Pathways and Network Based Analysis of Candidate Genes to Reveal Cross-Talk and Specificity in the Sorghum (Sorghum bicolor (L.) Moench) Responses to Drought and It's Co-occurring Stresses

Drought alone or in combination with other stresses forms the major crop production constraint worldwide. Sorghum, one of the most important cereal crops is affected by drought alone or in combination with co-occurring stresses; notwithstanding, sorghum has evolved adaptive responses to combined stresses. Furthermore, an impressive number of sorghum genes have been investigated for drought tolerance. However, the molecular mechanism underling drought response remains poorly understood. We employed a systems biology approach to elucidate regulatory and broad functional features of these genes. Their interaction network would provide insight into understanding the molecular mechanisms of drought tolerance and underpinning signal pathways. Functional analysis was undertaken to determine significantly enriched genesets for pathways involved in drought tolerance. Analysis of distinct pathway cross-talk network was performed and drought-specific subnetwork was extracted. Investigation of various data sources such as gene expression, regulatory pathways, sorghumCyc, sorghum protein-protein interaction (PPI) and Gene Ontology (GO) revealed 14 major drought stress related hub genes (DSRhub genes). Significantly enriched genesets have shown association with various biological processes underlying drought-related responses. Key metabolic pathways were significantly enriched in the drought-related genes. Systematic analysis of pathways cross-talk and gene interaction network revealed major cross-talk pathway modules associated with drought tolerance. Further investigation of the major DSRhub genes revealed distinct regulatory genes such as ZEP, NCED, AAO, and MCSU and CYP707A1. These were involved in the regulation of ABA biosynthesis and signal transduction. Other protein families, namely, aldehyde and alcohol dehydrogenases, mitogene activated protein kinases (MAPKs), and Ribulose-1,5-biphosphate carboxylase (RuBisCO) were shown to be involved in the drought-related responses. This shows a diversity of complex functional features in sorghum to respond to various abiotic stresses. Finally, we constructed a drought-specific subnetwork, characterized by unique candidate genes that were associated with DSRhub genes. According to our knowledge, this is the first in sorghum drought investigation that introduces pathway and network-based candidate gene approach for analysis of drought tolerance. We provide novel information about pathways cross-talk and signaling networks used in further systems level analysis for understanding the molecular mechanism behind drought tolerance and can, therefore, be adapted to other model and non-model crops

Draft genome sequence of <i>Bacillus</i> sp. strain X and <i>Salarachaeum</i> sp. strain III isolated from Lake Karum, Danakil Depression, Ethiopia

Here, we report the draft genome sequences of strains of Bacillus and Salarachaeum that were isolated from hypersaline water samples collected from Lake Karum, Danakil Depression, Ethiopia. The sequences pave the way for more targeted studies into the potential biological activities and secondary metabolite synthesis of these organisms

Combined assessment of tuberculosis case notification rate and infection control at health facilities of Dale districts, Sidama Zone, Southern Ethiopia

Background Mycobacterium tuberculosis (TB) is the deadliest disease that claims millions of deaths globally. Ethiopia is among the countries heavily hit by the disaster. Despite the effective directly observed treatment and TB infection control (TBIC) measures provided by the world health organization (WHO), the rate of new cases increased daily throughout the country. Healthcare workers (HCWs) are at highest risk serving without having the necessary facility in place while overcrowding of patients exacerbated TB transmission. The study aimed to assess TBIC implementation and analyze case notification rate (CNR) of smear-positive pulmonary TB in the selected health facilities at Dale district, Sidama Zone, Southern Ethiopia. Methods Seven health care facilities have been visited in the study area and smear-positive pulmonary TB notification rate was determined retrospectively during the years 2012 to 2014. Data on smear positive test results and demographic characteristics were collected from the TB unit registries. A structured questionnaire, facility survey, and observation checklists were used to assess the presence of TBIC plans at the health care facilities. Results The overall case notification rate of smear-positive pulmonary tuberculosis was 5.3% among all 7696 TB suspected patients. The odds of being diagnosed with smear-positive TB were 24% more in males than in females (adj OR = 1.24, 95% CI: (1.22, 1.55). Moreover, in the study area, only 28% of the facilities have been practiced TB infection control and 71% of the facilities assigned a focal person for the TBIC plan. The implementation of environmental control measures in the facilities was ranged between 16–83%. N95 particulate respirators were found only in 14% of the facilities. Conclusion TB CNR in Dale district was low. Moreover, implementations of TBIC in Dale district health facilities were poor when the survey was done. Hence, urgent measures should be taken to reverse the burden of TB

Correction: Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species.

