Construction of a plant-transformation-competent BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.).
Construction of a plant-transformation-competent BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.).
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DOI：
10.1186/1471-2164-14-208
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发表时间：
2013-03-28
期刊：
影响因子：
4.4
通讯作者：
Zhang HB
中科院分区：
文献类型：
--
作者：
Lee MK;Zhang Y;Zhang M;Goebel M;Kim HJ;Triplett BA;Stelly DM;Zhang HB
棉花是世界主要农作物之一，对世界纺织和能源工业具有重要意义，是研究植物多倍化、纤维素生物合成和细胞壁生物发生的模式物种。本文报道了多倍体陆地棉BIBAC文库的构建和比较基因组序列分析。与其可能的二倍体祖先种之一雷蒙地棉(G.raimondii Ulbr.)我们构建了棉花BIBAC文库，该文库可以通过农杆菌或基因枪法在不同植物中进行大分子量DNA转化。文库包含76,800个克隆，平均插入大小为135kb，提供了使用单拷贝探针从文库获得至少一个阳性克隆的大约99%的可能性。通过鉴定含有纤维发育、纤维纤维素生物合成、种子脂肪酸代谢、棉花-线虫互作和白叶枯病抗性重要基因的BIBAC，验证了文库的质量和实用性。为了深入了解陆地棉基因组及其与G.raimondii的关系，我们从文库中随机挑选了近10,000个BIBAC末端(BESS)进行测序，大约每250kb对应于陆地棉基因组的1个BES。反转录元件Gypsy/DIRS1家族在陆地棉基因组中占主导地位，占所有转座元件的77%以上。从BESS中鉴定出1,269个简单序列重复序列(SSR)，其中1,006个为新发现，为棉花基因组研究提供了新的标记。令人惊讶的是，比较序列分析显示，陆地棉与雷蒙地棉在基因组序列水平上的差异比预期的要大得多。陆地棉D-和A-亚基因组与陆地棉基因组的亲缘关系似乎没有显著差异，尽管陆地棉含有D基因组(D5)。该文库代表了棉花及其近缘物种的第一个BIBAC文库，从而为陆地棉基因组的综合物理作图、大规模基因组测序和大规模功能分析提供了有用的工具。比较序列分析提供了对陆地棉基因组的洞察，以及多倍体陆地棉与其二倍体假定祖先种G.raimondii分化和进化的可能机制。
Cotton, one of the world’s leading crops, is important to the world’s textile and energy industries, and is a model species for studies of plant polyploidization, cellulose biosynthesis and cell wall biogenesis. Here, we report the construction of a plant-transformation-competent binary bacterial artificial chromosome (BIBAC) library and comparative genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.) with one of its diploid putative progenitor species, G. raimondii Ulbr. We constructed the cotton BIBAC library in a vector competent for high-molecular-weight DNA transformation in different plant species through either Agrobacterium or particle bombardment. The library contains 76,800 clones with an average insert size of 135 kb, providing an approximate 99% probability of obtaining at least one positive clone from the library using a single-copy probe. The quality and utility of the library were verified by identifying BIBACs containing genes important for fiber development, fiber cellulose biosynthesis, seed fatty acid metabolism, cotton-nematode interaction, and bacterial blight resistance. In order to gain an insight into the Upland cotton genome and its relationship with G. raimondii, we sequenced nearly 10,000 BIBAC ends (BESs) randomly selected from the library, generating approximately one BES for every 250 kb along the Upland cotton genome. The retroelement Gypsy/DIRS1 family predominates in the Upland cotton genome, accounting for over 77% of all transposable elements. From the BESs, we identified 1,269 simple sequence repeats (SSRs), of which 1,006 were new, thus providing additional markers for cotton genome research. Surprisingly, comparative sequence analysis showed that Upland cotton is much more diverged from G. raimondii at the genomic sequence level than expected. There seems to be no significant difference between the relationships of the Upland cotton D- and A-subgenomes with the G. raimondii genome, even though G. raimondii contains a D genome (D5). The library represents the first BIBAC library in cotton and related species, thus providing tools useful for integrative physical mapping, large-scale genome sequencing and large-scale functional analysis of the Upland cotton genome. Comparative sequence analysis provides insights into the Upland cotton genome, and a possible mechanism underlying the divergence and evolution of polyploid Upland cotton from its diploid putative progenitor species, G. raimondii.
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影响因子：
4.4
作者：
Lin L;Pierce GJ;Bowers JE;Estill JC;Compton RO;Rainville LK;Kim C;Lemke C;Rong J;Tang H;Wang X;Braidotti M;Chen AH;Chicola K;Collura K;Epps E;Golser W;Grover C;Ingles J;Karunakaran S;Kudrna D;Olive J;Tabassum N;Um E;Wissotski M;Yu Y;Zuccolo A;ur Rahman M;Peterson DG;Wing RA;Wendel JF;Paterson AH
通讯作者：
Paterson AH
影响因子：
5.4
作者：
Feng, Jiuhuan;Vick, Brady A.;Jan, C. C.
通讯作者：
Jan, C. C.
影响因子：
11.4
作者：
Hu, Yan;Guo, Wang-Zhen;Zhang, Tian-Zhen
通讯作者：
Zhang, Tian-Zhen
影响因子：
3.5
作者：
He, LM;Du, CG;Zhang, HB
通讯作者：
Zhang, HB
影响因子：
3.1
作者：
Li, Yaning;Uhm, Taesik;Zhang, Hong-Bin
通讯作者：
Zhang, Hong-Bin