Construction of a chromosome-scale long-read reference genome assembly for potato.
Construction of a chromosome-scale long-read reference genome assembly for potato.
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DOI：
10.1093/gigascience/giaa100
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发表时间：
2020-09-23
期刊：
影响因子：
9.2
通讯作者：
Buell CR
中科院分区：
文献类型：
--
作者：
Pham GM;Hamilton JP;Wood JC;Burke JT;Zhao H;Vaillancourt B;Ou S;Jiang J;Buell CR
在世界范围内，栽培马铃薯，马铃薯L.，是第一大蔬菜作物，也是重要的粮食安全作物。本文报道了S. tuberosum Group Escherija，于2011年发表，使用具有短读序列数据的全基因组鸟枪测序方法。目前先进的测序技术现在允许以最低的成本产生接近完整的、高质量的染色体规模的基因组组装。在这里，我们提出了DM 1 -3 516 R44基因组序列（v6.1）的更新版本，使用Oxford Nanopore Technologies长读段与邻近连接支架（Hi-C）偶联，产生染色体规模的组装。新的（v6.1）组装代表了估计的844 Mb基因组的741.6 Mb序列（87.8%），其中741.5 Mb是无缺口的，731.2 Mb锚定在12条染色体上。使用Oxford Nanopore Technologies全长互补DNA测序，可以注释32，917个高置信度的蛋白质编码基因，编码44，851个基因模型，与以前的注释相比，这些基因模型具有显著改善的保守直系同源物的代表性。新的组装提高了邻接性，N50重叠群大小增加了595倍，重叠群数量减少了99%，N50支架大小增加了44倍，LTR组装指数得分为13.56，将其置于参考基因组质量类别中。改进的组装还允许通过与源自CENH 3核小体的测序读数比对来注释着丝粒。获得先进的测序技术和改进的软件，可以生成高质量、长读段、染色体规模的组装和改进的马铃薯参考基因型注释数据集，这将促进旨在改善农艺性状和理解基因组进化的研究。
Worldwide, the cultivated potato, Solanum tuberosum L., is the No. 1 vegetable crop and a critical food security crop. The genome sequence of DM1–3 516 R44, a doubled monoploid clone of S. tuberosum Group Phureja, was published in 2011 using a whole-genome shotgun sequencing approach with short-read sequence data. Current advanced sequencing technologies now permit generation of near-complete, high-quality chromosome-scale genome assemblies at minimal cost. Here, we present an updated version of the DM1–3 516 R44 genome sequence (v6.1) using Oxford Nanopore Technologies long reads coupled with proximity-by-ligation scaffolding (Hi-C), yielding a chromosome-scale assembly. The new (v6.1) assembly represents 741.6 Mb of sequence (87.8%) of the estimated 844 Mb genome, of which 741.5 Mb is non-gapped with 731.2 Mb anchored to the 12 chromosomes. Use of Oxford Nanopore Technologies full-length complementary DNA sequencing enabled annotation of 32,917 high-confidence protein-coding genes encoding 44,851 gene models that had a significantly improved representation of conserved orthologs compared with the previous annotation. The new assembly has improved contiguity with a 595-fold increase in N50 contig size, 99% reduction in the number of contigs, a 44-fold increase in N50 scaffold size, and an LTR Assembly Index score of 13.56, placing it in the category of reference genome quality. The improved assembly also permitted annotation of the centromeres via alignment to sequencing reads derived from CENH3 nucleosomes. Access to advanced sequencing technologies and improved software permitted generation of a high-quality, long-read, chromosome-scale assembly and improved annotation dataset for the reference genotype of potato that will facilitate research aimed at improving agronomic traits and understanding genome evolution.
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