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Cytokinin oxidase/dehydrogenase (CKX) regulates cytokinin levels in plants which are vital for plant growth and development. However, there is a paucity of evidence regarding their role in controlling embryo/seed development in pigeonpea. This comprehensive study provides information on the identification and characterization of CKX genes in pigeonpea. A genome-wide analysis identified 18 CKX genes, each with distinct structure, expression patterns, and possible diverse functions. Domain analysis revealed the presence of the sequences including FAD and CK-Binding domain, and subcellular localization analysis showed that almost 50 % of them reside within the nucleus. They were observed to be located unevenly on chromosome numbers 2, 4, 6, 7, and 11 with a majority of them present on the scaffolds. The 8 homologous pairs and various orthologous gene pairs provided further insights into their evolution pattern. Further, SNP/Indels variation in CKX genes and haplotype groups among contrasting genotypes for SNPP (seed number per pod) were analyzed. Spatiotemporal expression analysis revealed the significant expression pattern of CcCKX15, CcCKX17, and CcCKX2 in genotypes carrying low SNPP reiterating their possible role as negative regulators. These genes can be potential targets to undertake seed and biomass improvement in pigeonpea.
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BACKGROUND: Bemisia tabaci, a significant agricultural pest in Asia, contains distinct genetic groups, Asia-1 and Asia II-1. Understanding its reproductive biology, particularly the role of ejaculatory bulb proteins (EBPs) in mating, is crucial. However, EBPs in B. tabaci were not well characterised until this study. METHODS AND RESULTS: The EBPs have been characterised in the Asia-1 and Asia II-1 genetic groups of the whitefly B. tabaci, prevalent in Asia. The transcriptomic analysis yielded over 40,000,000 and 30,000,000 annotated transcripts, respectively, from Asia II-1 and Asia-1. Differential gene expression revealed the presence of 270 upregulated and 198 downregulated genes, with significant differences between these two genetic groups. Orphan genes (1992 numbers) were identified in both genetic groups. We report, for the first time, full-length sequences of EBP genes from B. tabaci. The 10 EBPs each deduced in B. tabaci Asia-1 and Asia II-1 are structurally akin to chemosensory proteins having four conserved cysteine residues. Additionally, we did domain analysis, protein structure prediction, mapping of these EBPs in the chromosomes of B. tabaci, and phylogenetic analysis to track their evolutionary lineage. We have specifically demonstrated the transfer of EBPs from males to females during mating using qPCR and further validated the transfer of EBPs through RNAi. Specifically, we targeted the highly expressed EBPs (EBP-3, 7, and 8 in BtAsia1; EBP-8, 9, and 10 in BtAsia II-1) through feeding bioassays of dsRNAs. Tracking by qPCR revealed that the females, when mated with dsRNA-treated males, did not show expression of the specific EBP, suggesting that the silencing of these genes in males hinders the transfer of EBP to females during mating. CONCLUSION: Our findings provide novel insights into the genomic contours of EBPs in B. tabaci and underscore the potential of RNAi-based strategies for pest management by disrupting the reproductive processes.
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Hemípteros , Proteínas de Insectos , Interferencia de ARN , Animales , Hemípteros/genética , Proteínas de Insectos/genética , Proteínas de Insectos/metabolismo , Masculino , Femenino , Filogenia , Reproducción/genética , Perfilación de la Expresión Génica/métodos , Conducta Sexual Animal/fisiología , Asia , Transcriptoma/genéticaRESUMEN
BACKGROUND: Heat stress is a detrimental abiotic stress that limits the development of many plant species and is linked to a variety of cellular and physiological problems. Heat stress affects membrane fluidity, which leads to negative effects on cell permeability and ion transport. Research reveals that heat stress causes severe damage to cells and leads to rapid accumulation of reactive oxygen species (ROS), which could cause programmed cell death. METHODS AND RESULTS: This current study aimed to validate the role of Triticum aestivum Salt Stress Root Protein (TaSSRP) in plants' tolerance to heat stress by modulating its expression in tobacco plants. The Relative Water Content (RWC), total chlorophyll content, and Membrane Stability Index (MSI) of the seven distinct transgenic lines (T0 - 2, T0 - 3, T0 - 6, T0 - 8, T0 - 9, T0 - 11, and T0 - 13), increased in response to heat stress. Despite the fact that the same tendency was detected in wild-type (WT) plants, changes in physio-biochemical parameters were greater in transgenic lines than in WT plants. The expression analysis revealed that the transgene TaSSRP expressed from 1.00 to 1.809 folds in different lines in the transgenic tobacco plants. The gene TaSSRP offered resistance to heat stress in Nicotiana tabacum, according to the results of the study. CONCLUSION: These findings could help to improve our knowledge and understanding of the mechanism underlying thermotolerance in wheat, and the novel identified gene TaSSRP could be used in generating wheat varieties with enhanced tolerance to heat stress.
