Draft assemblies for 177 bird species enhance genus-level coverage.
Publisher DOI
PubMed ID
42104960
Abstract
Background
With over 10,000 recognized species, birds constitute one of the most diverse and widely distributed vertebrate groups. Although avian genomics has advanced rapidly over the past decade, substantial gaps remain across the global avifauna. Filling these gaps is essential for understanding macroevolutionary patterns, population structure, and the molecular basis of ecological and behavioral diversity. Worldwide museum collections represent invaluable resources for filling these gaps, yet the typically degraded DNA and limited quantities from historical specimens have posed significant challenges for generating high-quality genome assemblies.Results
Here, the Bird Genome 10 K (B10K) Project adopted low-input sequencing strategies that reduce costs while improving assembly quality compared with earlier order- and family-level genomes. Using mainly stLFR, complemented by 10X Genomics and standard next-generation sequencing, we assembled 177 avian genomes from museum specimens and tissue collections representing 161 genera, including 102 newly sequenced at the genomic level. The assemblies average ∼1.2 Gb in size, with scaffold N50 = 8.03 Mb, contig N50 = 120 kb, 93% BUSCO completeness, and Merqury QV score of 56.Conclusions
These genomes greatly expand avian taxonomic coverage and demonstrate the efficiency of low-input sequencing for generating high-quality assemblies from limited and often degraded material sourced from museum specimens. This resource provides a foundation for comparative genomics, conservation genetics, and evolutionary studies across the avian tree of life.
With over 10,000 recognized species, birds constitute one of the most diverse and widely distributed vertebrate groups. Although avian genomics has advanced rapidly over the past decade, substantial gaps remain across the global avifauna. Filling these gaps is essential for understanding macroevolutionary patterns, population structure, and the molecular basis of ecological and behavioral diversity. Worldwide museum collections represent invaluable resources for filling these gaps, yet the typically degraded DNA and limited quantities from historical specimens have posed significant challenges for generating high-quality genome assemblies.Results
Here, the Bird Genome 10 K (B10K) Project adopted low-input sequencing strategies that reduce costs while improving assembly quality compared with earlier order- and family-level genomes. Using mainly stLFR, complemented by 10X Genomics and standard next-generation sequencing, we assembled 177 avian genomes from museum specimens and tissue collections representing 161 genera, including 102 newly sequenced at the genomic level. The assemblies average ∼1.2 Gb in size, with scaffold N50 = 8.03 Mb, contig N50 = 120 kb, 93% BUSCO completeness, and Merqury QV score of 56.Conclusions
These genomes greatly expand avian taxonomic coverage and demonstrate the efficiency of low-input sequencing for generating high-quality assemblies from limited and often degraded material sourced from museum specimens. This resource provides a foundation for comparative genomics, conservation genetics, and evolutionary studies across the avian tree of life.
Date Issued
2026-01-21
Publication Type
Article
Subject(s)
Subjects
biodiversity
•
birds
•
genome sequencing
Language(s)
en
Author(s)
Chen, Guangji | |
Wang, Shuang | |
Bilyeli Øksnebjerg, Daniel | |
Nielsen, Sascha Dreyer | |
Dai, Wei | |
Jiang, Wei | |
Liang, Jing | |
Han, Wei | |
Zhou, Chengran | |
Li, Qiye | |
Petersen, Bent | |
Monadjem, Ara | |
Bhembe, Zamekile D | |
Maphalala, Machawe | |
Ocampo, Diego | |
Sandoval, Luis | |
Fickel, Jörns | |
Greenwood, Alex D | |
Szentiks, Claudia A | |
Roller, Marco | |
Birks, Sharon M | |
Leaché, Adam D | |
Rico-Guevara, Alejandro | |
Fuchs, Jérôme | |
Vy, Nguyen Tran | |
Hvilsom, Christina | |
Berner, Juliana Andrea | |
Lifjeld, Jan Terje | |
Johnsen, Arild | |
Johannessen, Lars Erik | |
Labuschagne, Kim | |
Jønsson, Knud Andreas | |
Irestedt, Martin | |
Reeve, Andrew Hart | |
Joseph, Leo | |
Hellgren, Olof | |
Brumfield, Robb T | |
Burg, Theresa M | |
Illera, Juan Carlos | |
Aleixo, Alexandre | |
Rheindt, Frank E | |
Nishiumi, Isao | |
Quesada, Javier | |
Dumbacher, John P | |
Andersen, Michael J | |
Witt, Christopher C | |
Phillips, Richard A | |
Prum, Richard | |
Zyskowski, Kristof | |
Goodman, Steven M | |
Raherilalao, Marie Jeanne | |
Ottosson, Ulf | |
Barshep, Yahkat | |
Ivande, Sam | |
Brlík, Vojtěch | |
Okposio, Emmanuel | |
Koane, Bonny | |
Haryoko, Tri | |
Jarvis, Erich D | |
Rahbek, Carsten | |
Lei, Fumin | |
Graves, Gary R | |
Feng, Shaohong | |
Hosner, Peter A | |
Gilbert, M Thomas P | |
Zhang, Guojie |
Additional Credits
Journal
GigaScience
Publisher
Oxford University Press
ISSN
2047-217X
Access(Rights)
open.access