An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data
An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data
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DOI：
10.1186/s12864-020-6657-2
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发表时间：
2020-04-02
期刊：
影响因子：
4.4
通讯作者：
Sakakibara, Yasubumi
中科院分区：
文献类型：
--
作者：
Jayakumar, Vasanthan;Ishii, Hiromi;Sakakibara, Yasubumi
普通绒猴（Callithrix jacchus）是研究最多的灵长类模式生物之一。然而，公共数据库中的绒猴基因组高度碎片化，充满了序列空白，阻碍了与绒猴基因组学和转录组学相关的研究进展。结果在这里，我们利用单分子，长读段序列数据，以改善和更新现有的基因组组装和报告一个接近完整的基因组的普通绒猴。该组装体大小为2.79 Gb，重叠群N50长度为6.37 Mb，染色体支架N50长度为143.91 Mb，代表了迄今为止最连续和高质量的绒猴基因组。大约90%的组装基因组以长度超过1 Mb的重叠群表示，与先前公布的绒猴基因组相比，其邻近性提高了约104倍。超过98%的来自先前公布的基因组的缺口被成功填补，这提高了基因组和转录组数据到组装基因组的映射率。结论更新后的高质量普通绒猴基因组组装体与以前版本的绒猴基因组组装体相比在不同程度上有所改进。这将使研究灵长类基因组学的研究人员能够更有效地将基因组应用于其基因组和转录组序列数据。
Background The common marmoset (Callithrix jacchus) is one of the most studied primate model organisms. However, the marmoset genomes available in the public databases are highly fragmented and filled with sequence gaps, hindering research advances related to marmoset genomics and transcriptomics. Results Here we utilize single-molecule, long-read sequence data to improve and update the existing genome assembly and report a near-complete genome of the common marmoset. The assembly is of 2.79 Gb size, with a contig N50 length of 6.37 Mb and a chromosomal scaffold N50 length of 143.91 Mb, representing the most contiguous and high-quality marmoset genome up to date. Approximately 90% of the assembled genome was represented in contigs longer than 1 Mb, with approximately 104-fold improvement in contiguity over the previously published marmoset genome. More than 98% of the gaps from the previously published genomes were filled successfully, which improved the mapping rates of genomic and transcriptomic data on to the assembled genome. Conclusions Altogether the updated, high-quality common marmoset genome assembly provide improvements at various levels over the previous versions of the marmoset genome assemblies. This will allow researchers working on primate genomics to apply the genome more efficiently for their genomic and transcriptomic sequence data.