Liu Jia, Mei Desheng, Li Yunchang, Huang Shunmou, Hu Qiong
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, People's Republic of China.
PLoS One. 2014 Sep 5;9(9):e105775. doi: 10.1371/journal.pone.0105775. eCollection 2014.
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.
野芥菜是一种具有强大生物活性的杂草。尽管它是一种有问题的一年生杂草，会影响农作物产量，但它是一种有价值的外来种质资源。它可用于拓宽芸苔属作物的遗传背景，这些作物具有诸如抗黑胫病（黑斑病菌）、菌核病（核盘菌）和角果开裂（由FUL基因引起）等优良农艺性状。然而，由于缺乏基因组资源，关于野芥菜的遗传研究报道较少。在本研究中，我们首次进行了从头转录组测序，以生成野芥菜的综合数据集。我们使用Illumina双末端测序技术对野芥菜的花转录组进行测序，获得了40,981,443条 reads，并将其组装成131,278个转录本。我们从头组装了96,562个高质量单基因，平均长度为832 bp。共鉴定出33,662个全长ORF完整序列，并使用KEGG通路数据库将41,415个单基因映射到128条通路上。将注释后的单基因与白菜、甘蓝、油菜和拟南芥进行比较。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/信号传导相关。与这些序列数据集均不匹配的单基因被认为是野芥菜特有的。此外，还发现了21,321个简单序列重复。我们的研究将增加目前可用的十字花科资源，并为未来芸苔属作物遗传改良的基因组研究提供一个平台。