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Regulación de la Expresión Génica de las Plantas , Respuesta al Choque Térmico , Nicotiana , Proteínas de Plantas , Plantas Modificadas Genéticamente , Triticum , Nicotiana/genética , Nicotiana/metabolismo , Triticum/genética , Triticum/metabolismo , Plantas Modificadas Genéticamente/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Respuesta al Choque Térmico/genética , Especies Reactivas de Oxígeno/metabolismo , Raíces de Plantas/metabolismo , Raíces de Plantas/genética , Termotolerancia/genética , Clorofila/metabolismo , Tolerancia a la Sal/genéticaRESUMEN
The P-type ATPase superfamily genes are the cation and phospholipid pumps that transport ions across the membranes by hydrolyzing ATP. They are involved in a diverse range of functions, including fundamental cellular events that occur during the growth of plants, especially in the reproductive organs. The present work has been undertaken to understand and characterize the P-type ATPases in the pigeonpea genome and their potential role in anther development and pollen fertility. A total of 59 P-type ATPases were predicted in the pigeonpea genome. The phylogenetic analysis classified the ATPases into five subfamilies: eleven P1B, eighteen P2A/B, fourteen P3A, fifteen P4, and one P5. Twenty-three pairs of P-type ATPases were tandemly duplicated, resulting in their expansion in the pigeonpea genome during evolution. The orthologs of the reported anther development-related genes were searched in the pigeonpea genome, and the expression profiling studies of specific genes via qRT-PCR in the pre- and post-meiotic anther stages of AKCMS11A (male sterile), AKCMS11B (maintainer) and AKPR303 (fertility restorer) lines of pigeonpea was done. Compared to the restorer and maintainer lines, the down-regulation of CcP-typeATPase22 in the post-meiotic anthers of the male sterile line might have played a role in pollen sterility. Furthermore, the strong expression of CcP-typeATPase2 in the post-meiotic anthers of restorer line and CcP-typeATPase46, CcP-typeATPase51, and CcP-typeATPase52 in the maintainer lines, respectively, compared to the male sterile line, clearly indicates their potential role in developing male reproductive organs in pigeonpea.
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Cajanus , Regulación de la Expresión Génica de las Plantas , Filogenia , Proteínas de Plantas , Polen , Polen/genética , Polen/crecimiento & desarrollo , Cajanus/genética , Cajanus/crecimiento & desarrollo , Cajanus/enzimología , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , ATPasas Tipo P/genética , ATPasas Tipo P/metabolismo , Fertilidad/genética , Flores/genética , Flores/crecimiento & desarrollo , Infertilidad Vegetal/genética , Perfilación de la Expresión Génica , Genoma de PlantaRESUMEN
The present study explores the kitchen waste okra peels derived synthesis of nitrogen doped carbon dots (N-CDs) via simple carbonization followed by reflux method. The synthesized N-CDs was characterized using, TEM, XPS, FTIR, XRD, Raman, UV-Visible and Fluorescence Spectroscopy. The N-CDs emits bright blue emission at 420 nm with 12 % of quantum yield as well as it follows excitation dependent emission. Further, the N-CDs were employed as a fluorescence sensor for detection of hazardous metal ions and nitro compounds. Among various metal ions and nitro compounds, the N-CDs shows fluorescence quenching response towards Cr6+, and Mn7+ metal ions as well as 4-nitroaniline (4-NA) and picric acid (PA) with significant hypsochromic and bathochromic shift for Mn7+, 4-NA and PA respectively. The developed fluorescent probe shows relatively low limit of detection (LOD) of 1.46 µg/mL, 1.05 µg/mL, 2.1 µg/mL and 2.2 µg/mL for the above analytes respectively. The N-CDs did not show any significant interference with coexisting ions and successfully applied for real water sample analysis. In addition, circular economy approach was employed for adsorption of dyes by reactivating leftover waste carbon residue which was obtained after reflux. Thus, the kitchen waste valorization and circular economy approach based N-CDs have potential applications in the field of detection of emerging pollutants, and environmental remediation.
