【成功案例】百迈客云助力董文轩老师 使用 真核生物有参考基因组的转录组分析平台 辅助研究,发表《比较转录组分析和形态学对杏品种(Prunus armeniaca L.)的内果皮切割的研究》

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摘要:

一个完整和硬化的内果皮是核果的典型特征。 然而,“Liehe”(LE)杏品种具有薄,软,可切割的内皮,其厚度和木质素含量分别占“金西红”(JG)杏(具有正常硬化内果皮)的60.39%和63.76%。为了了解LE杏表型背后的分子机制,本研究使用Illumina HiSeq TM 2500对Prunus armeniaca L.进行比较转录组测序。

本研究中鉴定出了63,170条unigenes(15,469条unigene的长度大于1,000 bp),25,356条unigenes得到了功能注释。利用通路富集及表达模式分析来分析差异表达基因,在LE杏中编码苯丙素生物合成参与的关键酶的差异表达基因显著下调,例如,在盛花期后15,21,30,49天中,编码肉桂醇脱氢酶的CAD基因表达水平在LE杏中仅为JG品种的1.3%,0.7%,0.2%和2.7%。此外,确定了调节次级壁和木质素生物合成的转录因子,特别是对于二级壁增厚因子1(NST 1),其在盛花期后15天和21天,LE杏中的表达水平分别仅为JG品种的2.8%和9.3%。

本研究中的比较转录组可以用于了解LE杏中内切皮表型的分子机制,这种新的杏基因组资源和候选基因为进一步研究杏内果皮发育期间的木质素提供了有用的参考。转录因子(如NST1)可调节参与苯丙素途径的基因,影响内皮的发育和木质化。

本文主流程和k-means均值聚类都用了百迈客云平台。

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.

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