利用 Hi-C 测序提高牙鲆（Plecoglossus altivelis）基因组草图质量。
Improvement of the ayu (Plecoglossus altivelis) draft genome using Hi-C sequencing.
机构信息
Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, 108-8477, Japan.
出版信息
BMC Res Notes. 2023 May 30;16(1):92. doi: 10.1186/s13104-023-06362-7.
OBJECTIVE
The ayu or sweetfish Plecoglossus altivelis is ray-finned fish that is widely distributed in East Asia. The genome size of ayu was estimated at approximately 420 Mb. Previously, we reported on ayu draft genome assembly by whole-genome shotgun using Illumina short reads and PacBio long reads; however, the assembly was not to chromosome level. Therefore, to improve the draft genome sequence of ayu to chromosome level, we performed in situ Hi-C sequencing as a source of linkage information.
RESULTS
The ayu genome assembly yielded 28 large scaffolds that corresponded to the karyotype of ayu (n = 28). The resulting ayu genome assembly has a N50 scaffold length of 17.0 Mb, improved from 4.3 Mb. The high-quality reference genome will be helpful for phylogenetic research on bony fishes and for breeding programs in ayu aquaculture.
目的
真鲷或甜鱼 Plecoglossus altivelis 是一种分布于东亚的硬骨鱼类。真鲷的基因组大小约为 420Mb。此前，我们曾使用 Illumina 短读长和 PacBio 长读长对真鲷的基因组草图进行了全基因组鸟枪法测序，但组装结果未达到染色体水平。因此，为了将真鲷的基因组草图序列提升到染色体水平，我们进行了原位 Hi-C 测序以获取连锁信息。
结果
真鲷基因组组装得到了 28 个与真鲷染色体（n=28）相对应的大支架。组装得到的真鲷基因组的 N50 支架长度为 17.0Mb，优于之前的 4.3Mb。高质量的参考基因组将有助于骨鱼类的系统发育研究和真鲷水产养殖的选育计划。
Zotero 插件