近日,，由廣東省農(nóng)業(yè)科學(xué)院作物研究所梁炫強(qiáng)研究員,、陳小平博士,，山東省農(nóng)業(yè)科學(xué)院花生研究所所長(zhǎng)禹山林研究員及國(guó)際半干旱熱帶作物研究所（ICRISAT）基因組中心負(fù)責(zé)人Rajeev Kumar Varshney等完成的花生轉(zhuǎn)錄組de novo測(cè)序的結(jié)果發(fā)表于Plant Biotechnology Journal。該雜志創(chuàng)刊于2003年,，影響因子5.44,，是專注于應(yīng)用植物科學(xué)的期刊。本研究是中國(guó)花生基因組計(jì)劃取得的又一階段性成果,，測(cè)序和部分信息分析工作均在Macrogen千年基因完成,。
花生(Arachis hypogaea L.)是我國(guó)重要的油料和經(jīng)濟(jì)作物，因其“地上開花,，地下結(jié)莢”的特性被稱之為“落花生”,。花生受精后子房柄（又稱果針）開始伸長(zhǎng)并啟動(dòng)向地性生長(zhǎng),，從而將子房帶入地下,，到達(dá)一定深度后子房開始膨大并發(fā)育成莢果。研究表明,，黑暗和機(jī)械刺激是果針發(fā)育的必要條件,，而溫度、水分,、空氣,、營(yíng)養(yǎng)等外界因素也影響果針發(fā)育的過(guò)程。因此,，果針能否入土關(guān)系到花生能否正常結(jié)莢,。但由于目前尚未完成花生全基因組圖譜的繪制，關(guān)于果針發(fā)育的分子機(jī)制目前尚不明確,，本研究將從轉(zhuǎn)錄組水平闡明影響果針發(fā)育的關(guān)鍵基因,。
本研究應(yīng)用Roche 454（GS FLX Titanium）測(cè)序平臺(tái)，分別對(duì)花生的地上果針（AP）和2個(gè)不同發(fā)育時(shí)期的地下果針（SP1和SP2）進(jìn)行1/2 run轉(zhuǎn)錄組de novo測(cè)序,，得到274M（704,738條reads）,、290M（711,496條reads）和238M（609,841條reads）原始數(shù)據(jù)（raw data），測(cè)序reads的平均讀長(zhǎng)為396bp,，去除接頭等序列和低質(zhì)量值reads后獲得83%的有效數(shù)據(jù)（clean data）,。相關(guān)測(cè)序結(jié)果已提交至NCBI的SRA數(shù)據(jù)庫(kù)（www.ncbi.nlm.nih.gov/sra），登錄號(hào)為SRA053198。
AP,、SP1和SP2的測(cè)序數(shù)據(jù)合并后以Newbler（v2.6）和TGICL2.0分別進(jìn)行組裝,，并比較兩個(gè)軟件的組裝性能。組裝結(jié)果與現(xiàn)有的花生轉(zhuǎn)錄組數(shù)據(jù)合并去冗余后構(gòu)建花生轉(zhuǎn)錄組參考序列,，序列大小114.9M,，約是花生基因組大小的4.1%。組裝結(jié)果分別進(jìn)行功能基因預(yù)測(cè),、GO（gene ontology）分類,、KEGG（Kyoto Encyclopaedia of Genes and Genomes）代謝通路注釋和基因差異表達(dá)分析，結(jié)果表明在2194個(gè)差異表達(dá)基因中,，地上果針和地下果針?lè)謩e有859和1068個(gè)轉(zhuǎn)錄本的表達(dá)顯著性上調(diào),。在地上果針中，與光合作用和衰老相關(guān)的基因表達(dá)顯著上調(diào),，這2個(gè)基因很可能阻止了果針的膨大從而導(dǎo)致敗育,。本研究的結(jié)果為探索果針發(fā)育的分子機(jī)制提供了充分的理論依據(jù)，并為花生轉(zhuǎn)錄組和功能基因組的研究提供了更多的數(shù)據(jù)資源,。(生物谷Bioon.com)
DOI: 10.1111/pbi.12018
PMC:
PMID:
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.
