Draft assemblies for 177 bird species enhance genus-level coverage

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.

Authors

Institutions

Publication Details

Journal
GigaScience
Published
2026-05-08
DOI
https://doi.org/10.1093/gigascience/giag045
Primary Topic
Genomics and Phylogenetic Studies
Type
article
Field-Weighted Citation Impact
0.00
Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

Draft assemblies for 177 bird species enhance genus-level coverage

Bent Petersen, Adam D. Leaché, Ulf Ottosson, Isao Nishiumi et al.
GigaScience
Genomics and Phylogenetic Studies
article

Draft assemblies for 177 bird species enhance genus-level coverage

Bent Petersen, Adam D. Leaché, Ulf Ottosson, Isao Nishiumi, Ben Smit, Peter A. Hosner, Andrew Hart Reeve, Manuel Schweizer, Luis Sandoval, Diego Ocampo, Martin Irestedt, Shaohong Feng, Christina Hvilsom, Nguyen Tran Vy, Bonny Koane, Lars Erik Johannessen, Vojtěch Brlík, Jan Terje Lifjeld, Tri Haryoko, Kim Labuschagne, Knud A. Jønsson, Wei Dai, Alejandro Rico‐Guevara, Guojie Zhang, Marco Roller, Sharon Birks, Robb T. Brumfield, Kristof Zyskowski, Olof Hellgren, Arild Johnsen, Christopher C. Witt, Theresa M. Burg, Chengran Zhou, Zamekile D. Bhembe, Guangji Chen, Daniel Bilyeli Øksnebjerg, Claudia A. Szentiks, Qi Li, Jörns Fickel, Marie Jeanne Raherilalao, Juliana Andrea Berner, J. Quesada, Richard Prum, Sascha Dreyer Nielsen, Emmanuel Okposio, Jessica Lee, Jérôme Fuchs, Michael J Andersen, Frank E Rheindt, Fumin Lei, Alex D Greenwood, Gary R Graves, Juan Carlos Illera, Yahkat Barshep, Erich D Jarvis, Jing Liang, Wei Han, Machawe Maphalala, Wei Jiang, Leo Joseph, Ara Monadjem, John P Dumbacher, Steven M Goodman, Shuang Wang, Alexandre Aleixo, Sam Ivande, Richard A Phillips, Carsten Rahbek, M Thomas P Gilbert
article en

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.

GigaScience
BGI Group (China) (CN), University of Lethbridge (CA), University of Hohenheim (DE), Global Biodiversity Information Facility (DK), University of Bern (CH), Louisiana State University (US), University of Copenhagen (DK), Museum of Vertebrate Zoology (US), British Antarctic Survey (GB), Museu Paraense Emílio Goeldi (BR), Natural History Museum (GB), Houston Museum of Natural Science (US), American Museum of Natural History (US), National Museum of Natural History (US), University of Antananarivo (MG), University of Jos (NG), Vale (Brazil) (BR), National University of Singapore (SG), University of Eswatini (SZ), University of Potsdam (DE), University of Southern Denmark (DK), University of Oslo (NO), Lund University (SE), University of Veterinary Medicine Hannover, Foundation (DE), University of Washington (US), Rhodes University (ZA), Charles University (CZ), Swedish Museum of Natural History (SE), Field Museum of Natural History (US), Copenhagen Zoo (DK), Sir Run Run Shaw Hospital (CN), Indianapolis Zoo (US), Mammal Research Institute (PL), California Academy of Sciences (US), Universidad de Costa Rica (CR), South African National Biodiversity Institute (ZA), Natural History Museum of Bern (CH), Biodiversity Research Institute (US), Museu de Ciències Naturals de Barcelona (ES), Senckenberg Natural History Collections Dresden (DE), Institut de Systématique, Évolution, Biodiversité (FR), Seva Mandir (IN), Burke Museum of Natural History and Culture (US), Natural History Museum Aarhus (DK), New Guinea Binatang Research Center (PG), Institute of Zoology (KZ), National Biodiversity Institute (CR), Association Vahatra (MG), Botswana Geoscience Institute (BW), Southwestern College - New Mexico (US), Robert S. Peabody Museum of Archaeology (US), Vitensenteret i Trondheim (NO), Women's Hospital, School of Medicine, Zhejiang University (CN), Museum am Rothenbaum (DE), Leibniz Institute for Zoo and Wildlife Research (DE), National Museum of Nature and Science (JP), Hospital for Tropical Diseases (VN), Australian National Wildlife Collection (AU), Vale Technological Institute (BR), University of Chinese Academy of Sciences (CN), Institute of Zoology (CN), California State University, Fresno (US), University of Pretoria (ZA), University of Göttingen (DE), Freie Universität Berlin (DE), Rockefeller University (US)
Life in Land
Openalex Percentile: Top 8%
Genomics and Phylogenetic Studies
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.