Deep RNA-Seq to Unlock the Gene Bank of Floral Development in Sinapis arvensis

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（Sinapis arvensis）是一种生物活性较强的杂草。尽管其作为一种会造成农作物产量损失的有害一年生杂草，却也是极具价值的外来种质资源。它可用于拓宽芸苔属（Brassica）作物的遗传背景，赋予其抗黑胫病（由黑胫病菌Leptosphaeria maculans引起）、菌核病（由核盘菌Sclerotinia sclerotium引起）以及角果开裂（由FRUITFULL基因介导）等优良农艺性状。然而，由于基因组资源匮乏，目前针对野芥菜的遗传研究报道极少。本研究首次对野芥菜开展从头转录组测序，构建其全面的转录组数据集。我们采用Illumina双端测序技术对野芥菜的花组织转录组进行测序，共获得40,981,443条读段，经组装得到131,278条转录本。我们从头组装得到96,562条高质量单基因（unigene），平均长度为832 bp。共鉴定出33,662条完整开放阅读框（ORF）序列，同时通过KEGG通路数据库，将41,415条单基因注释到128条代谢通路中。我们将注释后的单基因与芜菁（Brassica rapa）、甘蓝（B. oleracea）、甘蓝型油菜（B. napus）及拟南芥（Arabidopsis thaliana）的蛋白序列进行比对。在这些单基因中，76,324条被鉴定为公共蛋白数据库中已注释序列的推定同源基因，其中1194条与植物激素信号转导相关，113条与赤霉素稳态/信号转导相关。未匹配到上述序列数据集的单基因被认为是野芥菜所特有的。此外，本研究共发现21,321个简单序列重复（SSR）位点。本研究将丰富十字花科（Brassicaceae）现有基因组资源，并为未来开展芸苔属作物遗传改良的基因组学研究提供支撑平台。