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KEY MESSAGE: In current study candidate gene (261 genes) based association mapping on 144 pigeonpea accessions for flowering time and related traits and 29 MTAs producing eight superior haplotypes were identified. In the current study, we have conducted an association analysis for flowering-associated traits in a diverse pigeonpea mini-core collection comprising 144 accessions using the SNP data of 261 flowering-related genes. In total, 13,449 SNPs were detected in the current study, which ranged from 743 (ICP10228) to 1469 (ICP6668) among the individuals. The nucleotide diversity (0.28) and Watterson estimates (0.34) reflected substantial diversity, while Tajima's D (-0.70) indicated the abundance of rare alleles in the collection. A total of 29 marker trait associations (MTAs) were identified, among which 19 were unique to days to first flowering (DOF) and/or days to fifty percent flowering (DFF), 9 to plant height (PH), and 1 to determinate (Det) growth habit using 3 years of phenotypic data. Among these MTAs, six were common to DOF and/or DFF, and four were common to DOF/DFF along with the PH, reflecting their pleiotropic action. These 29 MTAs spanned 25 genes, among which 10 genes clustered in the protein-protein network analysis, indicating their concerted involvement in floral induction. Furthermore, we identified eight haplotypes, four of which regulate late flowering, while the remaining four regulate early flowering using the MTAs. Interestingly, haplotypes conferring late flowering (H001, H002, and H008) were found to be taller, while those involved in early flowering (H003) were shorter in height. The expression pattern of these genes, as inferred from the transcriptome data, also underpinned their involvement in floral induction. The haplotypes identified will be highly useful to the pigeonpea breeding community for haplotype-based breeding.
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Cajanus , Flores , Haplotipos , Polimorfismo de Nucleótido Simple , Flores/genética , Flores/fisiología , Flores/crecimiento & desarrollo , Haplotipos/genética , Cajanus/genética , Cajanus/crecimiento & desarrollo , Polimorfismo de Nucleótido Simple/genética , Genes de Plantas/genética , Fenotipo , Regulación de la Expresión Génica de las Plantas , Estudios de Asociación Genética , Sitios de Carácter Cuantitativo/genéticaRESUMEN
Ziziphus nummularia an elite heat-stress tolerant shrub, grows in arid regions of desert. However, its molecular mechanism responsible for heat stress tolerance is unexplored. Therefore, we analysed whole transcriptome of Jaisalmer (heat tolerant) and Godhra (heat sensitive) genotypes of Z. nummularia to understand its molecular mechanism responsible for heat stress tolerance. De novo assembly of 16,22,25,052 clean reads yielded 276,029 transcripts. A total of 208,506 unigenes were identified which contains 4290 and 1043 differentially expressed genes (DEG) in TGO (treated Godhra at 42 °C) vs. CGO (control Godhra) and TJR (treated Jaisalmer at 42 °C) vs. CJR (control Jaisalmer), respectively. A total of 987 (67 highly enriched) and 754 (34 highly enriched) pathways were obsorved in CGO vs. TGO and CJR vs. TJR, respectively. Antioxidant pathways and TFs like Homeobox, HBP, ARR, PHD, GRAS, CPP, and E2FA were uniquely observed in Godhra genotype and SET domains were uniquely observed in Jaisalmer genotype. Further transposable elements were highly up-regulated in Godhra genotype but no activation in Jaisalmer genotype. A total of 43,093 and 39,278 simple sequence repeats were identified in the Godhra and Jaisalmer genotypes, respectively. A total of 10 DEGs linked to heat stress were validated in both genotypes for their expression under different heat stresses using quantitative real-time PCR. Comparing expression patterns of the selected DEGs identified ClpB1 as a potential candidate gene for heat tolerance in Z. nummularia. Here we present first characterized transcriptome of Z. nummularia in response to heat stress for the identification and characterization of heat stress-responsive genes. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-024-01431-y.
