Deep RNA-Seq to unlock the gene bank of floral development in Sinapis arvensis.
Deep RNA-Seq to unlock the gene bank of floral development in Sinapis arvensis.
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DOI：
10.1371/journal.pone.0105775
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Hu Q
中科院分区：
文献类型：
--
作者：
Liu J;Mei D;Li Y;Huang S;Hu Q
白芥是一种生物活性很强的杂草。尽管它是一种污染农作物产量的一年生杂草，但它是一种宝贵的外来种质资源。它可用于拓宽芸苔属作物的遗传背景，这些芸苔属作物具有期望的农业性状，如对黑胫病（Leptosphaeria maculans）、茎腐病（Sclerotinia sclerotium）和裂荚病（由FRUITFULL基因引起）的抗性。然而，很少有关于S.由于缺乏基因组资源，报道了一些野生的野生种。在本研究中，我们进行了从头转录组测序，以产生一个全面的数据集的S。阿文西斯第一次。我们采用Illumina双末端测序技术对S. Arvensis花转录组中，并产生40，981，443个读数，其组装成131，278个转录物。我们从头组装了96，562个高质量的unigenes，平均长度为832 bp。共鉴定了33，662个全长ORF完整序列，并使用KEGG Pathway数据库将41，415个unigenes定位到128个通路上。将注释的单基因与芜菁B进行比较。oleracea，B. B. napus和Arabidopsis thaliana。在这些单基因中，76，324个被鉴定为公共蛋白质数据库中注释序列的推定同源物，其中1194个与植物激素信号转导相关，113个与赤霉素稳态/信号转导相关。不匹配任何这些序列数据集的单基因被认为是S.阿文西斯此外，还发现了21，321个简单重复序列。本研究将丰富芸苔科植物的现有资源，并为芸苔属作物的遗传改良提供基因组研究平台。
Sinapis arvensis is a weed with strong biological activity. Despite being a problematic annual weed that contaminates agricultural crop yield, it is a valuable alien germplasm resource. It can be utilized for broadening the genetic background of Brassica crops with desirable agricultural traits like resistance to blackleg (Leptosphaeria maculans), stem rot (Sclerotinia sclerotium) and pod shatter (caused by FRUITFULL gene). However, few genetic studies of S. arvensis were reported because of the lack of genomic resources. In the present study, we performed de novo transcriptome sequencing to produce a comprehensive dataset for S. arvensis for the first time. We used Illumina paired-end sequencing technology to sequence the S. arvensis flower transcriptome and generated 40,981,443 reads that were assembled into 131,278 transcripts. We de novo assembled 96,562 high quality unigenes with an average length of 832 bp. A total of 33,662 full-length ORF complete sequences were identified, and 41,415 unigenes were mapped onto 128 pathways using the KEGG Pathway database. The annotated unigenes were compared against Brassica rapa, B. oleracea, B. napus and Arabidopsis thaliana. Among these unigenes, 76,324 were identified as putative homologs of annotated sequences in the public protein databases, of which 1194 were associated with plant hormone signal transduction and 113 were related to gibberellin homeostasis/signaling. Unigenes that did not match any of those sequence datasets were considered to be unique to S. arvensis. Furthermore, 21,321 simple sequence repeats were found. Our study will enhance the currently available resources for Brassicaceae and will provide a platform for future genomic studies for genetic improvement of Brassica crops.
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