Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq.
Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq.
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DOI：
10.1186/1471-2164-13-19
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发表时间：
2012-01-13
期刊：
影响因子：
4.4
通讯作者：
Chen KS
中科院分区：
文献类型：
--
作者：
Feng C;Chen M;Xu CJ;Bai L;Yin XR;Li X;Allan AC;Ferguson IB;Chen KS
杨梅（Myrica rubra Sieb.）Zucc）。是一种重要的亚热带水果作物，由于在发育和成熟过程中发生的快速和实质性变化，包括果实颜色和味道的变化，是果实品质研究的理想物种。然而，在分子水平上的研究受到缺乏序列数据的限制。本研究旨在通过RNA-Seq和生物信息学分析，获得杨梅果实发育过程中的转录本序列数据，并检测相关基因的表达，为深入了解果实成熟过程中品质变化的分子机制奠定基础。RNA-Seq产生1.92 G原始数据，然后从头组装成41，239个UniGenes，平均长度为531 bp。大约80%的UniGenes（32，805）针对公共蛋白质数据库进行注释，并确定了31，665个UniGenes的编码序列（CDS）。在果实成熟过程中，有超过3，600个UniGenes差异表达，其中826个上调，1，407个下调。这两种类型的UniGenes之间的GO比较和相互作用途径（Ipath）分析发现，能量相关的代谢增强，催化活性增加。所有参与花青素合成的基因在果实成熟过程中均表达上调，并伴随着果实颜色的变化。成熟果实中碳水化合物和酸代谢的重要变化可能与蔗糖磷酸合成酶（SPS）和谷氨酸脱羧酶（GAD）的表达有关。获得了杨梅基因的大量序列数据，并分析了杨梅果实成熟过程中基因的表达谱。对UniGenes进行了注释，为该物种的功能基因组研究提供了平台。利用途径定位和表达谱，研究了果实成熟过程中颜色和味道变化的分子机制。这为非模式多年生植物复杂代谢的研究提供了参考。
Chinese bayberry (Myrica rubra Sieb. and Zucc.) is an important subtropical fruit crop and an ideal species for fruit quality research due to the rapid and substantial changes that occur during development and ripening, including changes in fruit color and taste. However, research at the molecular level is limited by a lack of sequence data. The present study was designed to obtain transcript sequence data and examine gene expression in bayberry developing fruit based on RNA-Seq and bioinformatic analysis, to provide a foundation for understanding the molecular mechanisms controlling fruit quality changes during ripening. RNA-Seq generated 1.92 G raw data, which was then de novo assembled into 41,239 UniGenes with a mean length of 531 bp. Approximately 80% of the UniGenes (32,805) were annotated against public protein databases, and coding sequences (CDS) of 31,665 UniGenes were determined. Over 3,600 UniGenes were differentially expressed during fruit ripening, with 826 up-regulated and 1,407 down-regulated. GO comparisons between the UniGenes of these two types and interactive pathways (Ipath) analysis found that energy-related metabolism was enhanced, and catalytic activity was increased. All genes involved in anthocyanin biosynthesis were up-regulated during the fruit ripening processes, concurrent with color change. Important changes in carbohydrate and acid metabolism in the ripening fruit are likely associated with expression of sucrose phosphate synthase (SPS) and glutamate decarboxylase (GAD). Mass sequence data of Chinese bayberry was obtained and the expression profiles were examined during fruit ripening. The UniGenes were annotated, providing a platform for functional genomic research with this species. Using pathway mapping and expression profiles, the molecular mechanisms for changes in fruit color and taste during ripening were examined. This provides a reference for the study of complicated metabolism in non-model perennial species.
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DOI：
10.1111/j.1365-313x.2006.02964.x
发表时间：
2007-02
期刊：
The Plant journal : for cell and molecular biology
影响因子：
--
作者：
Espley RV;Hellens RP;Putterill J;Stevenson DE;Kutty-Amma S;Allan AC
通讯作者：
Allan AC
影响因子：
7
作者：
Li, Ruiqiang;Zhu, Hongmei;Wang, Jun
通讯作者：
Wang, Jun
影响因子：
7.4
作者：
KOCH, KE;AVIGNE, WT
通讯作者：
AVIGNE, WT
影响因子：
4.4
作者：
Crowhurst RN;Gleave AP;MacRae EA;Ampomah-Dwamena C;Atkinson RG;Beuning LL;Bulley SM;Chagne D;Marsh KB;Matich AJ;Montefiori M;Newcomb RD;Schaffer RJ;Usadel B;Allan AC;Boldingh HL;Bowen JH;Davy MW;Eckloff R;Ferguson AR;Fraser LG;Gera E;Hellens RP;Janssen BJ;Klages K;Lo KR;MacDiarmid RM;Nain B;McNeilage MA;Rassam M;Richardson AC;Rikkerink EH;Ross GS;Schröder R;Snowden KC;Souleyre EJ;Templeton MD;Walton EF;Wang D;Wang MY;Wang YY;Wood M;Wu R;Yauk YK;Laing WA
通讯作者：
Laing WA
影响因子：
4.4
作者：
Hahn DA;Ragland GJ;Shoemaker DD;Denlinger DL
通讯作者：
Denlinger DL