Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars.
Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars.
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DOI：
10.1186/1471-2164-13-657
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发表时间：
2012-11-21
期刊：
影响因子：
4.4
通讯作者：
Kwon SY
中科院分区：
文献类型：
--
作者：
Kim J;Park JH;Lim CJ;Lim JY;Ryu JY;Lee BW;Choi JP;Kim WB;Lee HY;Choi Y;Kim D;Hur CG;Kim S;Noh YS;Shin C;Kwon SY
玫瑰（Rosa sp.），属于蔷薇科，是最重要的经济观赏植物，占花卉市场的30%。然而，由于对玫瑰的高需求，玫瑰育种计划在分子资源方面受到限制，这可以大大提高和加速育种工作。更好地了解重要的基因，有助于重要的花发育和所需的表型将导致改善玫瑰品种。在这项研究中，我们分析了玫瑰miRNA和玫瑰花转录组，以产生一个数据库，阐述目前的知识，关于重要的花卉特征的调节。一个玫瑰遗传数据库将使不同的玫瑰品种之间的基因表达和调控通过miRNA的全面分析。我们从表达的序列中产生了超过50万个读段，总计超过1.1亿bp。由此，我们从蔷薇杂种：'Vital'、'Maroussia'和'Sympathy'和玫瑰玫瑰中产生了35，657、31，434、34，725和39，722个花单基因。，分别。单一基因被分配功能注释、结构域、代谢途径、基因本体（GO）术语、植物本体（PO）术语和MIPS功能目录（FunCat）术语。将玫瑰花转录本与来自蔷薇科成员（苹果、草莓和桃）和葡萄的全基因组序列的基因进行比较。我们还从Rosa的花组织中产生了大约4000万个小RNA读段，代表了267个独特的miRNA标签。在已鉴定的miRNAs中，有25个是新的miRNAs，有242个是保守的miRNAs。miRNA谱的统计分析揭示了共享的和物种特异性的miRNA，这可能会影响花的发育和表型。本研究构建了蔷薇属植物的miRNA和转录组数据库，并对4个蔷薇品种的花组织中的miRNA和转录组进行了分析。该数据库提供了一个全面的遗传资源，可用于更好地了解玫瑰花发育和识别重要表型的候选基因。
Roses (Rosa sp.), which belong to the family Rosaceae, are the most economically important ornamental plants—making up 30% of the floriculture market. However, given high demand for roses, rose breeding programs are limited in molecular resources which can greatly enhance and speed breeding efforts. A better understanding of important genes that contribute to important floral development and desired phenotypes will lead to improved rose cultivars. For this study, we analyzed rose miRNAs and the rose flower transcriptome in order to generate a database to expound upon current knowledge regarding regulation of important floral characteristics. A rose genetic database will enable comprehensive analysis of gene expression and regulation via miRNA among different Rosa cultivars. We produced more than 0.5 million reads from expressed sequences, totalling more than 110 million bp. From these, we generated 35,657, 31,434, 34,725, and 39,722 flower unigenes from Rosa hybrid: ‘Vital’, ‘Maroussia’, and ‘Sympathy’ and Rosa rugosa Thunb. , respectively. The unigenes were assigned functional annotations, domains, metabolic pathways, Gene Ontology (GO) terms, Plant Ontology (PO) terms, and MIPS Functional Catalogue (FunCat) terms. Rose flower transcripts were compared with genes from whole genome sequences of Rosaceae members (apple, strawberry, and peach) and grape. We also produced approximately 40 million small RNA reads from flower tissue for Rosa, representing 267 unique miRNA tags. Among identified miRNAs, 25 of them were novel and 242 of them were conserved miRNAs. Statistical analyses of miRNA profiles revealed both shared and species-specific miRNAs, which presumably effect flower development and phenotypes. In this study, we constructed a Rose miRNA and transcriptome database, and we analyzed the miRNAs and transcriptome generated from the flower tissues of four Rosa cultivars. The database provides a comprehensive genetic resource which can be used to better understand rose flower development and to identify candidate genes for important phenotypes.
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影响因子：
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作者：
Bolduc F;Hoareau C;St-Pierre P;Perreault JP
通讯作者：
Perreault JP
影响因子：
14.9
作者：
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Zhao PX
影响因子：
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作者：
Fahlgren N;Howell MD;Kasschau KD;Chapman EJ;Sullivan CM;Cumbie JS;Givan SA;Law TF;Grant SR;Dangl JL;Carrington JC
通讯作者：
Carrington JC
影响因子：
5.4
作者：
Debener, T;Mattiesch, L
通讯作者：
Mattiesch, L
影响因子：
14.9
作者：
Avraham, Shulamit;Tung, Chih-Wei;Ilic, Katica;Jaiswal, Pankaj;Kellogg, Elizabeth A.;McCouch, Susan;Pujar, Anuradha;Reiser, Leonore;Rhee, Seung Y.;Sachs, Martin M.;Schaeffer, Mary;Stein, Lincoln;Stevens, Peter;Vincent, Leszek;Zapata, Felipe;Ware, Doreen
通讯作者：
Ware, Doreen