| Endothelial type I interferon signaling modulates the vascular response to ischemic brain injury |
Kavli Affiliate: Erich Jarvis
| Authors: Giulio Formenti, Nivesh Jain, Jack A Medico, Marco Sollitto, Dmitry Antipov, Jennifer Balacco, Suziane Barcellos, Matthew T Biegler, Ines Borges, J King Chang, Ying Chen, Haoyu Cheng, Helena B Conceicao, Matthew Davenport, Lorraine C De Oliveira, Erick Duarte, Gillian P Durham, Jonathan Fenn, Niamh Forde, Juhyun Kim, Aleksey Komissarov, Bonhwang Koo, Sergey Koren, Pedro A F Galante, Kenji Gerhardt, Alice M Giani, Simona Giunta, Denis Larkin, Chul Lee, Heng Li, Kateryna Makova, Patrick Masterson, Terence Murphy, Kirsty McCaffrey, Rafael L V Mercuri, Yeojung Na, Mary J O Connell, Shujun Ou, Adam M Phillippy, Marina Popova, Arang Rhie, Francisco J Ruiz-Ruano, Simona Secomandi, Linnea Smeds, Alexander Suh, Tatiana Tilley, Niki Vontzou, Paul D Waters and Erich D Jarvis
| Summary:
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 (Taeniopygia guttata), 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.