ROCK PIGEON

Improved Genome
Assembly and
Annotation

MBB 211 – Group 3

December 9, 2019
 2

INTRODUCTION
 INTRODUCTION 3

 world's oldest
domesticated bird
 one of the most widely
distributed, diverse
morphology and behavior
among the avian species

 native to Europe, North

Africa, the Middle East,
Domestic Rock Pigeon (Columba livia)
and South Asia
 promising model for both avian and vertebrate evolutionary genetics for
understanding molecular basis
 a reference genome sequence of the rock pigeon (Cliv_1.0, current) was
recently assembled and updated (Cliv_2.0, updated), thereby facilitating
exploration of the molecular origins of diversity within and among breeds.
 METHODOLOGY 4

Process Technology
Genome Sequencing Illumina HiSeq platform
Genome Assembly HiRise
Repeat Identification RepeatScout
Repeat Assembly Sequencher
Repeat Annotation and Alignment RepeatMasker and
NCBI/RMBLAST v2.6.0+
RNA Sequencing Illumina HiSeq 2000
RNA Assembly Trinity v. r20131110
Genome Prediction MAKER by Augustus
Genetic map construction R/qtl v1.41-6
Genome masking and alignment WindowMasker and LAST
1 Sample extraction from female Danish tumbler pigeon
METHODOLOGY 5

2 Library construction
Chicago Method
3 Genome Sequencing
Illumina HiSeq
4 Genome Assembly
HiRise
5 Repeat Library from combine existing avian genome assemblies

6 Repeat Identification
RepeatScout
7 Repeat Assembly Danish tumbler pigeon
Sequencher
8 Repeat Classification TIRs
Non
RepeatMasker TE RepClass Perl Scripts
TE
TSDs
9 Consensus Sequence Comparison
TBLASTN
10 Library combining
RepeatModeler

11 Repeat Annotator
RepeatMasker + NCBI/RMBLAST
12 Percent divergence of consensus fragments
parseRM.pl script
13 RNA extraction from adult tissues
METHODOLOGY 6

14 RNA Sequencing
Illumina HiSeq 2000

15 Brain, Retina
Cliv_1.0 RNA-seq re-assembly
Subepidermis,
FastQC, FASTX-Toolkit Cochlear duct, Spleen,
Olfactory epithelium
16 RNA Assembly
Embryo
Trinity

17 Genome Annotation Racing homer

MAKER

18 Gene Prediction
MAKER by Augustus

19 Genotyping-by-Sequencing data were generated

Parlor roller
20 Reads were mapped to Cliv_2.1
Bowtie2

21 Genetic map construction

R/qtl

21 Assembly of sex-linked scaffolds and Z-chromosome linked scaffolds

2960 autosomal
21 Linkage group assembly 232 Z-linked markers
markers
 METHODOLOGY
7

22 Comparison of linkage map to the original genome assembly

Stacks and BLASTN

Hardmasking of Cliv_2.1 and colLiv2 genome assemblies

23
NCBI WindowMasker and LAST

15 Genome –scale dot plot

SynMap

Gene content comparison

16
Manual and BLASTN
 Results and 8

Discussion

N50 of Cliv_2.1 is greater up to fourfold

increase compared to Cliv_1.0

There is a major improvement

to the Cliv 2.1 assembly with a
substantial increase in scaffold
length

Figure 1 a.) assembly scaffolding contiguity comparison between

Cliv_1.0 (input scaffolds) and Cliv_2.1 (final scaffolds) assemblies
 Results and 9

Discussion

Summary of Cliv_2.1 annotation set with added new

gene models

AED values shifted to the left which indicates a greater model

concordance with the aligned transcriptome and protein homology
Results and 10

Discussion

(1,184)
Total number of
omitted genes in
the “old”
alignment, colLiv2
 11

CONCLUSION
• The improved and updated gene model annotations will further strengthen
ongoing and upcoming studies in the identification of genes responsible for
the phenotypic traits of interest
• Longer scaffolds will improve detection of regions

Remarks
• The addition of the expression profiles from various tissue
samples to the updated transcriptomic data is an upgrade from the
last alignment
• ??
 www.website.com 12

RESOURCES
(Levi 1986; Domyan and Shapiro 2017)

THANK YOU!