The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44.
The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44.
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DOI：
10.1371/journal.pone.0026801
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Buell CR
中科院分区：
文献类型：
--
作者：
Massa AN;Childs KL;Lin H;Bryan GJ;Giuliano G;Buell CR
马铃薯营养繁殖、同源四倍体和极端杂合性等复杂的生物学系统限制了马铃薯分子育种的进展。马铃薯基因组的可用性和伴随的基因互补与相应的基因结构，位置和功能注释是了解这种复杂植物和推进分子育种工作的强大资源。在这里，我们报告了一个参考的马铃薯转录组使用32个组织和生长条件从加倍的单倍体Solanum tuberosum组马铃薯克隆DM 1 -3 516 R44的基因组序列是可用的。超过5.5亿个RNA-Seq读数的分析允许检测和定量超过22，000个基因的表达水平。层次聚类和主成分分析捕获的生物学变异性，占组织之间的基因表达差异，表明组织特异性基因表达，和组织或条件限制表达的基因。利用基因共表达网络分析，我们确定了18个基因模块，代表马铃薯主要器官和发育阶段的组织特异性转录网络。这些信息为马铃薯研究以及茄科其他成员的研究提供了强有力的资源。
Advances in molecular breeding in potato have been limited by its complex biological system, which includes vegetative propagation, autotetraploidy, and extreme heterozygosity. The availability of the potato genome and accompanying gene complement with corresponding gene structure, location, and functional annotation are powerful resources for understanding this complex plant and advancing molecular breeding efforts. Here, we report a reference for the potato transcriptome using 32 tissues and growth conditions from the doubled monoploid Solanum tuberosum Group Phureja clone DM1-3 516R44 for which a genome sequence is available. Analysis of greater than 550 million RNA-Seq reads permitted the detection and quantification of expression levels of over 22,000 genes. Hierarchical clustering and principal component analyses captured the biological variability that accounts for gene expression differences among tissues suggesting tissue-specific gene expression, and genes with tissue or condition restricted expression. Using gene co-expression network analysis, we identified 18 gene modules that represent tissue-specific transcriptional networks of major potato organs and developmental stages. This information provides a powerful resource for potato research as well as studies on other members of the Solanaceae family.
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影响因子：
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Pachter L
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