Genome-wide landscape of alternative splicing events in brachypodium distachyon

Recently, Brachypodium distachyon has emerged as a model plant for studying monocot grasses and cereal crops. Using assembled expressed transcript sequences and subsequent mapping to the corresponding genome, we identified 1219 alternative splicing (AS) events spanning across 2021 putatively assembled transcripts generated from 941 genes. Approximately, 6.3% of expressed genes are alternatively spliced in B. distachyon. We observed that a majority of the identified AS events were related to retained introns (55.5%), followed by alternative acceptor sites (16.7%).We also observed a low percentage of exon skipping (5.0%) and alternative donor site events (8.8%). The 'complex event' that consists of a combination of two or more basic splicing events accounted for ~14.0%. Comparative AS transcript analysis revealed 163 and 39 homologous pairs between B. distachyon and Oryza sativa and between B. distachyon and Arabidopsis thaliana, respectively. In all, we found 16 AS transcripts to be conserved in all 3 species. AS events and related putative assembled transcripts annotation can be systematically browsed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/plant/). © The Author 2012

isomiR2Function: An integrated workflow for identifying MicroRNA variants in plants

© 2017 Yang, Sablok, Qiao, Nie and Wen. In plants, post transcriptional regulation by non-coding RNAs (ncRNAs), in particular miRNAs (19-24 nt) has been involved in modulating the transcriptional landscape in developmental, biotic and abiotic interactions. In past few years, considerable focus has been leveraged on delineating and deciphering the role of miRNAs and their canonical isomiRs in plants. However, proper classification and accurate prediction of plant isomiRs taking into account the relative features by which we define isomiRs, such as templated or non-templated is still lacking. In the present research, we present isomiR2Function, a standalone easily deployable tool that allows for the robust and high-throughput discovery of templated and non-templated isomiRs. Additionally, isomiR2Function allows for identification of differentially expressed isomiRs and in parallel target prediction based on both transcripts or PARE-Seq either using Targetfinder or Cleaveland. isomiR2Function allows for the functional enrichment of the detected targets using TopGO package. Benchmarking of isomiR2Function revealed highly accurate prediction and classification of isomiRs as compared to the previously developed isomiR prediction tools. Additionally, the downstream implementation of additional features allows isomiR2Function to be classified as a single standalone tool for isomiR profiling from discovery to functional roles. All in all, isomiR2Function allows the streamline processing of the miRNA-seq for the identification and characterization of isomiRs with minimal efforts. isomiR2Function can be accessed through: https://gi thub.com/347033139/isomiR2Function

Transcriptomics profiling of Indian mustard (Brassica juncea) under arsenate stress identifies key candidate genes and regulatory pathways

© 2015 Srivastava, Srivastava, Sablok, Deshpande and Suprasanna. Arsenic (As) is a non-essential element, a groundwater pollutant, whose uptake by plants produces toxic effects. The use of As-contaminated groundwater for irrigation can affect the crop productivity. Realizing the importance of the Brassica juncea as a crop plant in terms of oil-yield, there is a need to unravel mechanistic details of response to As stress and identify key functional genes and pathways. In this research, we studied time-dependent (4–96 h) transcriptome changes in roots and shoots of B. juncea under arsenate [As(V)] stress using Agilent platform. Among the whole transcriptome profiled genes, a total of 1,285 genes showed significant change in expression pattern upon As(V) exposure. The differentially expressed genes were categorized to various signaling pathways including hormones (jasmonate, abscisic acid, auxin, and ethylene) and kinases. Significant effects were also noticed on genes related to sulfur, nitrogen, CHO, and lipid metabolisms along with photosynthesis. Biochemical assays were conducted using specific inhibitors of glutathione and jasmonate biosynthesis, and kinases. The inhibitor studies revealed interconnection among sulfur metabolism, jasmonate, and kinase signaling pathways. In addition, various transposons also constituted a part of the altered transcriptome. Lastly, we profiled a set of key functional up- and down-regulated genes using real-time RT-PCR, which could act as an early indicators of the As stress

