An Annotated Draft Genome of the Mountain Hare (Lepus timidus)
An Annotated Draft Genome of the Mountain Hare (Lepus timidus)
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DOI：
10.1093/gbe/evz273
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发表时间：
2020-01-01
影响因子：
3.3
通讯作者：
Melo-Ferreira, Jose
中科院分区：
文献类型：
--
作者：
Marques, Joao P.;Seixas, Fernando A.;Melo-Ferreira, Jose
野兔（Lepus属）提供了重复和经常大量的渐渗杂交和惊人的地方适应的明确例子。迄今为止，对这一群体的基因组研究依赖于与欧洲兔（耳兔）参考基因组的比较。在这里，我们报道了野兔（Lepus timidus）的第一个全新的参考基因组草案，并评估了使用新参考基因组与使用兔参考基因组进行全基因组重测序分析的有效性。采用ALLPATHS-LG方案，结合重叠对和配对对Illumina测序（77x覆盖）对基因组进行组装。该装配包含32294个支架，总长度为2.7 Gb，支架N50为3.4 Mb。基于家兔参考文献的重新支架将支架总数减少到4205个，支架N50为194 Mb。根据基因含量和直接比对，发现其中22个支架与家兔染色体对应。通过结合从头算预测、同源性搜索和转录组数据，我们注释了24,578个蛋白质编码基因，其中683个基因完全来自野兔特异性转录组数据。因此，野兔参考基因组是发现和研究野兔特异性变异的新资源。当将全基因组重测序数据映射到新的野兔草图基因组或基于兔子基因组的替代参考时，获得了类似的杂合度估计和推断的人口统计学历史概况。我们的结果验证了先前基于参考的策略，并表明染色体尺度的野兔草图基因组应该能够对野兔进行染色体范围的分析和基因组扫描。
Hares (genus Lepus) provide clear examples of repeated and often massive introgressive hybridization and striking local adaptations. Genomic studies on this group have so far relied on comparisons to the European rabbit (Otyctolagus cuniculus) reference genome. Here, we report the first de novo draft reference genome for a hare species, the mountain hare (Lepus timidus), and evaluate the efficacy of whole-genome re-sequencing analyses using the new reference versus using the rabbit reference genome. The genome was assembled using the ALLPATHS-LG protocol with a combination of overlapping pair and mate-pair Illumina sequencing (77x coverage). The assembly contained 32,294 scaffolds with a total length of 2.7 Gb and a scaffold N50 of 3.4 Mb. Re-scaffolding based on the rabbit reference reduced the total number of scaffolds to 4,205 with a scaffold N50 of 194 Mb. A correspondence was found between 22 of these hare scaffolds and the rabbit chromosomes, based on gene content and direct alignment. We annotated 24,578 protein coding genes by combining ab-initio predictions, homology search, and transcriptome data, of which 683 were solely derived from hare-specific transcriptome data. The hare reference genome is therefore a new resource to discover and investigate hare-specific variation. Similar estimates of heterozygosity and inferred demographic history profiles were obtained when mapping hare whole-genome re-sequencing data to the new hare draft genome or to alternative references based on the rabbit genome. Our results validate previous reference-based strategies and suggest that the chromosome-scale hare draft genome should enable chromosome-wide analyses and genome scans on hares.