Comparative genomic data of the Avian Phylogenomics Project.
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 Neognat...
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ftdukeunivdsp:oai:localhost:10161/9322 2023-11-12T03:59:39+01:00 Comparative genomic data of the Avian Phylogenomics Project. Zhang, Guojie Li, Bo Li, Cai Gilbert, M Thomas P Jarvis, Erich D Wang, Jun Avian Genome Consortium 2014 application/pdf application/octet-stream https://hdl.handle.net/10161/9322 http://www.ncbi.nlm.nih.gov/pubmed/25671091 unknown 10.1186/2047-217X-3-26 http://hdl.handle.net/10161/9321 10161/9321 http://www.ncbi.nlm.nih.gov/pubmed/25671091 https://hdl.handle.net/10161/9322 Avian genomes Phylogenomics Whole genome sequencing Other article 2014 ftdukeunivdsp 2023-10-17T09:36:47Z 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 ... Other/Unknown Material Adelie penguin peregrine falcon Duke University Libraries: DukeSpace Finch ENVELOPE(167.383,167.383,-72.567,-72.567) |
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Duke University Libraries: DukeSpace |
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ftdukeunivdsp |
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topic |
Avian genomes Phylogenomics Whole genome sequencing |
spellingShingle |
Avian genomes Phylogenomics Whole genome sequencing Zhang, Guojie Li, Bo Li, Cai Gilbert, M Thomas P Jarvis, Erich D Wang, Jun Avian Genome Consortium Comparative genomic data of the Avian Phylogenomics Project. |
topic_facet |
Avian genomes Phylogenomics Whole genome sequencing |
description |
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 ... |
format |
Other/Unknown Material |
author |
Zhang, Guojie Li, Bo Li, Cai Gilbert, M Thomas P Jarvis, Erich D Wang, Jun Avian Genome Consortium |
author_facet |
Zhang, Guojie Li, Bo Li, Cai Gilbert, M Thomas P Jarvis, Erich D Wang, Jun Avian Genome Consortium |
author_sort |
Zhang, Guojie |
title |
Comparative genomic data of the Avian Phylogenomics Project. |
title_short |
Comparative genomic data of the Avian Phylogenomics Project. |
title_full |
Comparative genomic data of the Avian Phylogenomics Project. |
title_fullStr |
Comparative genomic data of the Avian Phylogenomics Project. |
title_full_unstemmed |
Comparative genomic data of the Avian Phylogenomics Project. |
title_sort |
comparative genomic data of the avian phylogenomics project. |
publishDate |
2014 |
url |
https://hdl.handle.net/10161/9322 http://www.ncbi.nlm.nih.gov/pubmed/25671091 |
long_lat |
ENVELOPE(167.383,167.383,-72.567,-72.567) |
geographic |
Finch |
geographic_facet |
Finch |
genre |
Adelie penguin peregrine falcon |
genre_facet |
Adelie penguin peregrine falcon |
op_relation |
10.1186/2047-217X-3-26 http://hdl.handle.net/10161/9321 10161/9321 http://www.ncbi.nlm.nih.gov/pubmed/25671091 https://hdl.handle.net/10161/9322 |
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