RNA-seq analysis of transcriptome and glucosinolate metabolism in seeds and sprouts of broccoli (Brassica oleracea var. italic).
RNA-seq analysis of transcriptome and glucosinolate metabolism in seeds and sprouts of broccoli (Brassica oleracea var. italic).
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西兰花（Brassica oleracea var. italic）种子和芽中转录组和芥子油苷代谢的 RNA 测序分析
DOI：
10.1371/journal.pone.0088804
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Li J
中科院分区：
文献类型：
--
作者：
Gao J;Yu X;Ma F;Li J
西兰花（Brassica oleracea var. italica）是十字花科植物，是一种重要的蔬菜，含有高浓度的各种营养和功能性分子，尤其是具有抗癌作用的硫代葡萄糖苷。西兰花的芽苗比可食用的花球含有高10 - 100倍的萝卜硫素（抗癌的主要成分）。尽管西兰花芽苗具有重要的功能，但目前可用于其研究的遗传和基因组工具非常有限，这极大地限制了这种具有重要功能的蔬菜的发展。
总共获得了约8500万个251bp的读段。经过从头组装，并将组装后的转录本与拟南芥和美国国立生物技术信息中心（NCBI）的nr数据库进行比对，19441个最佳匹配的转录本被聚类为单基因，平均长度为2133bp。这些单基因根据其假定的功能类别进行了分类。对具有相似表达模式的所有单基因以及不同组织间差异表达的单基因进行了聚类分析，还进行了转录因子分析。我们鉴定出25个假定的硫代葡萄糖苷代谢基因，它们与拟南芥的直系同源基因具有62.04 - 89.72%的核苷酸序列同一性。这建立了一个与拟南芥具有高度共线性的西兰花硫代葡萄糖苷代谢途径。许多生物合成和降解基因在发芽后的表达量高于在种子中的表达量；尤其是黑芥子酶TGG2的表达量高20 - 130倍。这些结果以及先前关于这些基因在拟南芥中的研究报告和西兰花芽苗中硫代葡萄糖苷的浓度表明，硫代葡萄糖苷的分解产物可能在西兰花种子发芽和芽苗发育阶段发挥重要作用。
我们的研究提供了迄今为止西兰花最大的遗传资源。这些数据将为西兰花芽苗的进一步研究和基因工程铺平道路，也将为该物种及其近缘物种的基因组研究提供新的见解。
Background Broccoli (Brassica oleracea var. italica), a member of Cruciferae, is an important vegetable containing high concentration of various nutritive and functional molecules especially the anticarcinogenic glucosinolates. The sprouts of broccoli contain 10–100 times higher level of glucoraphanin, the main contributor of the anticarcinogenesis, than the edible florets. Despite the broccoli sprouts’ functional importance, currently available genetic and genomic tools for their studies are very limited, which greatly restricts the development of this functionally important vegetable. Results A total of ∼85 million 251 bp reads were obtained. After de novo assembly and searching the assembled transcripts against the Arabidopsis thaliana and NCBI nr databases, 19,441 top-hit transcripts were clustered as unigenes with an average length of 2,133 bp. These unigenes were classified according to their putative functional categories. Cluster analysis of total unigenes with similar expression patterns and differentially expressed unigenes among different tissues, as well as transcription factor analysis were performed. We identified 25 putative glucosinolate metabolism genes sharing 62.04–89.72% nucleotide sequence identity with the Arabidopsis orthologs. This established a broccoli glucosinolate metabolic pathway with high colinearity to Arabidopsis. Many of the biosynthetic and degradation genes showed higher expression after germination than in seeds; especially the expression of the myrosinase TGG2 was 20–130 times higher. These results along with the previous reports about these genes’ studies in Arabidopsis and the glucosinolate concentration in broccoli sprouts indicate the breakdown products of glucosinolates may play important roles in the stage of broccoli seed germination and sprout development. Conclusion Our study provides the largest genetic resource of broccoli to date. These data will pave the way for further studies and genetic engineering of broccoli sprouts and will also provide new insight into the genomic research of this species and its relatives.
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影响因子：
3.7
作者：
Fan H;Xiao Y;Yang Y;Xia W;Mason AS;Xia Z;Qiao F;Zhao S;Tang H
通讯作者：
Tang H
影响因子：
9.4
作者：
Gigolashvili, Tamara;Engqvist, Martin;Fluegge, Ulf-Ingo
通讯作者：
Fluegge, Ulf-Ingo
影响因子：
7.4
作者：
Celenza, JL;Quiel, JA;Bender, J
通讯作者：
Bender, J
影响因子：
7.2
作者：
Gigolashvili, Tamara;Berger, Bettina;Fluegge, Ulf-Ingo
通讯作者：
Fluegge, Ulf-Ingo
影响因子：
3.1
作者：
Chen, Yazhou;Yan, Xiufeng;Chen, Sixue
通讯作者：
Chen, Sixue