De novo transcriptomic analysis of Doum Palm (Hyphaene compressa) revealed an insight into its potential drought tolerance

BACKGROUND

Doum palms (Hyphaene compressa) perform a crucial starring role in the lives of Kenya's arid and semi-arid people for empowerment and sustenance. Despite the crop's potential for economic gain, there is a lack of genetic resources and detailed information about its domestication at the molecular level. Given the doum palm's vast potential as a widely distributed plant in semi-arid and arid climates and a source of many applications, coupled with the current changing climate scenario, it is essential to understand the molecular processes that provide drought resistance to this plant.

RESULTS

Assembly of the first transcriptome of doum palms subjected to water stress generated about 39.97 Gb of RNA-Seq data. The assembled transcriptome revealed 193,167 unigenes with an average length of 1655 bp, with 128,708 (66.63%) successfully annotated in seven public databases. Unigenes exhibited significant differentially expressed genes (DEGs) in well-watered and stressed-treated plants, with 45071 and 42457 accounting for up-regulated and down-regulated DEGs, respectively. GO term, KEGG, and KOG analysis showed that DEGs were functionally enriched cellular processes, metabolic processes, cellular and catalytic activity, metabolism, genetic information processing, signal transduction mechanisms, and posttranslational modification pathways. Transcription factors (TF), such as the MYB, WRKY, NAC family, FAR1, B3, bHLH, and bZIP, were the prominent TF families identified as doum palm DEGs encoding drought stress tolerance.

CONCLUSIONS

This study provides a complete understanding of DEGs involved in drought stress at the transcriptome level in doum palms. This research is, therefore, the foundation for the characterization of potential genes, leading to a clear understanding of its drought stress responses and providing resources for improved genetic modification.

Transcriptome Analysis Reveals Genes Associated with Flooding Tolerance in Mulberry Plants

Mulberry (Morus alba), a widely distributed economic plant, can withstand long-term flooding stress. However, the regulatory gene network underlying this tolerance is unknown. In the present study, mulberry plants were subjected to submergence stress. Subsequently, mulberry leaves were collected to perform quantitative reverse-transcription PCR (qRT-PCR) and transcriptome analysis. Genes encoding ascorbate peroxidase and glutathione S-transferase were significantly upregulated after submergence stress, indicating that they could protect the mulberry plant from flood damage by mediating ROS homeostasis. Genes that regulate starch and sucrose metabolism; genes encoding pyruvate kinase, alcohol dehydrogenase, and pyruvate decarboxylase (enzymes involved in glycolysis and ethanol fermentation); and genes encoding malate dehydrogenase and ATPase (enzymes involved in the TCA cycle) were also obviously upregulated. Hence, these genes likely played a key role in mitigating energy shortage during flooding stress. In addition, genes associated with ethylene, cytokinin, abscisic acid, and MAPK signaling; genes involved in phenylpropanoid biosynthesis; and transcription factor genes also showed upregulation under flooding stress in mulberry plants. These results provide further insights into the adaptation mechanisms and genetics of submergence tolerance in mulberry plants and could aid in the molecular breeding of these plants.

Transcriptome analysis of mulberry (Morus alba L.) leaves to identify differentially expressed genes associated with post-harvest shelf-life elongation

Present study deals with molecular expression patterns responsible for post-harvest shelf-life extension of mulberry leaves. Quantitative profiling showed retention of primary metabolite and accumulation of stress markers in NS7 and CO7 respectively. The leaf mRNA profiles was sequenced using the Illumina platform to identify DEGs. A total of 3413 DEGs were identified between the treatments. Annotation with Arabidopsis database has identified 1022 DEGs unigenes. STRING generated protein-protein interaction, identified 1013 DEGs nodes with p < 1.0e-16. KEGG classifier has identified genes and their participating biological processes. MCODE and BiNGO detected sub-networking and ontological enrichment, respectively at p ≤ 0.05. Genes associated with chloroplast architecture, photosynthesis, detoxifying ROS and RCS, and innate-immune response were significantly up-regulated, responsible for extending shelf-life in NS7. Loss of storage sucrose, enhanced activity of senescence-related hormones, accumulation of xenobiotics, and development of osmotic stress inside tissue system was the probable reason for tissue deterioration in CO7. qPCR validation of DEGs was in good agreement with RNA sequencing results, indicating the reliability of the sequencing platform. Present outcome provides a molecular insight regarding involvement of genes in self-life extension, which might help the sericulture industry to overcome their pre-existing problems related to landless farmers and larval feeding during monsoon.

