DOI: 10.5061/dryad.sxksn03f6
title: Synteny enabled upgrade of the Galapagos giant tortoise genome improves inferences of runs of homozygosity

description: 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. --
description: # Synteny enabled upgrade of the Galapagos giant tortoise genome improves
 inferences of runs of homozygosity Dataset DOI:
 [10.5061/dryad.sxksn03f6](10.5061/dryad.sxksn03f6) ## Description of the
 data and file structure The files herein consist of the final genome
 assembly, annotation file and filtered VCF files used for ROH analyses.
 ### Files and variables #### File:
 37GalTort\_FilteredSNPs\_cheloabing1.0.vcf.gz **Description:** VCF file of
 37 Galapapagos giant tortoise individuals used for ROH analyses based on
 genome version CheloAbing_1.0. This file can be opened and manipulated
 using the software vcftools, or R via the package vcfR. #### File:
 37GalTort\_FilteredSNPs\_cheloabing2.0.vcf.gz **Description:** VCF file of
 37 Galapapagos giant tortoise individuals used for ROH analyses based on
 genome version CheloAbing_2.0. This file can be opened and manipulated
 using the software vcftools, or R via the package vcfR. #### File:
 liftoff\_annotation\_1.0\_to\_2.0.gff.zip **Description:** the gff file of
 the annotation of ChelAbing_2.0. Once unzipped, this file can be opened in
 a standard text editor. #### File: CheloAbing2.0.fasta.zip
 **Description:** fasta file containing the ChelAbing_2.0 genome assembly.
 Once unzipped, this file can be opened in a standard text editor. ##
 Access information Other publicly accessible locations of the data: * This
 study made use of existing data available on the NCBI SRA under biosample
 SAMN07840320 and bioproject PRJNA761229.