SplicingTypesAnno: Annotating and quantifying alternative splicing events for RNA-Seq data

© 2015 Elsevier Ireland Ltd. Alternative splicing plays a key role in the regulation of the central dogma. Four major types of alternative splicing have been classified as intron retention, exon skipping, alternative 5 splice sites or alternative donor sites, and alternative 3 splice sites or alternative acceptor sites. A few algorithms have been developed to detect splice junctions from RNA-Seq reads. However, there are few tools targeting at the major alternative splicing types at the exon/intron level. This type of analysis may reveal subtle, yet important events of alternative splicing, and thus help gain deeper understanding of the mechanism of alternative splicing. This paper describes a user-friendly R package, extracting, annotating and analyzing alternative splicing types for sequence alignment files from RNA-Seq. SplicingTypesAnno can: (1) provide annotation for major alternative splicing at exon/intron level. By comparing the annotation from GTF/GFF file, it identifies the novel alternative splicing sites; (2) offer a convenient two-level analysis: genome-scale annotation for users with high performance computing environment, and gene-scale annotation for users with personal computers; (3) generate a user-friendly web report and additional BED files for IGV visualization. SplicingTypesAnno is a user-friendly R package for extracting, annotating and analyzing alternative splicing types at exon/intron level for sequence alignment files from RNA-Seq

Molecular dynamic simulation and inhibitor prediction of cysteine synthase structured model as a potential drug target for trichomoniasis

In our presented research, we made an attempt to predict the 3D model for cysteine synthase (A2GMG5-TRIVA) using homology-modeling approaches. To investigate deeper into the predicted structure, we further performed a molecular dynamics simulation for 10 ns and calculated several supporting analysis for structural properties such as RMSF, radius of gyration, and the total energy calculation to support the predicted structured model of cysteine synthase. The present findings led us to conclude that the proposed model is stereochemically stable. The overall PROCHECK G factor for the homology-modeled structure was -0.04. On the basis of the virtual screening for cysteine synthase against the NCI subset II molecule, we present the molecule 1-N, 4-N-bis [3-(1H-benzimidazol-2-yl) phenyl] benzene-1,4-dicarboxamide (ZINC01690699) having the minimum energy score (-13.0 Kcal/Mol) and a log P value of 6 as a potential inhibitory molecule used to inhibit the growth of T. vaginalis infection. © 2013 Satendra Singh et al

Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops

© 2015 Min et al. Background: Protein functional diversity at the post-transcriptional level is regulated through spliceosome mediated pre-mRNA alternative splicing (AS) events and that has been widely demonstrated to be a key player in regulating the functional diversity in plants. Identification and analysis of AS genes in cereal crop plants are critical for crop improvement and understanding regulatory mechanisms. Results: We carried out the comparative analyses of the functional landscapes of the AS using the consensus assembly of expressed sequence tags and available mRNA sequences in four cereal plants. We identified a total of 8,734 in Oryza sativa subspecies (ssp) japonica, 2,657 in O. sativa ssp indica, 3,971 in Sorghum bicolor, and 10,687 in Zea mays AS genes. Among the identified AS events, intron retention remains to be the dominant type accounting for 23.5 % in S. bicolor, and up to 55.8 % in O. sativa ssp indica. We identified a total of 887 AS genes that were conserved among Z. mays, S. bicolor, and O. sativa ssp japonica; and 248 AS genes were found to be conserved among all four studied species or ssp. Furthermore, we identified 53 AS genes conserved with Brachypodium distachyon. Gene Ontology classification of AS genes revealed functional assignment of these genes in many biological processes with diverse molecular functions. Conclusions: AS is common in cereal plants. The AS genes identified in four cereal crops in this work provide the foundation for further studying the roles of AS in regulation of cereal plant growth and development. The data can be accessed at Plant Alternative Splicing Databas

Evaluation of codon biology in citrus and poncirus trifoliata based on genomic features and frame corrected expressed sequence tags

