Construction of a chromosome-level Japanese stickleback species genome using ultra-dense linkage analysis with single-cell sperm sequencing.
Construction of a chromosome-level Japanese stickleback species genome using ultra-dense linkage analysis with single-cell sperm sequencing.
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DOI：
10.1093/nargab/lqac026
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发表时间：
2022-06
影响因子：
4.6
通讯作者：
Asakawa S
中科院分区：
文献类型：
--
作者：
Yoshitake K;Ishikawa A;Yonezawa R;Kinoshita S;Kitano J;Asakawa S
构建高等生物的基因组仍然很困难，因为它们的基因组序列必须通过连锁分析延伸到染色体的长度。在这项研究中，我们试图提供一个创新的替代传统的连锁分析，设计了一种方法，使用10× Genomics单细胞基因组测序文库的精子基因型，以产生一个连锁图没有杂交个体。利用日本棘鱼Gasterosteus nipponicus的精子组装基因组，单细胞基因分型产生1864430个非常密集的异源SNP，每个精子细胞的平均覆盖率为0.13×。总共使用了1665个精子，这比用于常规连锁分析的重组数量高一个数量级。然后根据单细胞基因分型数据的特点，改进了连锁分析工具scaffold extender with low depth linkage analysis（SELDLA），对数据进行分析。最后，我们能够确定456 Mb基因组中重叠群的染色体定位（97.1%）和方向（64.4%）。nipponicus，使用纳米孔测序。这种方法有望成为一个有用的工具，用于确定非模式生物的基因组的育种系统尚未建立的连锁分析。
It is still difficult to construct the genomes of higher organisms as their genome sequences must be extended to the length of the chromosome by linkage analysis. In this study, we attempted to provide an innovative alternative to conventional linkage analysis by devising a method to genotype sperm using 10× Genomics single-cell genome sequencing libraries to generate a linkage map without interbreeding individuals. A genome was assembled using sperm from the Japanese stickleback Gasterosteus nipponicus, with single-cell genotyping yielding 1 864 430 very dense hetero-SNPs and an average coverage per sperm cell of 0.13×. In total, 1665 sperm were used, which is an order of magnitude higher than the number of recombinations used for conventional linkage analysis. We then improved the linkage analysis tool scaffold extender with low depth linkage analysis (SELDLA) to analyze the data according to the characteristics of the single-cell genotyping data. Finally, we were able to determine the chromosomal location (97.1%) and orientation (64.4%) of the contigs in the 456 Mb genome of G. nipponicus, sequenced using nanopores. This method promises to be a useful tool for determining the genomes of non-model organisms for which breeding systems have not yet been established by linkage analysis.
影响因子：
4.6
作者：
Yoshitake K;Igarashi Y;Mizukoshi M;Kinoshita S;Mitsuyama S;Suzuki Y;Saito K;Watabe S;Asakawa S
通讯作者：
Asakawa S