Physiological and transcriptome analyses highlight multiple pathways involved in drought stress in Medicago falcata

Medicago falcata is one of the leguminous forage crops, which grows well in arid and semiarid region. To fully investigate the mechanism of drought resistance response in M. falcata, we challenged the M. falcata plants with 30% PEG-6000, and performed physiological and transcriptome analyses. It was found that, the activities of antioxidant enzymes (eg. SOD, POD, and CAT) and soluble sugar content were all increased in the PEG-treated group, as compared to the control group. Transcriptome results showed that a total of 706 genes were differentially expressed in the PEG-treated plants in comparison with the control. Gene enrichment analyses on differentially expressed genes revealed that a number of genes in various pathway were significantly enriched, including the phenylpropanoid biosynthesis (ko00940) and glycolysis/gluconeogenesis (ko00010), indicating the involvement of these key pathways in drought response. Furthermore, the expression levels of seven differentially expressed genes were verified to be involved in drought response in M. falcata by qPCR. Taken together, these results will provide valuable information related to drought response in M. falcata and lay a foundation for molecular studies and genetic breeding of legume crops in future research.

DNA Methylation Changes and Its Associated Genes in Mulberry (Morus alba L.) Yu-711 Response to Drought Stress Using MethylRAD Sequencing

Drought stress remains one of the most detrimental environmental cues affecting plant growth and survival. In this work, the DNA methylome changes in mulberry leaves under drought stress (EG) and control (CK) and their impact on gene regulation were investigated by MethylRAD sequencing. The results show 138,464 (37.37%) and 56,241 (28.81%) methylation at the CG and CWG sites (W = A or T), respectively, in the mulberry genome between drought stress and control. The distribution of the methylome was prevalent in the intergenic, exonic, intronic and downstream regions of the mulberry plant genome. In addition, we discovered 170 DMGs (129 in CG sites and 41 in CWG sites) and 581 DMS (413 in CG sites and 168 in CWG sites). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicates that phenylpropanoid biosynthesis, spliceosome, amino acid biosynthesis, carbon metabolism, RNA transport, plant hormone, signal transduction pathways, and quorum sensing play a crucial role in mulberry response to drought stress. Furthermore, the qRT-PCR analysis indicates that the selected 23 genes enriched in the KEGG pathways are differentially expressed, and 86.96% of the genes share downregulated methylation and 13.04% share upregulation methylation status, indicating the complex link between DNA methylation and gene regulation. This study serves as fundamentals in discovering the epigenomic status and the pathways that will significantly enhance mulberry breeding for adaptation to a wide range of environments.

Whole genome bisulfite sequencing methylome analysis of mulberry (Morus alba) reveals epigenome modifications in response to drought stress

DNA methylation plays a significant role in many biological processes. Although some studies of DNA methylation have been performed in woody plant, none is known about the methylation patterns of mulberry (Morus alba). In this study, we performed whole genome bisulfite sequencing under drought stress to generate a methylated cytosines map and assessed the effects of the changes on gene expression combined with transcriptomics. We found that the percentage of methylated cytosines varied depending on the local sequence context (CG, CHG and CHH) and external treatment (control, CK; drought stress, DS). The methylation levels under DS were 8.64% higher than that of CK, and differences that were mainly due to the contribution of mCG (6.24%). Additionally, there were 3,243 different methylation and expression associated genes. In addition, methylated genes were enriched within GO subcategories including catalytic activity, cellular process, metabolic process, response to stimulus and regulation of biological process. This is the first study to comprehensively present methylation patterns in mulberry and reveal widespread DNA methylation changes in response to drought stress, which has the potential to enhance our understanding of links between DNA methylation and the modulation of gene expression in plants subjected to abiotic stresses.

Transcriptomic and proteomic analyses of mulberry (Morus atropurpurea) fruit response to Ciboria carunculoides

The aim of this work was to gain insights into the molecular mechanisms and dynamics of the mulberry (Morus atropurpurea) fruit response to Ciboria carunculoides infection. A transcriptomic and proteomic study was carried out based on RNA sequencing and isobaric tags for relative and absolute quantification analysis, respectively. These data were then validated using quantitative real-time PCR and multiple reaction monitoring assays. Comparative analyses revealed that 9.0% of the transcriptome and 20.8% of the proteome were differentially regulated after C. carunculoides infection at the early stage (stage 1) and middle stage (stage 2), but correlation analysis revealed that only 145 genes were differentially regulated at both the transcriptome and proteome levels. The combined transcriptome and proteome analysis showed that plant hormone signal transduction, calcium-mediated defense signaling, transcription factors, and secondary metabolites were stimulated, whereas photosynthesis and cellular growth-related metabolism were suppressed after C. carunculoides infection. These finding provide theoretical foundation for disease resistance breeding of C. carunculoides. BIOLOGICAL SIGNIFICANCE: Ciboria carunculoides is a major fungal pathogen that infects mulberry fruit, leading to extensive damage and productivity loss. Despite this major impact, the mulberry fruit response to C. carunculoides infection has yet to be characterized. This study provides the first system-wide datasets with which to examine changes in the transcriptome and proteome after C. carunculoides infection in mulberry fruit. The results showed that plant hormone signal transduction, calcium-mediated defense signaling, and other pathways were stimulated, whereas photosynthesis and cellular growth-related metabolism were suppressed by C. carunculoides. These results will lead to a better understanding of the molecular mechanisms triggered in mulberry fruit in response to C. carunculoides infection and will provide new molecular targets for regulating defense responses to fungal pathogens in berry fruits.

Transcriptome analysis and identification of key genes involved in 1-deoxynojirimycin biosynthesis of mulberry (Morus alba L.)

Mulberry (Morus alba L.) represents one of the most commonly utilized plants in traditional medicine and as a nutritional plant used worldwide. The polyhydroxylated alkaloid 1-deoxynojirimycin (DNJ) is the major bioactive compounds of mulberry in treating diabetes. However, the DNJ content in mulberry is very low. Therefore, identification of key genes involved in DNJ alkaloid biosynthesis will provide a basis for the further analysis of its biosynthetic pathway and ultimately for the realization of synthetic biological production. Here, two cDNA libraries of mulberry leaf samples with different DNJ contents were constructed. Approximately 16 Gb raw RNA-Seq data was generated and de novo assembled into 112,481 transcripts, with an average length of 766 bp and an N50 value of 1,392. Subsequently, all unigenes were annotated based on nine public databases; 11,318 transcripts were found to be significantly differentially regulated. A total of 38 unique candidate genes were identified as being involved in DNJ alkaloid biosynthesis in mulberry, and nine unique genes had significantly different expression. Three key transcripts of DNJ biosynthesis were identified and further characterized using RT-PCR; they were assigned to lysine decarboxylase and primary-amine oxidase genes. Five CYP450 transcripts and two methyltransferase transcripts were significantly associated with DNJ content. Overall, the biosynthetic pathway of DNJ alkaloid was preliminarily speculated.

Mulberry (Morus spp.) has the features to treat as a potential perennial model system

Mulberry (Morus spp.), a commercially exploited tree species as the host of monophagous pest silk worm (Bombyx mori), belongs to the family Moraceae. The domesticated tree has diverse beneficial characters such as traits associated with rapid growth and biomass production, plant insect/microbe interaction, abiotic stress tolerance and the traits associated with nutritional and medicinal values; some of which have been exploited. Draft genome of Morus notabilis has been sequenced and a large volume of transcriptome and genomic resources have been generated. In this review an attempt has been made to examine the options for considering mulberry as another tree model system to study unique traits associated with perennial systems. The diverse traits and features in mulberry suggest that the system can be a "comprehensive trait integrated tree system" quite different from other model tree systems.

S. P, M. S. R, R. T, Naik VG. Association mapping of quantitative resistance to charcoal root rot in mulberry germplasm

Outbreaks of root rot disease in the productive South Indian sericulture belt have threatened the sustainability of the industry. Macrophomina phaseolina (Tassi) Goid. causing charcoal rot is the predominant pathogen to which all productive mulberry cultivars are susceptible. The present study was undertaken to identify molecular markers associated with charcoal rot resistance in mulberry. A mapping panel comprising 214 diverse entries from the Indian germplasm collection was assessed for charcoal rot resistance by artificial inoculation. Resistance to the pathogen was observed in 20 entries, and 51 were found to be moderately resistant. A total of 773 alleles generated across 105 SSR loci and 20,384 AFLP markers generated using 32 EcoRI-NN and MseI-CNN primer combinations were used in genetic analysis. The panel was weakly structured with two subpopulations. However, most entries were found to be admixtures. Survival of cuttings and number of roots per sapling were associated with root rot resistance. Association mapping was performed using different linear mixed models. Five AFLP markers explaining 9.6-12.7% of the total phenotypic variance were found to be significantly (p < 0.05) associated with root rot resistance. Significant associations were also detected in four AFLP markers for survival of cuttings, and these markers explained 10.7-14.2% of the total phenotypic variance. These markers should be validated using mapping populations derived from contrasting biparental combinations by linkage analysis for use in marker-assisted gene pyramiding for durable resistance. The resistant genotypes identified in this study will substantially contribute to genetic improvement of mulberry for charcoal rot resistance and can be integrated into conventional breeding programmes.

Improvement of abiotic stress adaptive traits in mulberry (Morus spp.): an update on biotechnological interventions

Mulberry (Morus spp.), being an economically important tree, is cultivated in China, India, Thailand, Brazil, Uzbekistan and other Countries across the globe, for its leaves to feed monophagous mulberry silkworm (Bombyx mori). The sustainability of silk industry is directly correlated with the production and continuous supply of high-quality mulberry leaves. In India, it is cultivated on large scale in tropical, sub-tropical and temperate regions under irrigated conditions for silkworm rearing. Drought, low temperature, high salinity and alkalinity, being experienced in widespread areas, are the major abiotic stresses, causing reduction in its potential foliage yield and quality. Further, climate change effects may worsen the productivity of mulberry in near future, not only in India but also across the globe. Although traditional breeding methods contributed immensely towards the development of abiotic stress-tolerant mulberry varieties, still there is lot of scope for implementation of modern genomic and molecular biology tools for accelerating mulberry genetic improvement programmes. This review discusses omics approaches, molecular breeding, plant tissue culture and genetic engineering techniques exploited for mulberry genetic improvement for abiotic stress tolerance. However, high-throughput biotechnological tools such as RNA interference, virus-induced gene silencing, epigenomics and genome editing tools need to be utilized in mulberry to accelerate the progress of functional genomics. The application of genomic tools such as genetic engineering, marker-assisted selection and genomic selection in breeding programmes can hasten the development of climate resilient and productive mulberry varieties leading to the vertical and horizontal expansion for quality silk production.

Comparative transcriptomics and comprehensive marker resource development in mulberry

BACKGROUND

High potential of Morus laevigata and Morus serrata has been proposed in the breeding programs for Morus sp. However, due to the lack of dense molecular markers this goal is still in its nascent stage and not yet realized. We thus, sequenced the transcriptomes of these two wild Morus species and utilized the data for marker development.

RESULTS

We generated 87.0 and 80.3 Mb of transcriptome data from M. laevigata and M. serrata, respectively. The transcriptomes from M. laevigata and M. serrata, were assembled into 95,181 and 85,269 transcripts, respectively, and annotated. We identified around 24,049 Simple Sequence Repeats (SSRs), 1,201,326 Single Nucleotide Polymorphisms (SNPs) and 67,875 Insertion-Deletions (InDels). The variants having a higher impact were also identified and their effect was further investigated.

CONCLUSIONS

The transcriptome resource from the wildly growing mulberry species developed in this study can find wide applicability in gene identification and/or characterization. It can also contribute immensely in the existing mulberry improvement programs.