Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers

Abstract

BackgroundSesame 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.ResultsSesame 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.ConclusionsThis 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.

Deyeuxia angustifolia's trancriptional response to elevated CO2 concentration in Sanjiang plain, Northeast China

“…Out of all unannotated unigenes (31,121), 58.57% unigenes that were shorter than 300 bp had no BLAST matches, whereas only 1.04% uigenes that were longer than 1000 bp had no matchest. We also observed the similar correlation in other studies [13,14,15]. This demonstrated that the lack of annotation for these unigenes could be ascribed to a genuine lack of hits to sequences in the database rather than a shorter sequence length .…”

Genomic Simple Sequence Repeat Markers Reveal Patterns of Genetic Relatedness and Diversity in Sesame

“…The trend also applied for trinucleotide SSRs with a predominance of AT-rich repeats, similar to our findings. Whether or not mononucleotide repeats are included in SSR surveys, all reports on genic SSR development in sesame indicate dinucleotide repeats as the predominant SSR type in coding sequences (Wei et al, 2008;Wei et al, 2011;Zhang et al, 2012;Yepuri et al, 2013;Wu et al, 2014). In addition, AG/CT was consistently found as the predominant motif in sesame genic SSRs.…”

“…Simple sequence repeats are widely used in plant molecular genetic studies because they are hypervariable, reproducible, relatively abundant, and provide extensive genome coverage (Powell et al, 1996). Reports on SSR marker development in sesame are limited and most work involved the development of genic SSRs, either from expressed sequence tag (EST) sequences in public databases (Wei et al, 2008;Yepuri et al, 2013) or transcriptome sequencing (Wei et al, 2011;Zhang et al, 2012;Wu et al, 2014). Fewer authors described genomic SSRs in sesame (Dixit et al, 2005;Spandana et al, 2012;Wei et al, 2014;Surapaneni et al, 2014).…”

De-novo characterization of the soft-shelled turtle Pelodiscus sinensis transcriptome using Illumina RNA-Seq technology

“…Recently, the development of high-throughput DNA sequencing strategies has provided a new means of both mapping and quantifying transcriptomes, which is the complete set of all transcripts for certain types of cells or tissues in a specific developmental stage or physiological condition. Transcriptome analysis is a way to yield comprehensive functional elements of the genome and reveal the molecular mechanisms involved in specific biological processes on gene structure and function (Wei et al, 2011).…”