Deep sequencing analysis of the transcriptomes of peanut aerial and subterranean young pods identifies candidate genes related to early embryo abortion
Deep sequencing analysis of the transcriptomes of peanut aerial and subterranean young pods identifies candidate genes related to early embryo abortion
复制标题
DOI：
10.1111/pbi.12018
复制
发表时间：
2013-01-01
影响因子：
13.8
通讯作者：
Liang, Xuanqiang
中科院分区：
文献类型：
--
作者：
Chen, Xiaoping;Zhu, Wei;Liang, Xuanqiang
花生的种子败育是由于钉钉不能深入土壤而造成的。对参与这些过程的基因的了解相对缺乏。在这里，我们使用RNA-seq来深入了解空中和地下豆荚的转录组。利用焦磷酸测序技术从1个空中（AP）和2个地下（SP1和SP2）荚果文库中获得了200多万个转录本reads，平均长度为396bp。组装后，在AP、SP1和SP2中分别从74974个转录本组装组（TACs）中鉴定出49632、49952和50494组。在这些数据集之间观察到基因表达水平明显的线性关系。总之，共鉴定出2194个差异表达的tac，真阳性率为99.0%，其中空中豆荚上调859个，地下豆荚上调1068个。功能分析显示，59342个（79.2%）TACs和42955个（57.3%）TACs分别可以通过与UniProt和基因本体术语分类中所编目的蛋白相似度来确定推测功能。共有2968个tac被映射到174个KEGG通路上，其中168个是空中和地下转录组共享的。参与光合作用的tac在荚果中显著上调和富集。此外，两个衰老相关基因在空中豆荚中被发现显著上调，这可能有助于空中豆荚中的胚胎流产，进而停止肿胀。本研究中产生的数据集为一些功能基因作为空中和地下豆荚发育的有力候选提供了证据，并有助于阐明在光照和黑暗条件下果实发育的进化意义。
The failure of peg penetration into the soil leads to seed abortion in peanut. Knowledge of genes involved in these processes is comparatively deficient. Here, we used RNA-seq to gain insights into transcriptomes of aerial and subterranean pods. More than 2 million transcript reads with an average length of 396bp were generated from one aerial (AP) and two subterranean (SP1 and SP2) pod libraries using pyrosequencing technology. After assembly, sets of 49632, 49952 and 50494 from a total of 74974 transcript assembly contigs (TACs) were identified in AP, SP1 and SP2, respectively. A clear linear relationship in the gene expression level was observed between these data sets. In brief, 2194 differentially expressed TACs with a 99.0% true-positive rate were identified, among which 859 and 1068 TACs were up-regulated in aerial and subterranean pods, respectively. Functional analysis showed that putative function based on similarity with proteins catalogued in UniProt and gene ontology term classification could be determined for 59342 (79.2%) and 42955 (57.3%) TACs, respectively. A total of 2968 TACs were mapped to 174 KEGG pathways, of which 168 were shared by aerial and subterranean transcriptomes. TACs involved in photosynthesis were significantly up-regulated and enriched in the aerial pod. In addition, two senescence-associated genes were identified as significantly up-regulated in the aerial pod, which potentially contribute to embryo abortion in aerial pods, and in turn, to cessation of swelling. The data set generated in this study provides evidence for some functional genes as robust candidates underlying aerial and subterranean pod development and contributes to an elucidation of the evolutionary implications resulting from fruit development under light and dark conditions.