Identification of resistance gene analogs of NBS-LRR gene family against dieback in Dalbergia sissoo
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PROVIDER: PRJEB58707 | ENA |
REPOSITORIES: ENA
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Project description:Dalbergia sissoo is an important timber tree, and dieback disease poses a dire threat to it toward extinction. The genomic record of D. sissoo is not available yet on any database; that is why it is challenging to probe the genetic elements involved in stress resistance. Hence, we attempted to unlock the genetics involved in dieback resistance through probing the NBS-LRR family, linked with mostly disease resistance in plants. We analyzed the transcriptome of D. sissoo under dieback challenge through DOP-rtPCR analysis using degenerate primers from conserved regions of NBS domain-encoded gene sequences. The differentially expressed gene sequences were sequenced and in silico characterized for predicting the expressome that contributes resistance to D. sissoo against dieback. The molecular and bioinformatic analyses predicted the presence of motifs including ATP/GTP-binding site motif A (P-loop NTPase domain), GLPL domain, casein kinase II phosphorylation site, and N-myristoylation site that are the attributes of proteins encoded by disease resistance genes. The physicochemical characteristics of identified resistance gene analogs, subcellular localization, predicted protein fingerprints, in silico functional annotation, and predicted protein structure proved their role in disease and stress resistance.
| S-EPMC9585183 | biostudies-literature
Project description:Dalbergia sissoo Roxb. (Shisham) is a timber-producing species of economic, cultural, and medicinal importance in the Indian subcontinent. In the past few decades, Shisham's dieback disease caused by the fungus Botryodiplodia theobromae has become an evolving issue in the subcontinent endangering its survival. To gain insights into this issue, a standard transcriptome assembly was deployed to assess the response of D. sissoo at the transcriptomic level under the stress of B. theobromae infection. For RNA isolation, the control and infected leaf tissue samples were taken from 1-year-old greenhouse-grown D. sissoo plants after 20 days of stem-base spore inoculation. cDNA synthesis was performed from these freshly isolated RNA samples that were then sent for sequencing. About 18.14 Gb (Giga base) of data was generated using the BGISEQ-500 sequencing platform. In terms of Unigenes, 513,821 were identified after a combined assembly of all samples and then filtering the abundance. The total length of Unigenes, their average length, N50, and GC-content were 310,523,693 bp, 604 bp, 1,101 bp, and 39.95% respectively. The Unigenes were annotated using 7 functional databases i.e., 200,355 (NR: 38.99%), 164,973 (NT: 32.11%), 123,733 (Swissprot: 24.08%), 142,580 (KOG: 27.75%), 139,588 (KEGG: 27.17%), 99,752 (GO: 19.41%), and 137,281 (InterPro: 26.72%). Furthermore, the Transdecoder detected 115,762 CDS. In terms of SSR (Simple Sequence Repeat) markers, 62,863 of them were distributed on 51,508 Unigenes and on the predicted 4673 TF (Transcription Factor) coding Unigenes. A total of 16,018 up- and 19,530 down-regulated Differentially Expressed Genes (DEGs) were also identified. Moreover, the Plant Resistance Genes (PRGs) had a count of 9230. We are hopeful that in the future, these identified Unigenes, SSR markers, DEGs and PRGs will provide the prerequisites for managing Shisham dieback disease, its breeding, and in tree improvement programs.
| S-EPMC10665356 | biostudies-literature
Project description:Plant immunity includes enemy recognition, signal transduction, and defensive response against pathogens. We experimented to identify the genes that contribute resistance against dieback disease to Dalbergia sissoo, an economically important timber tree. In this study, we investigated the role of three differentially expressed genes identified in the dieback-induced transcriptome in Dalbergia sissoo. The transcriptome was probed using DOP-rtPCR analysis. The identified RGAs were characterized in silico as the contributors of disease resistance that switch on under dieback stress. Their predicted fingerprints revealed involvement in stress response. Ds-DbRCaG-02-Rga.a, Ds-DbRCaG-04-Rga.b, and Ds-DbRCaG-06-Rga.c showed structural homology with the Transthyretin-52 domain, EAL associated YkuI_C domain, and Src homology-3 domain respectively, which are the attributes of signaling proteins possessing a role in regulating immune responses in plants. Based on in-silico structural and functional characterization, they were predicted to have a role in immune response regulation in D. sissoo.
| S-EPMC10613980 | biostudies-literature
Project description:Drought Stressed Transcriptome reads of Dalbergia sissoo
| PRJNA1174766 | ENA
Project description:Dalbergia sissoo predicted Proteome under dieback challenge
| PRJNA917224 | ENA
Project description:Dalbergia sissoo Transcriptome or Gene expression
| PRJNA1019111 | ENA
Project description:Here we report the NGS RNA-seq data of the D. sissoo treated with the Botryodiplodia theobromeae.
2023-12-07 | GSE220535 | GEO
Project description:Dalbergia sissoo is a woody plant with economic and medicinal value. As the pharmacological qualities and properties of the wood from this plant primarily depend on its extractives, in this study, the metabolomic analysis of extractives from its stems was carried out using UPLC-MS/MS. A total of 735 metabolites were detected from two groups of samples, heartwood and sapwood, with the largest number of terpenoids in type and the largest number of flavonoids in quantity. The PCA and cluster analysis showed significant differences in the metabolite composition between the two groups. The differential metabolites were mainly organic oxygen compounds, flavonoids, and isoflavones. Among the 105 differential metabolites, 26 metabolites were significantly higher in relative content in sapwood than in heartwood, while the other 79 metabolites were significantly higher in relative content in heartwood than in sapwood. KEGG metabolic pathway enrichment analysis showed that these differential metabolites were mainly enriched in three metabolic pathways: Flavonoid biosynthesis, isoflavonoid biosynthesis, and flavonoid and flavonol biosynthesis. This study provides a reference for metabolomics studies in Dalbergia and other woody plants.
| S-EPMC8953952 | biostudies-literature
Project description:Dalbergia sissoo is one of the most economically important trees in forestry, agroforestry, and horticulture. This tree species is severely threatened by dieback. Widespread dieback outbreaks and infestations have drastically destroyed billions of D. sissoo trees. Hence, we attempted to resolve the dieback etiology through phylogenomics associated with D. sissoo mortality. The Ceratocystis species was evaluated using morphologically investigated fungal isolates collected from dieback-affected tissue plants. Based on the symptomatology, we have differentiated dieback from Fusarium wilt and concluded that the Ceratocystis fimbriata sensu lato complex is causing shisham dieback in Pakistan. As the Ceratocystis species complex is a cryptic species complex, we used genomics and phylogenetic analysis for deciphering its evolutionary hierarchical order. The pathogen's operational taxonomy was unlocked with the help of phylogenomics, and it was discovered that isolates from D. sissoo represent a species distinct from the other species in the C. fimbriata sensu lato species complex. The name Ceratocystis dalbergicans sp. nov. has been given to the fungus causing dieback disease in D. sissoo.
| S-EPMC10043428 | biostudies-literature