title: Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research.
abstract: BACKGROUND
  The large and complex hexaploid genome has greatly hindered genomics studies of common wheat (Triticum aestivum, AABBDD). Here, we investigated transcripts in common wheat developing caryopses using the emerging single-molecule real-time (SMRT) sequencing technology PacBio RSII, and assessed the resultant data for improving common wheat genome annotation and grain transcriptome research.
  
  
  RESULTS
  We obtained 197,709 full-length non-chimeric (FLNC) reads, 74.6 % of which were estimated to carry complete open reading frame. A total of 91,881 high-quality FLNC reads were identified and mapped to 16,188 chromosomal loci, corresponding to 13,162 known genes and 3026 new genes not annotated previously. Although some FLNC reads could not be unambiguously mapped to the current draft genome sequence, many of them are likely useful for studying highly similar homoeologous or paralogous loci or for improving chromosomal contig assembly in further research. The 91,881 high-quality FLNC reads represented 22,768 unique transcripts, 9591 of which were newly discovered. We found 180 transcripts each spanning two or three previously annotated adjacent loci, suggesting that they should be merged to form correct gene models. Finally, our data facilitated the identification of 6030 genes differentially regulated during caryopsis development, and full-length transcripts for 72 transcribed gluten gene members that are important for the end-use quality control of common wheat.
  
  
  CONCLUSIONS
  Our work demonstrated the value of PacBio transcript sequencing for improving common wheat genome annotation through uncovering the loci and full-length transcripts not discovered previously. The resource obtained may aid further structural genomics and grain transcriptome studies of common wheat.
authors.affiliation: The State Key Laboratory of Plant cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. lldong@genetics.ac.cn.
authors.forename: Lingli
authors.initials: L
authors.lastname: Dong
authors.affiliation: Frasergen, Wuhan East Lake High-tech Zone, Wuhan, 430075, China. liuhongfang@frasergen.com.
authors.forename: Hongfang
authors.initials: H
authors.lastname: Liu
authors.affiliation: The State Key Laboratory of Plant cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. jczhang@genetics.ac.cn.
authors.forename: Juncheng
authors.initials: J
authors.lastname: Zhang
authors.affiliation: The State Key Laboratory of Plant cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. sjyang@genetics.ac.cn.|University of Chinese Academy of Sciences, Beijing, 100049, China. sjyang@genetics.ac.cn.
authors.forename: Shuangjuan
authors.initials: S
authors.lastname: Yang
authors.affiliation: Frasergen, Wuhan East Lake High-tech Zone, Wuhan, 430075, China. kongguanyi@frasergen.com.
authors.forename: Guanyi
authors.initials: G
authors.lastname: Kong
authors.affiliation: Frasergen, Wuhan East Lake High-tech Zone, Wuhan, 430075, China. jeffreychu@frasergen.com.|School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China. jeffreychu@frasergen.com.
authors.forename: Jeffrey S C
authors.initials: JS
authors.lastname: Chu
authors.affiliation: School of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430075, China. chenn@sfu.ca.|Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada. chenn@sfu.ca.
authors.forename: Nansheng
authors.initials: N
authors.lastname: Chen
authors.affiliation: The State Key Laboratory of Plant cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. dwwang@genetics.ac.cn.|The Collaborative Innovation Center for Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China. dwwang@genetics.ac.cn.
authors.forename: Daowen
authors.initials: D
authors.lastname: Wang
mesh_terms: D019295:Computational Biology / Q000379:methods; D020451:Contig Mapping; D002523:Edible Grain / Q000235:genetics*; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D056426:Genetic Loci; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D005983:Glutens / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D016366:Open Reading Frames; D059467:Transcriptome; D014908:Triticum / Q000235:genetics*
chemical_list: D005983:Glutens