05月03 【成功案例】百邁客云助力董文軒老師 使用 真核生物有參考基因組的轉(zhuǎn)錄組分析平臺(tái) 輔助研究，發(fā)表《比較轉(zhuǎn)錄組分析和形態(tài)學(xué)對(duì)杏品種（Prunus armeniaca L.）的內(nèi)果皮切割的研究》
摘要：
一個(gè)完整和硬化的內(nèi)果皮是核果的典型特征。 然而，“Liehe”（LE）杏品種具有薄，軟，可切割的內(nèi)皮，其厚度和木質(zhì)素含量分別占“金西紅”（JG）杏（具有正常硬化內(nèi)果皮）的60.39％和63.76％。為了了解LE杏表型背后的分子機(jī)制，本研究使用Illumina HiSeq TM?2500對(duì)Prunus armeniaca?L.進(jìn)行比較轉(zhuǎn)錄組測(cè)序。
本研究中鑒定出了63,170條unigenes（15,469條unigene的長(zhǎng)度大于1,000 bp），25,356條unigenes得到了功能注釋。利用通路富集及表達(dá)模式分析來(lái)分析差異表達(dá)基因，在LE杏中編碼苯丙素生物合成參與的關(guān)鍵酶的差異表達(dá)基因顯著下調(diào)，例如，在盛花期后15，21，30，49天中，編碼肉桂醇脫氫酶的CAD基因表達(dá)水平在LE杏中僅為JG品種的1.3％，0.7％，0.2％和2.7％。此外，確定了調(diào)節(jié)次級(jí)壁和木質(zhì)素生物合成的轉(zhuǎn)錄因子，特別是對(duì)于二級(jí)壁增厚因子1（NST 1），其在盛花期后15天和21天，LE杏中的表達(dá)水平分別僅為JG品種的2.8％和9.3％。
本研究中的比較轉(zhuǎn)錄組可以用于了解LE杏中內(nèi)切皮表型的分子機(jī)制，這種新的杏基因組資源和候選基因?yàn)檫M(jìn)一步研究杏內(nèi)果皮發(fā)育期間的木質(zhì)素提供了有用的參考。轉(zhuǎn)錄因子（如NST1）可調(diào)節(jié)參與苯丙素途徑的基因，影響內(nèi)皮的發(fā)育和木質(zhì)化。
本文主流程和k-means均值聚類(lèi)都用了百邁客云平臺(tái)。
英文摘要：
Background: A complete and hardened endocarp is a typical trait of drupe fruits. However, the ‘Liehe’ (LE) apricot cultivar has a thin, soft, cleavable endocarp that represents 60.39% and 63.76% of the thickness and lignin content, respectively, of the ‘Jinxihong’ (JG) apricot (with normal hardened-endocarp). To understand the molecular mechanisms behind the LE apricot phenotype, comparative transcriptomes of Prunus armeniaca L. were sequenced using Illumina HiSeqTM 2500.
Results: In this study, we identified 63,170 unigenes including 15,469 genes >1000 bp and 25,356 genes with Gene Function annotation. Pathway enrichment and expression patterns were used to characterize differentially expression genes. The DEGs encoding key enzymes involved in phenylpropanoid biosynthesis were significantly down-regulated in LE apricot. For example, CAD gene expression levels, encoding cinnamyl alcohol dehydrogenase, were only 1.3%, 0.7%, 0.2% and 2.7% in LE apricot compared with JG cultivar at 15, 21, 30, 49 days after full bloom (DAFB). Furthermore, transcription factors regulating secondary wall and lignin biosynthesis were identified. Especially for SECONDARY WALL THICKENING PROMOTING FACTOR 1 (NST 1), its expression levels in LE apricot were merely 2.8% and 9.3% compared with JG cultivar at 15 and 21 DAFB, respectively.
Conclusions: Our comparative transcriptome analysis was used to understand the molecular mechanisms underlie the endocarp-cleaving phenotype in LE apricot. This new apricot genomic resource and the candidate genes provide a useful reference for further investigating the lignification during development of apricot endocarp. Transcription factors such as NST1 may regulate genes involved in phenylpropanoid pathway and affect development and lignification of the endocarp.