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2 months ago | 
nature.com | DongAhn Yoo |Arang Rhie |Prajna hebbar |Francesca Antonacci |Glennis A. Logsdon |Brandon Pickett | +66 more
AbstractThe most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies1,2,3. Consequently, our understanding of the evolution of our species is incomplete. Here we present haplotype-resolved reference genomes and comparative analyses of six ape species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang.
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Feb 20, 2025 | 
nature.com | Simona Secomandi |Guido Roberto Gallo |Riccardo Rossi |Carlos Fernandes |Erich D. Jarvis |Andrea Bonisoli-Alquati | +1 more
Correction to: Nature Genetics https://doi.org/10.1038/s41588-024-02029-6, published online 8 January 2025. In the version of the article initially published, in Box 3, “(1.7 Gb versus 0.5 Mb)” should have read “(1.7 Gb versus 0.5 Gb)” and has now been corrected in the HTML and PDF versions of the article. About this articleSecomandi, S., Gallo, G.R., Rossi, R. et al. Author Correction: Pangenome graphs and their applications in biodiversity genomics. Nat Genet (2025).
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Jan 8, 2025 | 
nature.com | Simona Secomandi |Guido Roberto Gallo |Riccardo Rossi |Carlos Fernandes |Erich D. Jarvis |Andrea Bonisoli-Alquati | +1 more
AbstractComplete datasets of genetic variants are key to biodiversity genomic studies. Long-read sequencing technologies allow the routine assembly of highly contiguous, haplotype-resolved reference genomes. However, even when complete, reference genomes from a single individual may bias downstream analyses and fail to adequately represent genetic diversity within a population or species.
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Nov 19, 2024 | 
nature.com | Melissa Rincon-Sandoval |Linelle Abueg |Giulio Formenti |Erich D. Jarvis |Dahiana Arcila |Aaron Davis
AbstractHabitat transitions have shaped the evolutionary trajectory of many clades. Sea catfishes (Ariidae) have repeatedly undergone ecological transitions, including colonizing freshwaters from marine environments, leading to an adaptive radiation in Australia and New Guinea alongside non-radiating freshwater lineages elsewhere. Here, we generate and analyze one long-read reference genome and 66 short-read whole genome assemblies, in conjunction with genomic data for 54 additional species.
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Apr 22, 2024 | 
nature.com | Matteo Sebastianelli |Sifiso M. Lukhele |Simona Secomandi |Olivier Fedrigo |Ara Monadjem |Niels J. Dingemanse | +2 more
AbstractVocal rhythm plays a fundamental role in sexual selection and species recognition in birds, but little is known of its genetic basis due to the confounding effect of vocal learning in model systems. Uncovering its genetic basis could facilitate identifying genes potentially important in speciation. Here we investigate the genomic underpinnings of rhythm in vocal non-learning Pogoniulus tinkerbirds using 135 individual whole genomes distributed across a southern African hybrid zone.
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Apr 9, 2024 | 
nature.com | Wen Hu |Mark Diekhans |Jordan Marrocco |Lishomwa C. Ndhlovu |Teresa A. Milner |Erich D. Jarvis | +3 more
AbstractRNA isoforms influence cell identity and function. However, a comprehensive brain isoform map was lacking. We analyze single-cell RNA isoforms across brain regions, cell subtypes, developmental time points and species. For 72% of genes, full-length isoform expression varies along one or more axes. Splicing, transcription start and polyadenylation sites vary strongly between cell types, influence protein architecture and associate with disease-linked variation.
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Feb 6, 2024 | 
biorxiv.org | Elena N. Waidmann |Victor Yang |William Doyle |Erich D. Jarvis
AbstractVocal communication is a major component of animal social behavior. Vocalizations can be learned or innate, and can convey a variety of signals, including territorial limits, the presence of predators, or courtship intent. Mouse ultrasonic vocalizations (USVs) are a promising model in which to study mammalian vocal production circuits.
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Dec 7, 2023 | 
nature.com | Young Lee |Giulio Formenti |Jonathan Wood |Francoise Thibaud-Nissen |Chul Sang Lee |Erich D. Jarvis
AbstractChub mackerels (Scomber japonicus) are a migratory marine fish widely distributed in the Indo-Pacific Ocean. They are globally consumed for their high Omega-3 content, but their population is declining due to global warming. Here, we generated the first chromosome-level genome assembly of chub mackerel (fScoJap1) using the Vertebrate Genomes Project assembly pipeline with PacBio HiFi genomic sequencing and Arima Hi-C chromosome contact data.
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Oct 19, 2023 | 
nature.com | Ashley T. Sendell-Price |Mats Pettersson |Du Kang |Sylke Winkler |Adam M. Phillippy |Erich D. Jarvis | +5 more
AbstractSharks occupy diverse ecological niches and play critical roles in marine ecosystems, often acting as apex predators. They are considered a slow-evolving lineage and have been suggested to exhibit exceptionally low cancer rates. These two features could be explained by a low nuclear mutation rate. Here, we provide a direct estimate of the nuclear mutation rate in the epaulette shark (Hemiscyllium ocellatum).
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Aug 28, 2023 | 
nature.com | Joseph Guhlin |Jana Wold |Emily Koot |Patrick Biggs |Stephanie J. Galla |Lara Urban | +8 more
AbstractThe kākāpō is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analysed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a high-quality species-wide genetic variant callset.
