title: Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers.
abstract: BACKGROUND
  Sesame is an important oil crop, but limited transcriptomic and genomic data are currently available. This information is essential to clarify the fatty acid and lignan biosynthesis molecular mechanism. In addition, a shortage of sesame molecular markers limits the efficiency and accuracy of genetic breeding. High-throughput transcriptomic sequencing is essential to generate a large transcriptome sequence dataset for gene discovery and molecular marker development.
  
  
  RESULTS
  Sesame transcriptomes from five tissues were sequenced using Illumina paired-end sequencing technology. The cleaned raw reads were assembled into a total of 86,222 unigenes with an average length of 629 bp. Of the unigenes, 46,584 (54.03%) had significant similarity with proteins in the NCBI nonredundant protein database and Swiss-Prot database (E-value < 10-5). Of these annotated unigenes, 10,805 and 27,588 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. In total, 22,003 (25.52%) unigenes were mapped onto 119 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Furthermore, 44,750 unigenes showed homology to 15,460 Arabidopsis genes based on BLASTx analysis against The Arabidopsis Information Resource (TAIR, Version 10) and revealed relatively high gene coverage. In total, 7,702 unigenes were converted into SSR markers (EST-SSR). Dinucleotide SSRs were the dominant repeat motif (67.07%, 5,166), followed by trinucleotide (24.89%, 1,917), tetranucleotide (4.31%, 332), hexanucleotide (2.62%, 202), and pentanucleotide (1.10%, 85) SSRs. AG/CT (46.29%) was the dominant repeat motif, followed by AC/GT (16.07%), AT/AT (10.53%), AAG/CTT (6.23%), and AGG/CCT (3.39%). Fifty EST-SSRs were randomly selected to validate amplification and to determine the degree of polymorphism in the genomic DNA pools. Forty primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism among 24 sesame accessions.
  
  
  CONCLUSIONS
  This study demonstrates that Illumina paired-end sequencing is a fast and cost-effective approach to gene discovery and molecular marker development in non-model organisms. Our results provide a comprehensive sequence resource for sesame research.
authors.affiliation: Key Laboratory of Oil Crops Biology of the Ministry of Agriculture, Sesame Germplasm and Genetic Breeding Laboratory, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062, China.
authors.forename: Wenliang
authors.initials: W
authors.lastname: Wei
authors.forename: Xiaoqiong
authors.initials: X
authors.lastname: Qi
authors.forename: Linhai
authors.initials: L
authors.lastname: Wang
authors.forename: Yanxin
authors.initials: Y
authors.lastname: Zhang
authors.forename: Wei
authors.initials: W
authors.lastname: Hua
authors.forename: Donghua
authors.initials: D
authors.lastname: Li
authors.forename: Haixia
authors.initials: H
authors.lastname: Lv
authors.forename: Xiurong
authors.initials: X
authors.lastname: Zhang
mesh_terms: D018744:DNA, Plant / Q000235:genetics; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D015723:Gene Library; D017343:Genes, Plant; D018745:Genome, Plant; D053858:Metabolic Networks and Pathways; D018895:Microsatellite Repeats; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods; D031685:Sesamum / Q000235:genetics*; D059467:Transcriptome
chemical_list: D018744:DNA, Plant