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Improved Genome
Assembly and
Annotation
INTRODUCTION
INTRODUCTION 3
world's oldest
domesticated bird
one of the most widely
distributed, diverse
morphology and behavior
among the avian species
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
18 Gene Prediction
MAKER by Augustus
Parlor roller
20 Reads were mapped to Cliv_2.1
Bowtie2
2960 autosomal
21 Linkage group assembly 232 Z-linked markers
markers
METHODOLOGY
7
SynMap
Discussion
Discussion
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!