Synteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity DOI Creative Commons
Evelyn L. Jensen,

Chiara Marchisio,

Alexander Ochoa

et al.

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: April 1, 2025

ABSTRACT The utility and importance of whole‐genome sequences are recognized across various fields, including evolution conservation. However, for some taxa, like extinct species, using methods to generate contiguous genomes that rely on high‐quality DNA is impossible. In such cases, an alternative may be employ synteny‐based a genome from closely related taxon more complete genomes. Here we update the reference Pinta Island Galapagos giant tortoise ( Chelonoidis abingdonii ) without conducting additional sequencing through rescaffolding against most chromosome‐level assembly, Aldabra Aldabrachelys gigantea ). This effort resulted in much genome, CheloAbing_2.0, with N50 two orders magnitude longer large reductions L50 number gaps. We then examined impact CheloAbing_2.0 estimates runs homozygosity (ROH) resequencing data 37 individual tortoises 13 extant lineages test mechanisms by which fragmented assembly over‐ or underestimate extent ROH. use inbreeding, ROH proportion (F ), (N cumulative length (S were statistically different those derived earlier assembly. improved will serve as resource future efforts focusing ecology, evolution, conservation this species group. More broadly, our results highlight scaffolding promising generating needing types.

Language: Английский

Digest: Whole genomes delimit multiple species of Galapagos giant tortoises DOI Creative Commons
Tabitha R. Taberer

Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 9, 2025

Utilising whole genome sequencing and multiple species delimitation models, Gaughran et al. (2024) show support for up to 13 distinct living Galapagos giant tortoise species, in contrast the current classification of a single species. This result highlights potential rapidly radiating organisms on islands act as model systems investigating boundaries, helping settle taxonomic debates.

Language: Английский

Citations

0
Synteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity DOI Creative Commons
Evelyn L. Jensen,

Chiara Marchisio,

Alexander Ochoa

et al.

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: April 1, 2025

ABSTRACT The utility and importance of whole‐genome sequences are recognized across various fields, including evolution conservation. However, for some taxa, like extinct species, using methods to generate contiguous genomes that rely on high‐quality DNA is impossible. In such cases, an alternative may be employ synteny‐based a genome from closely related taxon more complete genomes. Here we update the reference Pinta Island Galapagos giant tortoise ( Chelonoidis abingdonii ) without conducting additional sequencing through rescaffolding against most chromosome‐level assembly, Aldabra Aldabrachelys gigantea ). This effort resulted in much genome, CheloAbing_2.0, with N50 two orders magnitude longer large reductions L50 number gaps. We then examined impact CheloAbing_2.0 estimates runs homozygosity (ROH) resequencing data 37 individual tortoises 13 extant lineages test mechanisms by which fragmented assembly over‐ or underestimate extent ROH. use inbreeding, ROH proportion (F ), (N cumulative length (S were statistically different those derived earlier assembly. improved will serve as resource future efforts focusing ecology, evolution, conservation this species group. More broadly, our results highlight scaffolding promising generating needing types.

Language: Английский

Citations

0