A reference genome for the Harpy Eagle reveals steady demographic decline and chromosomal rearrangements in the origin of Accipitriformes.

Autor: Canesin LEC; Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Belém, Brazil., Vilaça ST; Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Belém, Brazil., Oliveira RRM; Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Belém, Brazil., Al-Ajli F; Rockefeller University, New York, USA.; Katara Biodiversity Genomics Program, Katara Cultural Village Foundation, Doha, Qatar., Tracey A; Rockefeller University, New York, USA., Sims Y; Rockefeller University, New York, USA., Formenti G; Rockefeller University, New York, USA., Fedrigo O; Rockefeller University, New York, USA., Banhos A; Universidade Federal do Espírito Santo (UFES), Alegre, Brazil., Sanaiotti TM; Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil., Farias IP; Universidade Federal do Amazonas (UFAM), Manaus, Brazil., Jarvis ED; Rockefeller University, New York, USA.; Howard Hughes Medical Institute (HHMI), New York, USA., Oliveira G; Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Belém, Brazil., Hrbek T; Universidade Federal do Amazonas (UFAM), Manaus, Brazil.; Trinity University, San Antonio, USA., Solferini V; Universidade Estadual de Campinas (Unicamp), Campinas, Brazil., Aleixo A; Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Belém, Brazil. alexandre.aleixo@itv.org.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2024 Sep 12; Vol. 14 (1), pp. 19925. Date of Electronic Publication: 2024 Sep 12.
DOI: 10.1038/s41598-024-70305-w
Abstrakt: The Harpy Eagle (Harpia harpyja) is an iconic species that inhabits forested landscapes in Neotropical regions, with decreasing population trends mainly due to habitat loss, and currently classified as vulnerable. Here, we report on a chromosome-scale genome assembly for a female individual combining long reads, optical mapping, and chromatin conformation capture reads. The final assembly spans 1.35 Gb, with N50 scaffold equal to 58.1 Mb and BUSCO completeness of 99.7%. We built the first extensive transposable element (TE) library for the Accipitridae to date and identified 7,228 intact TEs. We found a burst of an unknown TE ~ 13-22 million years ago (MYA), coincident with the split of the Harpy Eagle from other Harpiinae eagles. We also report a burst of solo-LTRs and CR1 retrotransposons ~ 31-33 MYA, overlapping with the split of the ancestor to all Harpiinae from other Accipitridae subfamilies. Comparative genomics with other Accipitridae, the closely related Cathartidae and Galloanserae revealed major chromosome-level rearrangements at the basal Accipitriformes genome, in contrast to a conserved ancient genome architecture for the latter two groups. A historical demography reconstruction showed a rapid decline in effective population size over the last 20,000 years. This reference genome serves as a crucial resource for future conservation efforts towards the Harpy Eagle.
(© 2024. The Author(s).)
Databáze: MEDLINE
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