A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor
A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor
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DOI：
10.1073/pnas.1219082110
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发表时间：
2013-05-07
影响因子：
11.1
通讯作者：
Dvorak, Jan
中科院分区：
文献类型：
--
作者：
Luo, Ming-Cheng;Gu, Yong Q.;Dvorak, Jan
目前基因组测序技术的局限性要求构建大型植物基因组的高质量草图序列的物理图谱，例如小麦D-基因组祖先节节麦的基因组。去绘制一张埃厄星的物理地图。在tauschii基因组中，我们对461，706个细菌人工染色体克隆进行了指纹分析，组装了重叠群，设计了一个10 K的Ae。利用tauschii Infinium SNP阵列构建了一张包含7，185个标记的遗传图谱，并锚定在总长度为4.03 Gb的重叠群上。使用全基因组鸟枪读取，我们扩展了SNP标记序列，发现了17，093个基因和基因片段。我们发现，共线性的Ae。tauschii基因与二穗短柄草，水稻和高粱的系统发育距离下降，结构基因组进化率一直在所有调查的谱系在亚科Pooideae，包括Brachypodieae。我们获得了额外的信息，从12个祖先染色体的7个小麦染色体的进化，并发现了一种模式的着丝粒失活伴随着嵌套染色体插入草。我们发现，非共线基因的密度沿着Ae。tauschii染色体与重组率正相关，提出了一个原因，并表明新基因，例如抗病基因，优先位于高重组染色体区域。
The current limitations in genome sequencing technology require the construction of physical maps for high-quality draft sequences of large plant genomes, such as that of Aegilops tauschii, the wheat D-genome progenitor. To construct a physical map of the Ae. tauschii genome, we fingerprinted 461,706 bacterial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array, constructed a 7,185-marker genetic map, and anchored on the map contigs totaling 4.03 Gb. Using whole genome shotgun reads, we extended the SNP marker sequences and found 17,093 genes and gene fragments. We showed that collinearity of the Ae. tauschii genes with Brachypodium distachyon, rice, and sorghum decreased with phylogenetic distance and that structural genome evolution rates have been high across all investigated lineages in subfamily Pooideae, including that of Brachypodieae. We obtained additional information about the evolution of the seven Triticeae chromosomes from 12 ancestral chromosomes and uncovered a pattern of centromere inactivation accompanying nested chromosome insertions in grasses. We showed that the density of noncollinear genes along the Ae. tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions.