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

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>Arabidopsis </it>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.</p> <p>Conclusions</p> <p>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.</p

Multi-proxy analysis in defining sedimentary processes in very recent prodelta deposits: the Northern Phlegraean offshoreexample (Eastern Tyrrhenian Margin)

A multi-proxy analysis of Volturno River prodelta deposits in the outer shelf of Northern Phlegraean margin (Eastern Tyrrhenian Sea) has been carried out to reconstruct the sedimentary processes acting during recent times. The late Holocene sediments were characterized through Subbottom Chirp profiles coupled with sedimentological and petrophysical data. The chronostratigraphic framework was achieved by means of colorimetric parameter a* correlations with nearby dated marine sediment. A time interpretation of about 2,300 years BP is estimated for the sedimentary record collected in the cores. Seismic stratigraphic analysis shows late Holocene outer shelf deposits, characterized by fluid escape features and small-offset faults. However, the undisturbed sedimentation and the preservation of an internal geometry at decimetre scale, as detected by the sedimentological and petrophysical analysis, indicates a slow sliding without sediment reworking for this sedimentological body. So far a possible recent (\2,300 years BP) shear dominated downward displacement of high water content sediments, triggered by the occurrence of seismic activity, is inferred. Based on the depth-age conversion of the detected lithological features, a regular climatically driven change in the sediment supply of the prodelta depositional environment is suggested. The detection of spectrophotometry correlations of Holocene shelf margin sediments, several km apart, goes beyond the previous work and confirms even for continental shelf area the potential value of spectrophotometer data in high-resolution stratigraphic correlations