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..., , # 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

**Desc...,

全基因组序列的实用价值与重要性在演化与保护生物学等诸多领域已得到广泛认可。然而，对于部分类群（如已灭绝物种）而言，依赖高质量DNA获取连续基因组的传统方法已无法实施。此类场景下，可采用基于共线性（synteny）的替代方案：借助近缘类群的基因组序列，构建更为完整的基因组。本研究未开展额外测序，而是通过与亲缘关系最近的染色体级基因组组装——阿尔达布拉象龟（Aldabrachelys gigantea）的基因组进行重支架组装，更新了平塔岛加拉帕戈斯象龟（Chelonoidis abingdonii）的参考基因组。最终获得了连续性大幅提升的CheloAbing_2.0版本基因组，其N50值提升了两个数量级，L50值与缺口数量均显著降低。随后，我们利用基因组重测序数据，分析了CheloAbing_2.0基因组对纯合性片段（Runs of homozygosity, ROH）估算结果的影响……
# 基于共线性的加拉帕戈斯象龟基因组升级优化了纯合性片段的推断分析

数据集DOI：10.5061/dryad.sxksn03f6

## 数据与文件结构说明
本数据集包含用于纯合性片段分析的最终基因组组装结果、注释文件以及过滤后的VCF文件。

### 文件与变量说明

#### 文件：37GalTort_FilteredSNPs_cheloabing1.0.vcf.gz
**描述：** 本文件为基于CheloAbing_1.0版本基因组开展纯合性片段分析所用的37只加拉帕戈斯象龟个体的VCF文件。可通过vcftools软件或R语言的vcfR包打开并处理该文件。

#### 文件：37GalTort_FilteredSNPs_cheloabing2.0.vcf.gz
**描述：** 本文件为基于CheloAbing_2.0版本基因组开展纯合性片段分析所用的37只加拉帕戈斯象龟个体的VCF文件。可通过vcftools软件或R语言的vcfR包打开并处理该文件。

#### 文件：liftoff_annotation_1.0_to_2.0.gff.zip
**描述：** ……