Comparative genomic data of the Avian Phylogenomics Project

• Published in: GigaScience
• Main Authors: Zhang, Guojie, Li, Bo, Li, Cai, Gilbert, M Thomas P, Jarvis, Erich D, Wang, Jun
• Format: Article in Journal/Newspaper
• Language: English
• Published: BioMed Central Ltd; part of Springer Nature 2014
• Subjects: QH Natural history; QH426 Genetics; QL Zoology; Finch; Adelie penguin; peregrine falcon
• Online Access: https://kar.kent.ac.uk/57583/; https://kar.kent.ac.uk/57583/1/Zhang%26al2014%28GigaScience%20-%20Consortium%20list%29.xls; https://kar.kent.ac.uk/57583/2/Zhang%26al2014%28GigaScience%29.pdf; https://doi.org/10.1186/2047-217X-3-26

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 ...