A preliminary analysis of genome structure and composition in Gossypium hirsutum.
A preliminary analysis of genome structure and composition in Gossypium hirsutum.
复制标题
陆地棉基因组结构和组成的初步分析
DOI：
10.1186/1471-2164-9-314
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发表时间：
2008-07-01
期刊：
影响因子：
4.4
通讯作者：
Zhang T
中科院分区：
文献类型：
--
作者：
Guo W;Cai C;Wang C;Zhao L;Wang L;Zhang T
背景
陆地棉产量最高，占世界棉花产量的95%。破译陆地棉基因组无疑将为该物种的结构、功能和进化研究提供最终的参考和资源。在这里，我们使用GeneTrek和BAC标签信息方法来预测异源四倍体棉花基因组的一般组成和结构。
结果
陆地棉142个BAC序列。MAXXA被下载到http://www.ncbi.nlm.nih.gov并得到确认。这些BAC序列分析表明，四倍体棉花基因组包含70,000多个候选基因，在同源的A-和D-亚基因组区域有重复的基因拷贝。基因分布不均，基因组中既有富含基因的区域，也有无基因的区域。142个BAC中有21%缺乏基因。BAC基因密度为0~33.2个/100kb，而大多数基因岛只含有一个基因，平均每个岛含有1.5个基因。发现复古元素是主要成分，第一种是富含Ltr/吉普赛人，第二种是Ltr/Copia。大多数LTR反转录转座子被截断，呈嵌套式结构。此外，从70个BAC克隆中开发的SSR扩增出166个多态座位，标记在我们的骨干遗传图谱上。75%(125/166)的多态座位被标记在D-亚基因组上。通过对四倍体陆地棉扩增产物的分子大小进行综合分析。Maxxa，Acc.TM-1和海岛棉(G.barbadense cv.)海7124和二倍体草棉(G.herbaceum var.African anum和G.raimondii，37个BAC，12个来自A-亚基因组，25个来自D-亚基因组，进一步锚定到相应的亚基因组染色体上。通过对不同亚基因组BAC的大量基因序列比较，结果表明，内含子可能对棉属不同亚基因组大小没有贡献。
结论
这一研究使我们对棉花基因组的复杂性有了初步的了解，并为今后进行四倍体棉花全基因组测序奠定了基础。
Background
Upland cotton has the highest yield, and accounts for 95% of world cotton production. Decoding upland cotton genomes will undoubtedly provide the ultimate reference and resource for structural, functional, and evolutionary studies of the species. Here, we employed GeneTrek and BAC tagging information approaches to predict the general composition and structure of the allotetraploid cotton genome.
Results
142 BAC sequences from Gossypium hirsutum cv. Maxxa were downloaded http://www.ncbi.nlm.nih.gov and confirmed. These BAC sequence analysis revealed that the tetraploid cotton genome contains over 70,000 candidate genes with duplicated gene copies in homoeologous A- and D-subgenome regions. Gene distribution is uneven, with gene-rich and gene-free regions of the genome. Twenty-one percent of the 142 BACs lacked genes. BAC gene density ranged from 0 to 33.2 per 100 kb, whereas most gene islands contained only one gene with an average of 1.5 genes per island. Retro-elements were found to be a major component, first an enriched LTR/gypsy and second LTR/copia. Most LTR retrotransposons were truncated and in nested structures. In addition, 166 polymorphic loci amplified with SSRs developed from 70 BAC clones were tagged on our backbone genetic map. Seventy-five percent (125/166) of the polymorphic loci were tagged on the D-subgenome. By comprehensively analyzing the molecular size of amplified products among tetraploid G. hirsutum cv. Maxxa, acc. TM-1, and G. barbadense cv. Hai7124, and diploid G. herbaceum var. africanum and G. raimondii, 37 BACs, 12 from the A- and 25 from the D-subgenome, were further anchored to their corresponding subgenome chromosomes. After a large amount of genes sequence comparison from different subgenome BACs, the result showed that introns might have no contribution to different subgenome size in Gossypium.
Conclusion
This study provides us with the first glimpse of cotton genome complexity and serves as a foundation for tetraploid cotton whole genomesequencing in the future.
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影响因子：
7.4
作者：
Haberer, G;Young, S;Messing, J
通讯作者：
Messing, J
影响因子：
5.4
作者：
Paterson, AH;Saranga, Y;Wright, RJ
通讯作者：
Wright, RJ
DOI：
10.1073/pnas.0509473102
发表时间：
2005-12-27
影响因子：
11.1
作者：
Devos, KM;Ma, JX;Bennetzen, JL
通讯作者：
Bennetzen, JL
影响因子：
14.9
作者：
Deutsch, M;Long, M
通讯作者：
Long, M
影响因子：
4.2
作者：
Sanmiguel, P;Bennetzen, JL
通讯作者：
Bennetzen, JL