Citrus, as one of the globally important fruit trees, has been an object of interest for understanding genetics and evolutionary process in fruit crops. Meta-analyses of 19 Citrus species, including 4 globally and economically important Citrus sinensis, Citrus clementina, Citrus reticulata, and 1 Citrus relative Poncirus trifoliata, were performed. We observed that codons ending with A- or T- at the wobble position were preferred in contrast to C- or G- ending codons, indicating a close association with AT richness of Citrus species and P. trifoliata. The present study postulates a large repertoire of a set of optimal codons for the Citrus genus and P. trifoliata and demonstrates that GCT and GGT are evolutionary conserved optimal codons. Our observation suggested that mutational bias is the dominating force in shaping the codon usage bias (CUB) in Citrus and P. trifoliata. Correspondence analysis (COA) revealed that the principal axis [axis 1; COA/relative synonymous codon usage (RSCU)] contributes only a minor portion (~10.96%) of the recorded variance. In all analysed species, except P. trifoliata, Gravy and aromaticity played minor roles in resolving CUB. Compositional constraints were found to be strongly associated with the amino acid signatures in Citrus species and P. trifoliata. Our present analysis postulates compositional constraints in Citrus species and P. trifoliata and plausible role of the stress with GC3 and coevolution pattern of amino acid. © The Author 2012

Clinical effects of Xinmailong therapy in patients with chronic heart failure

In the last 100 years, intensive studies have been done on the identification of the systematic approaches to find the cure for the chronic heart failure, however the mystery remains unresolved due to its complicated pathogenesis and ineffective early diagnosis. The present investigation was aimed to evaluate the potential effects of the traditional chinese medicine, Xinmailong, on the chronic heart failure (CHF) patients as compared to the standard western medical treatment available so far. In our study, we selected two groups of voluntary CHF patients at the Xiangya Hospital, which were allowed to administrate Xinmailong or standard treatments, respectively. Another group of voluntary healthy individuals were recruited as the control group. The treatment effectiveness was measured by five symptomatic factors, i.e. angiotensin II (Ang_II), high sensitivity C-reactive protein (hs_CRP), Left Ventricular End Systolic Volume Index (LVESVI), left ventricular ejection fraction (LVEF) and pro-B-type natriuretic peptide (NT_proBNP), between the control group and the CHF patients at different stages of drug administration and in different treatment groups. The timeline for the full dose administration was set to 15 days and five measurements as indicated above were taken on every 0, 7th and 15th day of the drug administration respectively. In the conducted study, similar symptomatic measurements were observed on day 0 in both treatment groups, and slight improvements were observed on 7th day. It was observed that after a full course of drug administration for 15 days, both of the treatment groups achieved statistically significant improvements in all the five measures, but Xinmailong was found to be more (almost double) statistically significant as compared with the available drug treatments for chronic heart failure. © Ivyspring International Publisher

Identification of Low Temperature Stress Regulated Transcript Sequences and Gene Families in Italian Cypress

© 2014, Springer Science+Business Media New York. Cold acclimation is a complex transcriptionally controlled process regulated by many different genes and genic-interactions in plants. The northward spreading of woody species is mainly limited by winter harshness. To increase our knowledge about the biological processes underlying cold acclimation, plants evolved in warmer climates can serve as models. In this work, a Suppression Subtractive Hybridization approach using PCR-select was used to isolate Italian cypress (Cupressus sempervirens L.) transcript sequences putatively expressed under low temperature stress. After assessing the reliability of the subtractive step, a total of 388 clones were selected and sequenced. Following sequence assembly and removal of the redundant cDNAs, 156 unique transcripts were identified and annotated in order to assign them a putative functional class. Most of the identified transcripts were functionally classified pertaining to stress in cellular and chloroplast membranes, which are previously known to be severely damaged by cold treatment. Among the identified functional gene families, the extensively represented ones were dehydrins, early light-inducible proteins, senescence-associated genes and oleosins. The last three gene families were further selected for phylogenetic analysis, with the corresponding protein sequences across the complete genomes of the model plants Populus trichocarpa, Vitis vinifera, Physcomitrella patens, and Arabidopsis thaliana. The relationship with the ortholog sequences coming from these species and their further implications are discussed