Supporting data for "Entering the era of conservation genomics: Cost-effective assembly of the African wild dog genome using linked reads"

A high-quality reference genome assembly is a valuable tool for the study of non-model organisms across disciplines. Genomic techniques can provide important insights about past population sizes, local adaptation, and even aid in the development of breeding management plans. This information can be particularly important for fields like conservation genetics, where endangered species require critical and immediate attention. However, funding for genomic-based methods can be sparse for conservation projects, as costs for general species management can consume budgets. Here we report the generation of high-quality reference genomes for the African wild dog (Lycaon pictus) at a low cost, thereby facilitating future studies of this endangered canid. We generated assemblies for three individuals from whole blood samples using the linked-read 10x Genomics Chromium system. The most continuous assembly had a scaffold N50 of 21 Mb, a contig N50 of 83 Kb, and completely reconstructed 95% of conserved mammalian genes as reported by BUSCO v2, indicating a high assembly quality. Thus, we show that 10x Genomics Chromium data can be used to effectively generate high-quality genomes of mammal species from Illumina short-read data of intermediate coverage (~25-50x). Interestingly, the wild dog shows a much higher heterozygosity than other species of conservation concern, possibly as a result of its behavioral ecology. The availability of reference genomes for non-model organisms will facilitate better genetic monitoring of threatened species such as the African wild dog and help researchers and conservationists to better understand the ecology and adaptability of those species in a changing environment.

高质量参考基因组组装（reference genome assembly）是跨学科开展非模式生物（non-model organisms）研究的宝贵工具。基因组学技术可为物种过往种群规模、本地适应性等研究提供重要见解，甚至可辅助制定育种管理方案。这类信息对于保护遗传学（conservation genetics）等领域尤为关键，因为濒危物种亟需得到高度重视与及时救助。然而，保护项目中基于基因组学的研究方法往往经费匮乏，常规物种管理的开销常会耗尽项目整体预算。本研究成功以低成本完成了非洲野犬（Lycaon pictus）的高质量参考基因组组装，为这一濒危犬科动物（canid）的后续研究奠定基础。我们采用连锁读长（linked-read）10x Genomics Chromium测序系统，对3份来自全血样本的个体进行了基因组组装。其中连续性最优的组装结果，其支架N50（scaffold N50）为21 Mb，重叠群N50（contig N50）为83 Kb，经BUSCO v2评估显示，完整重建了95%的哺乳动物保守单拷贝基因，表明该组装质量优异。综上，本研究证实，依托约25-50倍中间覆盖度的Illumina短读长测序数据（Illumina short-read data），可借助10x Genomics Chromium测序数据高效构建哺乳动物的高质量基因组。值得注意的是，非洲野犬的杂合度（heterozygosity）显著高于其他受保护关注的物种，这一现象可能与其行为生态学特征相关。非模式生物参考基因组的获取，将有助于对非洲野犬等受威胁物种开展更精准的遗传监测，同时帮助研究者与保护工作者更好地理解这些物种在环境变化下的生态学特征与适应性能力。