Improving Nelumbo nucifera genome assemblies using high-resolution genetic maps and BioNano genome mapping reveals ancient chromosome rearrangements
Improving Nelumbo nucifera genome assemblies using high-resolution genetic maps and BioNano genome mapping reveals ancient chromosome rearrangements
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DOI：
10.1111/tpj.13894
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发表时间：
2018-05-01
期刊：
影响因子：
7.2
通讯作者：
Ding, Yi
中科院分区：
文献类型：
--
作者：
Gui, Songtao;Peng, Jing;Ding, Yi
遗传和物理图谱是锚由下一代测序产生的片段化基因组草图组装的有力工具。目前，莲的两个基因组草图，即“中国古董”和“中国太子”的基因组草图已经发布。然而，目前还没有关于这些序列是如何组装成n.nucifera染色体的信息。物理图谱的缺乏和可用遗传图谱的分辨率不足阻碍了烟草染色体的组装。本研究利用181个F（2）个体的限制性内切酶位点相关DNA测序数据构建了含2371个bin标记[217577个单核苷酸多态性（SNP）]的珠母贝连锁图谱，并通过添加197个SSR标记进行了验证。此外，构建了一个覆盖86.20%的“中国太子”基因组的BioNano光学图谱。基于BioNano光学图谱对“中国太子”的草图组装进行了改进，显示支架N50从0.989增加到1.48Mb。利用多图谱组合，将97.9%的中国台子草图装配中的骨架和97.6%的中国古董草图装配中的骨架锚定到假染色体上，并鉴定了假染色体上的沿着着丝粒区域。提出了一个进化的方案，以达到现代N。nucifera核型的七个祖先真双子叶植物染色体。本研究提供了高分辨率的连锁图谱、光学图谱和染色体水平的基因组组装。nucifera，对我国的栽培和育种具有重要的参考价值。被子植物比较和进化基因组学研究的展望。
Genetic and physical maps are powerful tools to anchor fragmented draft genome assemblies generated from next-generation sequencing. Currently, two draft assemblies of Nelumbo nucifera, the genomes of 'China Antique' and 'Chinese Tai-zi', have been released. However, there is presently no information on how the sequences are assembled into chromosomes in N.nucifera. The lack of physical maps and inadequate resolution of available genetic maps hindered the assembly of N.nucifera chromosomes. Here, a linkage map of N.nucifera containing 2371 bin markers [217577 single nucleotide polymorphisms (SNPs)] was constructed using restriction-site associated DNA sequencing data of 181F(2) individuals and validated by adding 197 simple sequence repeat (SSR) markers. Additionally, a BioNano optical map covering 86.20% of the 'Chinese Tai-zi' genome was constructed. The draft assembly of Chinese Tai-zi' was improved based on the BioNano optical map, showing an increase of the scaffold N50 from 0.989 to 1.48Mb. Using a combination of multiple maps, 97.9% of the scaffolds in the Chinese Tai-zi' draft assembly and 97.6% of the scaffolds in the China Antique' draft assembly were anchored into pseudo-chromosomes, and the centromere regions along the pseudo-chromosomes were identified. An evolutionary scenario was proposed to reach the modern N. nucifera karyotype from the seven ancestral eudicot chromosomes. The present study provides the highest-resolution linkage map, the optical map and chromosome level genome assemblies for N. nucifera, which are valuable for the breeding and cultivation of N. nucifera and future studies of comparative and evolutionary genomics in angiosperms.