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Modifications within the epigenome of an organism in response to external environmental conditions allow it to withstand the hostile stress factors. Drought in chickpea is a severely limiting abiotic stress factor which is known to cause huge yield loss. To analyse the methylome of chickpea in response to drought stress conditions and how it affects gene expression, we performed whole-genome bisulfite sequencing (WGBS) and RNA-seq of two chickpea genotypes which contrast for drought tolerance. It was observed that the mCHH was most variable under drought stress and the drought tolerant (DT) genotype exhibited substantial genome-wide hypomethylation as compared to the drought sensitive (DS) genotype. Specifically, there was substantial difference in gene expression and methylation for the ribosomal genes for the tolerant and sensitive genotypes. The differential expression of these genes was in complete agreement with earlier reported transcriptomes in chickpea. Many of these genes were hypomethylated (q < 0.01) and downregulated under drought stress (p < 0.01) in the sensitive genotype. The gene RPS6 (ribosomal protein small subunit) was found to be downregulated and hypomethylated in the drought sensitive genotype which could possibly lead to reduced ribosomal biosynthesis. This study provides novel insights into regulation of drought-responsive genes in chickpea.
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Cicer , Metilación de ADN , Sequías , Regulación de la Expresión Génica de las Plantas , Estrés Fisiológico , Cicer/genética , Metilación de ADN/genética , Estrés Fisiológico/genética , Genotipo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Perfilación de la Expresión GénicaRESUMEN
MicroRNAs (miRNAs) are small non-coding conserved molecules with lengths varying between 18-25nt. Plants miRNAs are very stable, and probably they might have been transferred across kingdoms via food intake. Such miRNAs are also called exogenous miRNAs, which regulate the gene expression in host organisms. The miRNAs present in the cluster bean, a drought tolerant legume crop having high commercial value, might have also played a regulatory role for the genes involved in nutrients synthesis or disease pathways in animals including humans due to dietary intake of plant parts of cluster beans. However, the predictive role of miRNAs of cluster beans for gene-disease association across kingdoms such as cattle and humans are not yet fully explored. Thus, the aim of the present study is to (i) find out the cluster bean miRNAs (cb-miRs) functionally similar to miRNAs of cattle and humans and predict their target genes' involvement in the occurrence of complex diseases, and (ii) identify the role of cb-miRs that are functionally non-similar to the miRNAs of cattle and humans and predict their targeted genes' association with complex diseases in host systems. Here, we predicted a total of 33 and 15 functionally similar cb-miRs (fs-cb-miRs) to human and cattle miRNAs, respectively. Further, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed the participation of targeted genes of fs-cb-miRs in 24 and 12 different pathways in humans and cattle, respectively. Few targeted genes in humans like LCP2, GABRA6, and MYH14 were predicted to be associated with disease pathways of Yesinia infection (hsa05135), neuroactive ligand-receptor interaction (hsa04080), and pathogenic Escherichia coli infection (hsa05130), respectively. However, targeted genes of fs-cb-miRs in humans like KLHL20, TNS1, and PAPD4 are associated with Alzheimer's, malignant tumor of the breast, and hepatitis C virus infection disease, respectively. Similarly, in cattle, targeted genes like ATG2B and DHRS11 of fs-cb-miRs participate in the pathways of Huntington disease and steroid biosynthesis, respectively. Additionally, the targeted genes like SURF4 and EDME2 of fs-cb-miRs are associated with mastitis and bovine osteoporosis, respectively. We also found a few cb-miRs that do not have functional similarity with human and cattle miRNAs but are found to target the genes in the host organisms and as well being associated with human and cattle diseases. Interestingly, a few genes such as NRM, PTPRE and SUZ12 were observed to be associated with Rheumatoid Arthritis, Asthma and Endometrial Stromal Sarcoma diseases, respectively, in humans and genes like SCNN1B associated with renal disease in cattle.
