The complexity of alternative splicing and landscape of tissue-specific expression in lotus (Nelumbo nucifera) unveiled by Illumina- and single-molecule real-time-based RNA-sequencing.

Alternative splicing (AS) plays a critical role in regulating different physiological and developmental processes in eukaryotes, by dramatically increasing the diversity of the transcriptome and the proteome. However, the saturation and complexity of AS remain unclear in lotus due to its limitation of rare obtainment of full-length multiple-splice isoforms. In this study, we apply a hybrid assembly strategy by combining single-molecule real-time sequencing and Illumina RNA-seq to get a comprehensive insight into the lotus transcriptomic landscape. We identified 211,802 high-quality full-length non-chimeric reads, with 192,690 non-redundant isoforms, and updated the lotus reference gene model. Moreover, our analysis identified a total of 104,288 AS events from 16,543 genes, with alternative 3' splice-site being the predominant model, following by intron retention. By exploring tissue datasets, 370 tissue-specific AS events were identified among 12 tissues. Both the tissue-specific genes and isoforms might play important roles in tissue or organ development, and are suitable for 'ABCE' model partly in floral tissues. A large number of AS events and isoform variants identified in our study enhance the understanding of transcriptional diversity in lotus, and provide valuable resource for further functional genomic studies.

Genome-Wide DNA Methylation Profiling in the Lotus (Nelumbo nucifera) Flower Showing its Contribution to the Stamen Petaloid.

DNA methylation is a vital epigenetic modification. Methylation has a significant effect on the gene expression influencing the regulation of different physiological processes. Current studies on DNA methylation have been conducted on model plants. Lotus (Nelumbo nucifera) is a basic eudicot exhibiting variations during development, especially in flower formation. DNA methylation profiling was conducted on different flower tissues of lotuses through whole genome bisulfite sequencing (WGBS) to investigate the effects of DNA methylation on its stamen petaloid. A map of methylated cytosines at the single base pair resolution for the lotus was constructed. When the stamen was compared with the stamen petaloid, the DNA methylation exhibited a global decrease. Genome-wide relationship analysis between DNA methylation and gene expression identified 31 different methylation region (DMR)-associated genes, which might play crucial roles in floral organ formation, especially in the stamen petaloid. One out of 31 DMR-associated genes, NNU_05638 was homolog with Plant U-box 33 (PUB33). The DNA methylation status of NNU_05638 promoter was distinct in three floral organs, which was confirmed by traditional bisulfite sequencing. These results provide further insights about the regulation of stamen petaloids at the epigenetic level in lotus.

Culture and HIV/AIDS in Africa: promoting reproductive health in light of spouse-sharing practice among the Okun people, Nigeria.

The Okun tribe, numbering about a million persons, accepts sexual relations between men and wives of their male kin. We identified and used features of spouse sharing that affect reproductive health to develop an interactive, community-based intervention. The intervention promoted discussion of spouse sharing as a risk factor in HIV/AIDS transmission, knowledge of AIDS/sexually transmitted diseases (STDs), perception of risk and alternative behaviors to avoid contracting HIV/AIDS. The intervention effects were evaluated using data collected in baseline and follow-up surveys in May 1999 and June 2000 among 1018 sexually active respondents in two sets of Okun communities - one with and the other without intervention. The intervention significantly increased knowledge of HIV/AIDS, perception of risk of contracting the disease and the intention to discontinue spouse sharing in the intervention communities. Those who perceived themselves at risk of contracting HIV/AIDS were more likely to express intention to discontinue spouse sharing (odds ratio 2.87) than those who did not. It was recommended that future community-based interventions to address traditional practices that could transmit HIV/AIDS should address the aspects of the practice that could transmit the disease and actively involve the people to make impact.