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

Characterization of the natural variation in Arabidopsis thaliana metabolome by the analysis of metabolic distance

Metabolite fingerprinting is widely used to unravel the chemical characteristics of biological samples. Multivariate data analysis and other statistical tools are subsequently used to analyze and visualize the plasticity of the metabolome and/or the relationship between those samples. However, there are limitations to these approaches for example because of the multi-dimensionality of the data that makes interpretation of the data obtained from untargeted analysis almost impossible for an average human being. These limitations make the biological information that is of prime importance in untargeted studies be partially exploited. Even in the case of full exploitation, current methods for relationship elucidation focus mainly on between groups variation and differences. Therefore, a measure that is capable of exploiting both between- and within-group biological variation would be of great value. Here, we examined the natural variation in the metabolome of nine Arabidopsis thaliana accessions grown under various environmental conditions and established a measure for the metabolic distance between accessions and across environments. This data analysis approach shows that there is just a minor correlation between genetic and metabolic diversity of the nine accessions. On the other hand, it delivers so far in Arabidopsis unexplored chemical information and is shown to be biologically relevant for resistance studies

Genotypic and environmental interaction in advanced lines of wheat under salt-affected soils environment of Punjab

Wheat cultivars of diverse origin including approved varieties of different provinces of Pakistan i.e. Punjab, NWFP and Sindh were tested against different salinity levels in laboratory as well as in naturally saline fields in different ecological zones. Initially, 16 genotypes were studied for germination test at 6 different salinity levels ranging from 0-25 dS/m (2, 5, 10, 15, 20, 25, EC= dS/m). Then, out of 16 cultivars, 11 were studied for the relative growth rate at different levels of salinity and after their study in the laboratory, 9 genotypes were selected for testing in the naturally saline areas of Punjab province. Under germination percentage study, the varieties viz. Pasban-90, Sarsabz, Bakhtawar, 93032 and 933118 were less affected than other varieties. As regards the relative plant growth, varieties viz. Sarsabz, Bakhtawar, and Pasban-90 were tolerant to salinity at seedling stage while Inqlab was graded as sensitive to salt stress. Regarding field performance, significant differences were observed in the varieties grown under different saline environments and varieties x environment interaction. Varieties x environment (Lin) interaction was non significant while nonlinear interaction (pooled deviation) was significant. Based on overall yield performance, the Sarsabz variety produced the highest seed yield (4.37 T/ha) followed by Bakhtawar (4.24 T/ha) and Pasban-90 (3.93 T/ha). Regression coefficient values showed non significant differences to unity while standard deviation to regression showed significant differences to zero. These results indicated that the genotypes viz. Sarsabaz, Bakhtawar and Pasban-90 are better tolerant to saline environment as compared to others. The two genotypes, Marvi and 25219 had low regression values and can fit under stress environment

The Role of HIV-Related Knowledge and Ethnicity in Determining HIV Risk Perception and Willingness to Undergo HIV Testing Among Rural Women in Burkina Faso

We conducted a random community based survey of 300 young (15–29 years) rural women in Nouna, Burkina Faso. Only one-third of women were aware that a person could have HIV without having symptoms and these women were significantly more likely to classify themselves to be at high risk for getting HIV. Furthermore, multiple partners, Bwaba ethnicity and having mentioned a health worker as a source of HIV information were significantly associated with perceived high personal risk. Perceived willingness to participate in VCT was high (69%). The dissemination of information on the asymptomatic nature of HIV infection could potentially be very important in forming risk perception, awareness, and their willingness to participate in HIV interventions.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44011/1/10461_2005_Article_3905.pd

Lymphadenectomy prior to rat hind limb allotransplantation prevents graft-versus-host disease in chimeric hosts

In previous rat studies, the use of mixed allogeneic chimerism (MAC) to induce host tolerance to hind limb allografts has resulted in severe graft-versus-host disease (GVHD). The purpose of this study was to determine if immunocompetent cells in bone marrow (BM) and/or lymph nodes (LNs) of transplanted limbs were responsible for inducing GVHD in mixed chimeric hosts. [ACI --> Wistar Furth] chimeric rats received ACI hind limbs that were non-irradiated, irradiated (1050 cGy) or lymphadenectomized. Rejection, GVHD and donor chimerism was assessed. Chimeric hosts rejected none of their limbs. However, hosts of non-irradiated hind limbs succumbed to GVHD 22.4 +/- 0.8 days after transplantation. In contrast, chimeras that received irradiated or lymphadenectomized ACI hind limbs showed no clinical or histological signs of GVHD at 5 months. We conclude that mixed chimeric hosts are susceptible to GVHD due to the immunocompetent cell load provided by the LNs, not the BM, of hind limb allografts