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Comparative genomic data of the Avian Phylogenomics Project

Zhang, Guojie, Li, Bo, Li, Cai, Gilbert, M Thomas P, Jarvis, Erich D, Wang, Jun (2014) Comparative genomic data of the Avian Phylogenomics Project. GigaScience, 3 (1). Article Number 26. ISSN 2047-217X. (doi:10.1186/2047-217X-3-26) (KAR id:57583)

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Abstract

BACKGROUND

The evolutionary relationships of modern birds are among the most challenging to understand in systematic biology and have been debated for centuries. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders, and used the genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomics analyses (Jarvis et al. in press; Zhang et al. in press). Here we release assemblies and datasets associated with the comparative genome analyses, which include 38 newly sequenced avian genomes plus previously released or simultaneously released genomes of Chicken, Zebra finch, Turkey, Pigeon, Peregrine falcon, Duck, Budgerigar, Adelie penguin, Emperor penguin and the Medium Ground Finch. We hope that this resource will serve future efforts in phylogenomics and comparative genomics.

FINDINGS

The 38 bird genomes were sequenced using the Illumina HiSeq 2000 platform and assembled using a whole genome shotgun strategy. The 48 genomes were categorized into two groups according to the N50 scaffold size of the assemblies: a high depth group comprising 23 species sequenced at high coverage (>50X) with multiple insert size libraries resulting in N50 scaffold sizes greater than 1 Mb (except the White-throated Tinamou and Bald Eagle); and a low depth group comprising 25 species sequenced at a low coverage (~30X) with two insert size libraries resulting in an average N50 scaffold size of about 50 kb. Repetitive elements comprised 4%-22% of the bird genomes. The assembled scaffolds allowed the homology-based annotation of 13,000?~?17000 protein coding genes in each avian genome relative to chicken, zebra finch and human, as well as comparative and sequence conservation analyses.

CONCLUSIONS

Here we release full genome assemblies of 38 newly sequenced avian species, link genome assembly downloads for the 7 of the remaining 10 species, and provide a guideline of genomic data that has been generated and used in our Avian Phylogenomics Project. To the best of our knowledge, the Avian Phylogenomics Project is the biggest vertebrate comparative genomics project to date. The genomic data presented here is expected to accelerate further analyses in many fields, including phylogenetics, comparative genomics, evolution, neurobiology, development biology, and other related areas.

Item Type: Article
DOI/Identification number: 10.1186/2047-217X-3-26
Additional information: eCollection 2014; PubMed Central PMCID: PMC4322804
Subjects: Q Science > QH Natural history
Q Science > QH Natural history > QH426 Genetics
Q Science > QL Zoology
Divisions: Divisions > Division of Natural Sciences > School of Biosciences
Signature Themes: Food Systems, Natural Resources and Environment
Depositing User: Mike Romanov
Date Deposited: 29 Sep 2016 19:10 UTC
Last Modified: 05 Aug 2021 13:10 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/57583 (The current URI for this page, for reference purposes)
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