Synteny enabled upgrade of the Galapagos giant tortoise genome improves inferences of runs of homozygosity

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