Development of di-nucleotide microsatellite markers and construction of genetic linkage map in mango (Mangifera indica L.)

Forty-two di-nucleotide microsatellite, or simple-sequence repeat (SSR), markers were developed using CA and CTenriched genomic libraries of Mangifera indica L. Six cultivated mangoes and two wild species were tested for primer amplifications. Most loci could amplify M. caloneura Kruz and M. foetida. The average number of alleles per locus was 4.4. The average expected heterozygosity and the maximum polymorphism information content value were 0.57 and 0.53, respectively. The SSRs developed in this study together with 65 SSRs and 145 restriction fragment length polymorphism (RFLP) markers reported previously were used in the genetic linkage analysis. A partial genetic linkage map was constructed based on 31 F1 progenies from a cross between ‘Alphonso’ and ‘Palmer’. The map spanned a distance of 529.9 centiMorgan (cM) and consisted of 9 microsatellite markers (6 from this study) and 67 RFLP markers. The new SSR markers and the present map will be useful for mango genetic studies and breeding applications in the future

Genome-wide association study and genomic prediction for resistance against Streptococcus agalactiae in hybrid red tilapia (Oreochromis spp.)

Streptococcosis is a major disease that causes severe mortality in tilapia aquaculture worldwide. Although the conventional BLUP family selection to enhance disease resistance in a commercial red tilapia stock was successful, the response was low due to the low heritability of the traits. An alternative strategy is the utilization of genomic information to identify the best performing candidates within families. In this study, we performed genome-wide association studies for red tilapia resistance to Streptococcus agalactiae using 11,480 SNPs within 110 families represented by 1020 fish. Nineteen SNP markers were found to explain similar to 10% of the genetic variation. We compared the accuracies of genomic prediction using the pedigree-based (PBLUP), marker-based (GBLUP), and Bayesian models. The prediction accuracy was assessed by performing ten replicates of five-fold cross-validation. In each replicate, approximately 80% of the data (n similar to 816) were sampled for the training set and the remaining data (n similar to 204) were used for the validation. The BayesB model yielded the highest accuracies (0.31 and 0.20) followed by GBLUP (0.25 and 0.15) and PBLUP (0.15 and 0.06) for days to death and binary trait

EnHERV: Enrichment analysis of specific human endogenous retrovirus patterns and their neighboring genes.

Human endogenous retroviruses (HERVs) are flanked by long terminal repeats (LTRs), which contain the regulation part of the retrovirus. Remaining HERVs constitute 7% to 8% of the present day human genome, and most have been identified as solo LTRs. The HERV sequences have been associated with several molecular functions as well as certain diseases in human, but their roles in human diseases are yet to be established. We designed EnHERV to make accessible the identified endogenous retrovirus repetitive sequences from Repbase Update (a database of eukaryotic repetitive elements) that are present in the human genome. Defragmentation process was done to improve the RepeatMasker annotation output. The defragmented elements were used as core database in EnHERV. EnHERV is available at http://sysbio.chula.ac.th/enherv and can be searched using either gene lists of user interest or HERV characteristics. Besides the search function, EnHERV also provides an enrichment analysis function that allows users to perform enrichment analysis between selected HERV characteristics and user-input gene lists, especially genes with the expression profile of a certain disease. EnHERV will facilitate exploratory studies of specific HERV characteristics that control gene expression patterns related to various disease conditions. Here we analyzed 25 selected HERV groups/names from all four HERV superfamilies, using the sense and anti-sense directions of the HERV and gene expression profiles from 49 specific tissue and disease conditions. We found that intragenic HERVs were associated with down-regulated genes in most cancer conditions and in psoriatic skin tissues and associated with up-regulated genes in immune cells particularly from systemic lupus erythematosus (SLE) patients. EnHERV allowed the analysis of how different types of LTRs were differentially associated with specific gene expression profiles in particular disease conditions for further studies into their mechanisms and functions

Snake Venom Metalloproteinases and Their Peptide Inhibitors from Myanmar Russell’s Viper Venom

Russell’s viper bites are potentially fatal from severe bleeding, renal failure and capillary leakage. Snake venom metalloproteinases (SVMPs) are attributed to these effects. In addition to specific antivenom therapy, endogenous inhibitors from snakes are of interest in studies of new treatment modalities for neutralization of the effect of toxins. Two major snake venom metalloproteinases (SVMPs): RVV-X and Daborhagin were purified from Myanmar Russell’s viper venom using a new purification strategy. Using the Next Generation Sequencing (NGS) approach to explore the Myanmar RV venom gland transcriptome, mRNAs of novel tripeptide SVMP inhibitors (SVMPIs) were discovered. Two novel endogenous tripeptides, pERW and pEKW were identified and isolated from the crude venom. Both purified SVMPs showed caseinolytic activity. Additionally, RVV-X displayed specific proteolytic activity towards gelatin and Daborhagin showed potent fibrinogenolytic activity. These activities were inhibited by metal chelators. Notably, the synthetic peptide inhibitors, pERW and pEKW, completely inhibit the gelatinolytic and fibrinogenolytic activities of respective SVMPs at 5 mM concentration. These complete inhibitory effects suggest that these tripeptides deserve further study for development of a therapeutic candidate for Russell’s viper envenomation

Comparative Transcriptomic Analysis of Genes in the 20-Hydroxyecdysone Biosynthesis in the Fern <i>Microsorum scolopendria</i> towards Challenges with Foliar Application of Chitosan

Microsorum scolopendria is an important medicinal plant that belongs to the Polypodiaceae family. In this study, we analyzed the effects of foliar spraying of chitosan on growth promotion and 20-hydroxyecdysone (20E) production in M. scolopendria. Treatment with chitosan at a concentration of 50 mg/L in both young and mature sterile fronds induced the highest increase in the amount of accumulated 20E. Using RNA sequencing, we identified 3552 differentially expressed genes (DEGs) in response to chitosan treatment. The identified DEGs were associated with 236 metabolic pathways. We identified several DEGs involved in the terpenoid and steroid biosynthetic pathways that might be associated with secondary metabolite 20E biosynthesis. Eight upregulated genes involved in cholesterol and phytosterol biosynthetic pathway, five upregulated genes related to the methylerythritol 4-phosphate (MEP) and mevalonate (MVA) pathways, and several DEGs that are members of cytochrome P450s and ABC transporters were identified. Quantitative real-time RT-PCR confirmed the results of RNA-sequencing. Taken together, we showed that chitosan treatment increased plant dry weight and 20E accumulation in M. scolopendria. RNA-sequencing and DEG analyses revealed key enzymes that might be related to the production of the secondary metabolite 20E in M. scolopendria

HERV truncation pattern distribution.

<p>Percentage and number of each HERV truncation pattern in the HERV elements resulting from the defragmentation process.</p

Solo LTRs used in the enrichment analysis in EnHERV.

<p>Solo LTRs used in the enrichment analysis in EnHERV.</p

Number of defragmented and non-defragmented elements.

<p>Graph shows a number of defragmented and non-defragmented elements in relation to distance parameters.</p

The number of defragmented elements, resulting from HERV defragmentation using REannotate with different values of distance parameters, and their coverage percentages.

<p>The number of defragmented elements, resulting from HERV defragmentation using REannotate with different values of distance parameters, and their coverage percentages.</p