C a ja- G 07 0 1|1 -8

ac m u 0 1 ta - A SU N U 3 - E - 8
*2 6 02 |1 -8 9
2- -6 a m

E X M M a a m u - BB * 0 0 7 9

C a ja- G* 07 0 |1 -89

ac ca M
- * 8

| 1 -JS A N E0 0 1 -EX X 2 9
2- am mu u-B *0 54 9

4 01 |1 -8 9
C a a- G* 20 01 |1 89
EX X2 M

M a
2 |

C aj a- G* 17 02 |1- 9

01 |1 -8 9

- 8 U U 3 - E 2- - 1
M |P -B B* 09 3

ac
C aj a- * 7 03 1-8 9

9 E0 0 1 -E X 1| 0 | P
16 u - * 6
M am seu 20 097 9

|1 -8 9
C j -G *1

M
3- - E X2- 2 - 2 Pse s e
C a a j a - G * 1 72 0 12 | 1 - - 8 9 C F V

-8 9
M aa m u u - B | 1 - 8* 0 1
3- -E

C a ja - G * 1 3 0 1 | 1 - A
M m -B *1 9

9
C a ja - G * 1 0 h u s 9

EX X 23 4 | u u
E0 01

M a m u - B * 1 41 6

C a ja - G * 1 3 c c |1 - 8 9

2- 2 - 7 |P P s |1-8 | 1 - 8
M am u-B *04 9

C a ja - G ix ja 0 3 - 8
SU U

M a m uu - B * 1 3 2

C a ja h r 1 3 0 4 |1 - 8 9 - 8 9

5| | P se e u 9 9
M amu -B* *08 4
-J AN

EX

C ll it G * 3 2 |1 |1 9
M aa m u - B * 01 8 95

C aa ja - - G * 11 2 0 3 0 1 |1 - 8

Ps s e u| | 1
1
C a ja - G * 2 0 3 0 2 9
ta A

M
3-

X 2 M a m u - BB * 0 57 5

eu u | 1-8 - 8 9
C a ja G * 1 2 0 |1 -8 9
at a -

u *0 5

C a ja - G * 1 2 0 4 |1 -8
E0

M a |P s e - B * 0 4 8

C a ja - * 1 0 1 -8 9

|1 1 - 9
ul tt

M m u -Bu |1 -87 2

C a ja -G * 2 2 0 4 |1 -8 9
-E X M aa m u -B * 0 8 9
m la

-8 8 9
C ja -G * 0 9 5 |1 9
SU

2 -3 m u * 0 8

C a ja -G * 0 9 00 6 |1 -8 9
0 |P -B * 4 9
a mu

C a ja -G *0 9 8 |1 -8 9

9
035

C a ja -G *0 9 0 1 |1 -8
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9
C a ja -G *0 9 0 |1 -8 9
M a m s e u |1*0 9 8
-

C a ja -G 9 0 3 |1 -8 9
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u -B -8 9

C a ja -G *0 9 0 7 -8 9
ta
ac a

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at

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-8

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12|1 -89

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08 |1 -8

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Caja-G*08 19|1-89
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ac

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tt a -J
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tt a -J

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am

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|1 -
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cac

89
am
Ma

cac

aca
Ma

Mac

Figure 6: The phylogenetic tree using germline EX2 sequences from five WGS assemblies: two from C. jacchus and
three from M. mulatta. Next, the allelic sequences of M. mulatta (blue) and C jacchus (green) obtained from the
IDP-MHC database were aligned with the EX2 WGS sequences. Clades are collapsed to improve the visualization of
the results. Also, consensus sequences (brown) were aligned with the EX2 sequences to identify clades.

datasets by MHCfinder cannot guarantee the obtained across a wide range of primate
exact number of MHC-I genes within a partic- species. Until now, sequences were obtained
ular species, it can make claims in studies of from the genomes or cDNA sequences of
several species or taxanomic orders. only few specific primates ((Heimbruch et al.,
For the first time, a large number of 2015; Uda et al., 2005; Yan et al., 2013)).
germline MHC-I gene sequences have been Moreover, this work can shed more light on
13
bioRxiv preprint first posted online Feb. 15, 2018; doi: http://dx.doi.org/10.1101/266064. The copyright holder for this preprint
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
All rights reserved. No reuse allowed without permission.
previous studies of nonhuman primates that
have identified expressed MHC-I alleles, at-
tempting to classify these sequences without
exact knowledge of the genes present in these
species.
Given the ability to construct phyloge-
netic trees from the MHC-I exons of various
species, it is possible to group the evolution-
ary origin of these genes and more precisely
infer orthologs and paralogs. Here, sequences
of exon EX2 were used to construct such trees;
EX2 being the most discriminative constituent
of the MHC-I gene, while EX3 and EX4 alone
cannot resolve clades. The results indicate
that the diversification of these genes has been
driven by birth and death processes, thereby
explaining the large number of pseudogenes.
The results presented here demonstrate that
the classical HLA-A, -B and -C genes found
in Hominids were generated recently, coincid-
ing with the separation from Old World mon-
keys. In non-Hominid primates, orthologs to
these genes can no longer be found, but in-
stead there are paralogs that proceeded from a
common ancestor. The sequences from Cerco-
pithecus are practically absent, except for one
sequence from M. mulatta, which is of interest
since it corresponds to a gene having a large
amount of allelic variability. Similar to these
genes, which are quasi-specific to Hominids,
there are other genes that are specific to Cer-
copithecus and Platyrrhini. Taken together,
data from this study provides evidence of rapid
birth and death processes. The absence of or-
thologs to HLA-A, -B and C in Cercopithecus,
and to a lesser extent in Platyrrhini, may ex-
plain the generation and/or expansion of other
clades consisting of genes that have the func-
tions of the classical MHC-I. Confirmation of
this hypothesis is confirmed in several cases,
as seen in M. Mulatta, for which an allelic vari-
ation is seen that is not present in Hominids,
while in C. jacchus a gene was identified be-
14
longing to the HLA-G that is responsible for
most of the allelic variation.
The presence of orthologs to the nonclas-
sical genes (HLA-E, HLA-F, HLA-G and
HLA-H) in non Hominid primates indicates
a previous origin prior to the separation from
New World monkeys. In Prosimians, no or-
thologs were found, thereby raising the ques-
tion whether the separation between the clas-
sical and nonclassical MHC-I is general to
all mammals or specific to Platyrrhini and
Catarrhini. Similar results are found by other
authors (Piontkivska & Nei, 2003; Fukami-
Kobayashi et al., 2005).
The birth and death processes observed in
the data are similar to that which occurs in the
variable (V) regions of immunoglobulin (IG)
and T-cell receptor (TCR) genes. In the case of
MHC-I, the situation is more complex because
a viable replication process involves at least
six separate exons. The birth and death process
must be related to the adaptability and survival
of the species. This evolutionary mechanism
creates a greater genetic variability in genes
that must present antigen, as well as in those
that must recognize antigen. Nonetheless, it is
still unknown why some species possess more
V genes and/or MHC-I genes than others, or
whether the absolute number of such genes
provides the species with immunological ad-
vantages. More studies are needed to clarify
whether correlaciones exists between the num-
ber of these genes and to establish if coevolu-
tion processes are at play.
bioRxiv preprint first posted online Feb. 15, 2018; doi: http://dx.doi.org/10.1101/266064. The copyright holder for this preprint
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
All rights reserved. No reuse allowed without permission.
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