title: Deep RNA-Seq to unlock the gene bank of floral development in Sinapis arvensis.
abstract: 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.
authors.affiliation: 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.
authors.forename: Jia
authors.initials: J
authors.lastname: Liu
authors.affiliation: 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.
authors.forename: Desheng
authors.initials: D
authors.lastname: Mei
authors.affiliation: 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.
authors.forename: Yunchang
authors.initials: Y
authors.lastname: Li
authors.affiliation: 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.
authors.forename: Shunmou
authors.initials: S
authors.lastname: Huang
authors.affiliation: 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.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Hu
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology; D018076:DNA, Complementary; D035264:Flowers / Q000235:genetics* / Q000254:growth & development; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D018749:RNA, Plant; D012091:Repetitive Sequences, Nucleic Acid; D017423:Sequence Analysis, RNA; D015398:Signal Transduction; D031226:Sinapis / Q000235:genetics* / Q000254:growth & development; D059467:Transcriptome
chemical_list: D018076:DNA, Complementary; D018749:RNA, Plant