[This corrects the article DOI: 10.1371/journal.pone.0192678.]

Mining the Microbiome of Lake Afdera to Gain Insights into Microbial Diversity and Biosynthetic Potential

Microorganisms inhabiting hypersaline environments have received significant attention due to their ability to thrive under poly-extreme conditions, including high salinity, elevated temperatures and heavy metal stress. They are believed to possess biosynthetic gene clusters (BGCs) that encode secondary metabolites as survival strategy and offer potential biotechnological applications. In this study, we mined BGCs in shotgun metagenomic sequences generated from Lake Afdera, a hypersaline lake in the Afar Depression, Ethiopia. The microbiome of Lake Afdera is predominantly bacterial, with Acinetobacter (18.6%) and Pseudomonas (11.8%) being ubiquitously detected. A total of 94 distinct BGCs were identified in the metagenomic data. These BGCs are found to encode secondary metabolites with two main categories of functions: (i) potential pharmaceutical applications (nonribosomal peptide synthase NRPs, polyketide synthase, others) and (ii) miscellaneous roles conferring adaptation to extreme environment (bacteriocins, ectoine, others). Notably, NRPs (20.6%) and bacteriocins (10.6%) were the most abundant. Furthermore, our metagenomic analysis predicted gene clusters that enable microbes to defend against a wide range of toxic metals, oxidative stress and osmotic stress. These findings suggest that Lake Afdera is a rich biological reservoir, with the predicted BGCs playing critical role in the survival and adaptation of extremophiles

Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (<i>Sorghum bicolor</i> (L.) Moench) and related model species

<div><p>Background</p><p>Crop response to the changing climate and unpredictable effects of global warming with adverse conditions such as drought stress has brought concerns about food security to the fore; crop yield loss is a major cause of concern in this regard. Identification of genes with multiple responses across environmental stresses is the genetic foundation that leads to crop adaptation to environmental perturbations.</p><p>Methods</p><p>In this paper, we introduce an integrated approach to assess candidate genes for multiple stress responses across-species. The approach combines ontology based semantic data integration with expression profiling, comparative genomics, phylogenomics, functional gene enrichment and gene enrichment network analysis to identify genes associated with plant stress phenotypes. Five different ontologies, viz., Gene Ontology (GO), Trait Ontology (TO), Plant Ontology (PO), Growth Ontology (GRO) and Environment Ontology (EO) were used to semantically integrate drought related information.</p><p>Results</p><p>Target genes linked to Quantitative Trait Loci (QTLs) controlling yield and stress tolerance in sorghum (<i>Sorghum bicolor</i> (L.) Moench) and closely related species were identified. Based on the enriched GO terms of the biological processes, 1116 sorghum genes with potential responses to 5 different stresses, such as drought (18%), salt (32%), cold (20%), heat (8%) and oxidative stress (25%) were identified to be over-expressed. Out of 169 sorghum drought responsive QTLs associated genes that were identified based on expression datasets, 56% were shown to have multiple stress responses. On the other hand, out of 168 additional genes that have been evaluated for orthologous pairs, 90% were conserved across species for drought tolerance. Over 50% of identified maize and rice genes were responsive to drought and salt stresses and were co-located within multifunctional QTLs. Among the total identified multi-stress responsive genes, 272 targets were shown to be co-localized within QTLs associated with different traits that are responsive to multiple stresses. Ontology mapping was used to validate the identified genes, while reconstruction of the phylogenetic tree was instrumental to infer the evolutionary relationship of the sorghum orthologs. The results also show specific genes responsible for various interrelated components of drought response mechanism such as drought tolerance, drought avoidance and drought escape.</p><p>Conclusions</p><p>We submit that this approach is novel and to our knowledge, has not been used previously in any other research; it enables us to perform cross-species queries for genes that are likely to be associated with multiple stress tolerance, as a means to identify novel targets for engineering stress resistance in sorghum and possibly, in other crop species.</p></div

Description of sorghum target genes associated with QTLs known for drought tolerance.

