Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids.
Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids.
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DOI：
10.1038/s41598-017-14885-w
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发表时间：
2017-11-10
影响因子：
4.6
通讯作者：
Chen ZJ
中科院分区：
文献类型：
--
作者：
Saski CA;Scheffler BE;Hulse-Kemp AM;Liu B;Song Q;Ando A;Stelly DM;Scheffler JA;Grimwood J;Jones DC;Peterson DG;Schmutz J;Chen ZJ
像许多农作物一样，栽培的棉花是异源四倍体，基因组很大(~2.5千兆碱基对)。A和D两个亚基因组高度相似，但大小不相等，重复丰富，这对使用标准方法进行准确的基因组重建构成了巨大的挑战。在这里，我们报告了BAC文库、亚基因组特定物理图谱的发展，以及将导致陆地棉参考级基因组组装的新一代测序方法。构建了三个BAC文库，指纹图谱，并与BAC末端序列(BES)整合，形成从头开始的全基因组物理图谱。BAC图谱通过与二倍体前体D基因组参考序列的比对和密集分布的BES锚点和计算过滤来对子基因组进行划分。用FISH和来自BES的SNP标记的遗传作图对物理图谱进行了验证。两对同源染色体，A11/D11和A12/D12，被用来评估多重测序方法的完整性和可扩展性。这些结果代表了陆地棉第一个亚基因组锚定的物理图谱，以及新一代全基因组测序方法，这将导致异源多倍体棉花的参考级组装，并为其他多倍体物种的测序提供一般策略。
Like those of many agricultural crops, the cultivated cotton is an allotetraploid and has a large genome (~2.5 gigabase pairs). The two sub genomes, A and D, are highly similar but unequally sized and repeat-rich, which pose significant challenges for accurate genome reconstruction using standard approaches. Here we report the development of BAC libraries, sub genome specific physical maps, and a new-generation sequencing approach that will lead to a reference-grade genome assembly for Upland cotton. Three BAC libraries were constructed, fingerprinted, and integrated with BAC-end sequences (BES) to produce a de novo whole-genome physical map. The BAC map was partitioned by sub genomes through alignment to the diploid progenitor D-genome reference sequence with densely spaced BES anchor points and computational filtering. The physical maps were validated with FISH and genetic mapping of SNP markers derived from BES. Two pairs of homeologous chromosomes, A11/D11 and A12/D12, were used to assess multiplex sequencing approaches for completeness and scalability. The results represent the first sub genome anchored physical maps of Upland cotton, and a new-generation approach to the whole-genome sequencing, which will lead to the reference-grade assembly of allopolyploid cotton and serve as a general strategy for sequencing other polyploid species.
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影响因子：
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Beasley, JO
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