The Diversity of Sequence and Chromosomal Distribution of New Transposable Element-Related Segments in the Rye Genome Revealed by FISH and Lineage Annotation.
The Diversity of Sequence and Chromosomal Distribution of New Transposable Element-Related Segments in the Rye Genome Revealed by FISH and Lineage Annotation.
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DOI：
10.3389/fpls.2017.01706
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发表时间：
2017
影响因子：
5.6
通讯作者：
Hu Z
中科院分区：
文献类型：
--
作者：
Zhang Y;Fan C;Li S;Chen Y;Wang RR;Zhang X;Han F;Hu Z
植物基因组中的转座因子（Transposable elements，TE）具有多样的结构、序列内容和拷贝数，是物种多样性和基因组进化的重要驱动因子。尽管利用高通量DNA测序技术已经获得了黑麦中TEs的全基因组统计汇总，但由于重复序列组装问题以及TEs的高动态和嵌套性质，黑麦中TEs的准确多样性以及它们的染色体分布和进化仍然是难以捉摸的。在这项研究中，使用基因组质粒文库构建结合斑点杂交和荧光原位杂交（FISH）分析，我们成功地分离出70个独特的FISH阳性TE相关序列，其中包括47个黑麦基因组特异性序列：30个与先前的FISH特征序列同源或部分同源，40个尚未被表征。在70个序列中，48个序列含有Ty 3/gypsy来源的片段，7个序列含有Ty 1/copia来源的片段，15个序列含有与多个TE家族同源的片段。在70个序列中发现了26个TE谱系，其中Wilma分布在除端粒以外的所有染色体区域，Abiba主要分布在着丝粒和近着丝粒区域，Wis、Carmilla和Inga分布在从远端区域向近着丝粒区域扩散的序列中，而Inga则分布在端粒附近区域。除DNA转座子谱系外，所有其他谱系均在显示从近端区域向远端区域分散的信号的序列中发现。在本研究中鉴定了高百分比（21.4%）的嵌合序列，并且它们在黑麦基因组中的高丰度表明新的TE可能通过重组和嵌套转座形成。我们的研究结果也证明了不同的TE谱系排列在黑麦的着丝粒和近着丝粒的位置，像Abiba谱系可能在其结构组织和功能中发挥作用。所有这些结果可能有助于理解黑麦中TE的多样性和进化，以及它们在黑麦基因组组织和进化中的驱动力。
Transposable elements (TEs) in plant genomes exhibit a great variety of structure, sequence content and copy number, making them important drivers for species diversity and genome evolution. Even though a genome-wide statistic summary of TEs in rye has been obtained using high-throughput DNA sequencing technology, the accurate diversity of TEs in rye, as well as their chromosomal distribution and evolution, remains elusive due to the repetitive sequence assembling problems and the high dynamic and nested nature of TEs. In this study, using genomic plasmid library construction combined with dot-blot hybridization and fluorescence in situ hybridization (FISH) analysis, we successfully isolated 70 unique FISH-positive TE-related sequences including 47 rye genome specific ones: 30 showed homology or partial homology with previously FISH characterized sequences and 40 have not been characterized. Among the 70 sequences, 48 sequences carried Ty3/gypsy-derived segments, 7 sequences carried Ty1/copia-derived segments and 15 sequences carried segments homologous with multiple TE families. 26 TE lineages were found in the 70 sequences, and among these lineages, Wilma was found in sequences dispersed in all chromosome regions except telomeric positions; Abiba was found in sequences predominantly located at pericentromeric and centromeric positions; Wis, Carmilla, and Inga were found in sequences displaying signals dispersed from distal regions toward pericentromeric positions; except DNA transposon lineages, all the other lineages were found in sequences displaying signals dispersed from proximal regions toward distal regions. A high percentage (21.4%) of chimeric sequences were identified in this study and their high abundance in rye genome suggested that new TEs might form through recombination and nested transposition. Our results also gave proofs that diverse TE lineages were arranged at centromeric and pericentromeric positions in rye, and lineages like Abiba might play a role in their structural organization and function. All these results might help in understanding the diversity and evolution of TEs in rye, as well as their driving forces in rye genome organization and evolution.
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影响因子：
3.7
作者：
Goriaux C;Théron E;Brasset E;Vaury C
通讯作者：
Vaury C
影响因子：
7
作者：
Bousios A;Diez CM;Takuno S;Bystry V;Darzentas N;Gaut BS
通讯作者：
Gaut BS
影响因子：
14.9
作者：
Gent JI;Dong Y;Jiang J;Dawe RK
通讯作者：
Dawe RK
DOI：
10.1093/dnares/dsm029
发表时间：
2008-02-29
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Tomita M;Shinohara K;Morimoto M
通讯作者：
Morimoto M
影响因子：
4.9
作者：
Bao W;Kojima KK;Kohany O
通讯作者：
Kohany O