<p>Description of sorghum target genes associated with QTLs known for drought tolerance.</p

Work-flow for gene-phenotype association across-species and stresses.

<p>This figure demonstrates the work flow for the gene-phenotype association in sorghum stress tolerance across species by comparing sorghum drought responsive genes with orthologs in maize, rice and Arabidopsis and across stresses by comparing these genes against salt, cold, heat and oxidative stresses. The Gramene database was used in identification of sorghum genes associated with stress phenotypes based on known stress related ontology terms for each identified plant ontology. Ensembl BioMart was used to get sorghum orthologs having transitive association with known drought regulated functions from related species. The work flow provides a protocol for a step-by-step screening procedure to identify promising gene-sets for multiple stress tolerance across species: 1) The protocol identifies plant ontologies to query genes and detects if the genes belong to the sorghum gene association or to the orthologous group. Where there is no direct sorghum gene association, the protocol looks for orthologous group. Only those genes with these features were retained, and others were discarded. 2) The genes that were not supported by the relevant ontology terms in each ontology group were again rejected and only those with drought and associated ontology terms were screened for the next step. Once merged from all ontology groups, only unique genes were captured by removing the duplicates. 3) Among these, only those which were supported by all ontology groups were used for functional GO enrichment analysis and all others were discarded. 4) Functional GO enrichment analysis based on the P-value, FDR < 0.01 were used to screen the genes associated with stresses under investigation. Only those which satisfied this threshold value were selected as the candidates for the next step. 5) Comparative analysis across species and across traits was undertaken based on the above selected candidates. Sorghum specific and orthologous genes with multi-stress responses were combined with enrichment network and expression profiling for integrative analysis. Sorghum orthologs in other species were selected for which phylogenetic analysis was done. <b>Key to legend</b>: * Response to oxidative stress; ** Drought tolerance.</p

Description of the GO enrichment analysis with enrichment level of the GO-terms in decreasing order, the corresponding number of drought responsive genes involved and the associated traits in each GO-category.

<p>Description of the GO enrichment analysis with enrichment level of the GO-terms in decreasing order, the corresponding number of drought responsive genes involved and the associated traits in each GO-category.</p

Circular representation of the polar formatted phylogenetic tree of the sorghum specific and orthologous genes.

<p>Group of genes were color-coded by orthology group identified for drought response in the other species evolutionarily related to sorghum. The tree represents labels that were aligned with default leaf sorting. Branches represent evolutionarily related ortholog clades. Branch lengths for which 'ignored' setting was adjusted were represented each by the numbers in decimal and the bootstrap values in absolute numbers (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192678#pone.0192678.s013" target="_blank">S10 Table</a>). The tree was reconstructed after removing the gaps using a bootstrap support of the 1,000 replicates to show the frequency of each internal node, clades in the tree. The red circular bootstrap symbol was used to indicate the bootstrap supported clades based on the values within the range of 100 (small dot)– 1000 (large dot) iterative replicates, where more than 75% of the clades showed the bootstrap above the commonly known threshold value (70%). The clades with the bootstrap values less than 5% were removed from the tree. The values for the robust bootstrap support were given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192678#pone.0192678.s013" target="_blank">S10 Table</a>. <b>Key to legend for the colored ranges:</b> SOA, Sorghum orthologs in Arabidopsis; SOM, sorghum orthologs in maize; SOMA, shared sorghum orthologs in maize and Arabidopsis; SOMR, shared sorghum orthologs in maize and rice; SOMRA, shared sorghum orthologs in maize, rice and Arabidopsis; SOR, sorghum orthologs in rice; SORA, shared sorghum orthologs in rice and Aabidopsis; Sorghum, sorghum specific genes; Sorghum_SOA, shared sorghum specific and sorghum orthologs in Arabidopsis; Sorghum_SOMA, shared sorghum specific and sorghum orthologs in maize and Arabidopsis; Sorghum_SOMR, shared sorghum specific and sorghum orthologs in maize and rice; Sorghum_SOMRA, shared sorghum specific and sorghum orthologs in maize, rice and Arabidopsis; Sorghum_SOR, shared sorghum specific and sorghum orthologs in rice; Sorghum_SORA, shared sorghum specific and sorghum orthologs in rice and Arabidopsis.</p