近日，由广东省农业科学院作物研究所梁炫强研究员、陈小平博士，山东省农业科学院花生研究所所长禹山林研究员及国际半干旱热带作物研究所（ICRISAT）基因组中心负责人Rajeev Kumar Varshney等完成的花生转录组de novo测序的结果发表于Plant Biotechnology Journal。该杂志创刊于2003年，影响因子5.44，是专注于应用植物科学的期刊。本研究是中国花生基因组计划取得的又一阶段性成果，测序和部分信息分析工作均在Macrogen千年基因完成。
花生(Arachis hypogaea L.)是我国重要的油料和经济作物，因其“地上开花，地下结荚”的特性被称之为“落花生”。花生受精后子房柄（又称果针）开始伸长并启动向地性生长，从而将子房带入地下，到达一定深度后子房开始膨大并发育成荚果。研究表明，黑暗和机械刺激是果针发育的必要条件，而温度、水分、空气、营养等外界因素也影响果针发育的过程。因此，果针能否入土关系到花生能否正常结荚。但由于目前尚未完成花生全基因组图谱的绘制，关于果针发育的分子机制目前尚不明确，本研究将从转录组水平阐明影响果针发育的关键基因。
本研究应用Roche 454（GS FLX Titanium）测序平台，分别对花生的地上果针（AP）和2个不同发育时期的地下果针（SP1和SP2）进行1/2 run转录组de novo测序，得到274M（704,738条reads）、290M（711,496条reads）和238M（609,841条reads）原始数据（raw data），测序reads的平均读长为396bp，去除接头等序列和低质量值reads后获得83%的有效数据（clean data）。相关测序结果已提交至NCBI的SRA数据库（www.ncbi.nlm.nih.gov/sra），登录号为SRA053198。
AP、SP1和SP2的测序数据合并后以Newbler（v2.6）和TGICL2.0分别进行组装，并比较两个软件的组装性能。组装结果与现有的花生转录组数据合并去冗余后构建花生转录组参考序列，序列大小114.9M，约是花生基因组大小的4.1%。组装结果分别进行功能基因预测、GO（gene ontology）分类、KEGG（Kyoto Encyclopaedia of Genes and Genomes）代谢通路注释和基因差异表达分析，结果表明在2194个差异表达基因中，地上果针和地下果针分别有859和1068个转录本的表达显着性上调。在地上果针中，与光合作用和衰老相关的基因表达显着上调，这2个基因很可能阻止了果针的膨大从而导致败育。本研究的结果为探索果针发育的分子机制提供了充分的理论依据，并为花生转录组和功能基因组的研究提供了更多的数据资源。(生物谷Bioon.com)
DOI: 10.1111/pbi.12018
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Deep sequencing analysis of the transcriptomes of peanut aerial and subterranean young pods identifies candidate genes related to early embryo abortion
Xiaoping Chen1, Wei Zhu1,2, Sarwar Azam3,Heying Li4, Fanghe Zhu1, Haifen Li1, Yanbin Hong1, Haiyan Liu1, Erhua Zhang1, Hong Wu4,Shanlin Yu5, Guiyuan Zhou1, Shaoxiong Li1, Ni Zhong1, Shijie Wen1, Xingyu Li1, Steve J. Knapp6,Peggy Ozias-Akins6, Rajeev K. Varshney1,3,Xuanqiang Liang1,*
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 396 bp were generated from one aerial (AP) and two subterranean (SP1 and SP2) pod libraries using pyrosequencing technology. After assembly, sets of 49 632, 49 952 and 50 494 from a total of 74 974 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 59 342 (79.2%) and 42 955 (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.
