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The complete genome of a songbird

by Antipov, Dmitry , Giunta, Simona , Chen, Ying , Smeds, Linnéa , De Oliveira, Lorraine , Masterson, Patrick , Davenport, Matthew , Suh, Alexander , Tilley, Tatiana , Jarvis, Erich D , Galante, Pedro A , Koren, Sergey , Borges, Inês , Ou, Shujun , Li, Heng , O'Connell, Mary J , Chang, J King , Giani, Alice M , Mercuri, Rafael L V , Makova, Kateryna , Rhie, Arang , Biegler, Matthew , McCaffrey, Kirsty , Na, Yeojung , Vontzou, Niki , Sollitto, Marco , Fenn, Jonathan , Durham, Gillian , Lee, Chul , Medico, Jack A , Koo, Bonhwang , Forde, Niamh , Jain, Nivesh , Ruiz-Ruano, Francisco J , Balacco, Jennifer , Gerhardt, Kenji , Phillippy, Adam , Conceição, Helena , Secomandi, Simona , Formenti, Giulio , Kim, Juhyun , Duarte, Erick , Waters, Paul D , Popova, Marina , Murphy, Terence , Cheng, Haoyu , Larkin, Denis , Barcellos, Suziane , Komissarov, Aleksey

in Genomics

2025

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The complete genome of a songbird

in Genomics

2025

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The complete genome of a songbird

in Genomics

2025

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Journal Article

The complete genome of a songbird

Antipov, Dmitry,

Giunta, Simona,

Chen, Ying,

Smeds, Linnéa,

De Oliveira, Lorraine,

Masterson, Patrick,

Davenport, Matthew,

Suh, Alexander,

Tilley, Tatiana,

Jarvis, Erich D,

Galante, Pedro A,

Koren, Sergey,

Borges, Inês,

Ou, Shujun,

Li, Heng,

O'Connell, Mary J,

Chang, J King,

Giani, Alice M,

Mercuri, Rafael L V,

Makova, Kateryna,

Rhie, Arang,

Biegler, Matthew,

McCaffrey, Kirsty,

Na, Yeojung,

Vontzou, Niki,

Sollitto, Marco,

Fenn, Jonathan,

Durham, Gillian,

Lee, Chul,

Medico, Jack A,

Koo, Bonhwang,

Forde, Niamh,

Jain, Nivesh,

Ruiz-Ruano, Francisco J,

Balacco, Jennifer,

Gerhardt, Kenji,

Phillippy, Adam,

Conceição, Helena,

Secomandi, Simona,

Formenti, Giulio,

Kim, Juhyun,

Duarte, Erick,

Waters, Paul D,

Popova, Marina,

Murphy, Terence,

Cheng, Haoyu,

Larkin, Denis,

Barcellos, Suziane,

Komissarov, Aleksey

2025

Overview

Bird genomes are the smallest among amniotes, but remain challenging to assemble due to their structural complexity. This study presents the first fully phased, diploid, telomere-to-telomere (T2T) reference genome for the zebra finch ( ), a model organism for neuroscience and evolutionary genomics. Combining multiple sequencing strategies resulted in closing nearly all gaps, adding ~90 Mbp of previously missing sequence (7.8%). This includes T2T assemblies for all microchromosomes, including dot chromosomes, and the previously almost entirely missing chr16. The T2T genome is comprehensively annotated for genes, repeats, structural variants, and long-read methylation calls. Complete centromeric structures were assembled and annotated along with kinetochore binding sites. Relative to the previous high-quality reference of the Vertebrate Genomes Project, 2,778 (8.51%) previously unassembled or unannotated genes were identified, of which 9% overlap with segmental duplications. This first complete genome of a songbird, now the new public reference, illuminates avian genome architecture and function.

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Publisher

Cold Spring Harbor Laboratory

Subject

Genomics