Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order.
Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order.
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对 Haynaldia villosa 染色体 4V 的短臂进行流式排序测序，可深入了解其分子结构和虚拟基因顺序
DOI：
10.1186/s12864-017-4211-7
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发表时间：
2017-10-16
期刊：
影响因子：
4.4
通讯作者：
Wang X
中科院分区：
文献类型：
--
作者：
Xiao J;Dai K;Fu L;Vrána J;Kubaláková M;Wan W;Sun H;Zhao J;Yu C;Wu Y;Abrouk M;Wang H;Doležel J;Wang X
小麦草（Haynaldia villosa， H. villosa）是一种具有改良潜力的小麦种质。其基因组序列的可用性将促进其研究和应用。本研究采用流式细胞术对绒毛猴染色体4V （4VS）短臂进行了分选，并利用Illumina平台进行了测序。得到约170.6 Mb的组装序列。进一步分析表明，重复元件约占4VS的64.6%，而编码部分，对应于1977个注释基因，占手臂的1.5%。在小麦类群4第4AL、4BS、4DS染色体、短柄柄第1、4号染色体、水稻第3、11号染色体和高粱第1、5、8号染色体上检索并鉴定了4VS的同工区。基于基因组拉链分析，参考短柄藓类基因组构建了4VS基因组上735个基因位点的虚拟基因序列，与伊蚊的支架序列较为一致。陶氏染色体4D。在小麦第4群染色体上鉴定了包括Rht-1基因在内的多个克隆基因的同源等位基因。这些序列为小麦抗黄花叶病毒基因Wss1等位于4VS上的基因的定位和定位克隆提供了有价值的信息。对4VS的研究提供了对绒毛猴基因组的详细了解，也可以作为绒毛猴基因组剩余部分测序的模型。本文的在线版本（10.1186/s12864-017-4211-7）包含补充材料，授权用户可以使用。
Haynaldia villosa (H. villosa) has been recognized as a species potentially useful for wheat improvement. The availability of its genomic sequences will boost its research and application. In this work, the short arm of H. villosa chromosome 4V (4VS) was sorted by flow cytometry and sequenced using Illumina platform. About 170.6 Mb assembled sequences were obtained. Further analysis showed that repetitive elements accounted for about 64.6% of 4VS, while the coding fraction, which is corresponding to 1977 annotated genes, represented 1.5% of the arm. The syntenic regions of the 4VS were searched and identified on wheat group 4 chromosomes 4AL, 4BS, 4DS, Brachypodium chromosomes 1 and 4, rice chromosomes 3 and 11, and sorghum chromosomes 1, 5 and 8. Based on genome-zipper analysis, a virtual gene order comprising 735 gene loci on 4VS genome was built by referring to the Brachypodium genome, which was relatively consistent with the scaffold order determined for Ae. tauschii chromosome 4D. The homologous alleles of several cloned genes on wheat group 4 chromosomes including Rht-1 gene were identified. The sequences provided valuable information for mapping and positional-cloning genes located on 4VS, such as the wheat yellow mosaic virus resistance gene Wss1. The work on 4VS provided detailed insights into the genome of H. villosa, and may also serve as a model for sequencing the remaining parts of H. villosa genome. The online version of this article (10.1186/s12864-017-4211-7) contains supplementary material, which is available to authorized users.
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