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MicroARNs , Bovinos , Animales , MicroARNs/genética , Humanos , Cyamopsis/genética , ARN de Planta/genética , Enfermedades de los Bovinos/genéticaRESUMEN
Pigeonpea [Cajanus cajan (L.) Millspaugh] is an important grain legume crop with a broad range of 90 to 300 days for maturity. To identify the genomic variations associated with the early maturity, we conducted whole-genome resequencing of an early-maturing pigeonpea mutant TAT-10 and its wild type parent T21. A total of 135.67 and 146.34 million sequencing reads were generated for T21 and TAT-10, respectively. From this resequencing data, 1,397,178 and 1,419,904 SNPs, 276,741 and 292,347 InDels, and 87,583 and 92,903 SVs were identified in T21 and TAT-10, respectively. We identified 203 genes in the pigeonpea genome that are homologs of flowering-related genes in Arabidopsis and found 791 genomic variations unique to TAT-10 linked to 94 flowering-related genes. We identified three candidate genes for early maturity in TAT-10; Suppressor of FRI 4 (SUF4), Early Flowering In Short Days (EFS), and Probable Lysine-Specific Demethylase ELF6. The variations in ELF6 were predicted to be possibly damaging and the expression profiles of EFS and ELF6 also supported their probable role during early flowering in TAT-10. The present study has generated information on genomic variations associated with candidate genes for early maturity, which can be further studied and exploited for developing the early-maturing pigeonpea cultivars.
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Cajanus , Polimorfismo de Nucleótido Simple , Polimorfismo de Nucleótido Simple/genética , Genoma de Planta/genética , Genes de Plantas , Sitios de Carácter Cuantitativo , Genómica , Cajanus/genéticaRESUMEN
BACKGROUND: Despite plant's ability to adapt and withstand challenging environments, drought poses a severe threat to their growth and development. Although pigeon pea is already quite resistant to drought, the prolonged dehydration induced by the aberrant climate poses a serious threat to their survival and productivity. OBJECTIVE: Comparative physiological and transcriptome analyses of drought-tolerant (CO5) and drought-sensitive (CO1) pigeon pea genotypes subjected to drought stress were carried out in order to understand the molecular basis of drought tolerance in pigeon pea. METHODS: The transcriptomic analysis allowed us to examine how drought affects the gene expression of C. cajan. Using bioinformatics tools, the unigenes were de novo assembled, annotated, and functionally evaluated. Additionally, a homology-based sequence search against the droughtDB database was performed to identify the orthologs of the DEGs. RESULTS: 1102 potential drought-responsive genes were found to be differentially expressed genes (DEGs) between drought-tolerant and drought-sensitive genotypes. These included Abscisic acid insensitive 5 (ABI5), Nuclear transcription factor Y subunit A-7 (NF-YA7), WD40 repeat-containing protein 55 (WDR55), Anthocyanidin reductase (ANR) and Zinc-finger homeodomain protein 6 (ZF-HD6) and were highly expressed in the tolerant genotype. Further, GO analysis revealed that the most enriched classes belonged to biosynthetic and metabolic processes in the biological process category, binding and catalytic activity in the molecular function category and nucleus and protein-containing complex in the cellular component category. Results of KEGG pathway analysis revealed that the DEGs were significantly abundant in signalling pathways such as plant hormone signal transduction and MAPK signalling pathways. Consequently, in our investigation, we have identified and validated by qPCR a group of genes involved in signal reception and propagation, stress-specific TFs, and basal regulatory genes associated with drought response. CONCLUSION: In conclusion, our comprehensive transcriptome dataset enabled the discovery of candidate genes connected to pathways involved in pigeon pea drought response. Our research uncovered a number of unidentified genes and transcription factors that could be used to understand and improve susceptibility to drought.
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Cajanus , Transcriptoma , Cajanus/genética , Sequías , Perfilación de la Expresión Génica , GenotipoRESUMEN
Anguina tritici is the first plant-parasitic nematode described in literature, dating back to the year 1743. It is responsible for causing earcockle (seed gall) and tundu diseases in wheat and rye. Notably, this nematode has been observed to survive in an anhydrobiotic state for up to 32 years within wheat seed galls. These exceptional characteristics have inspired the sequencing of the A. tritici genome. In this study, we present the initial draft genome of A. tritici, obtained using the Illumina MiSeq platform with coverage of 60-fold. The genome is estimated to have a size of 164 Mb and comprises 39,965 protein-coding genes, exhibiting a GC content of 39.1%. The availability of this genome data will serve as a foundation for future functional biological investigations, particularly for genes whose functions remain unknown to this day.
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To unravel the plastid genome diversity among the cultivated groups of the pigeonpea germplasm, we characterized the SNP occurrence and distribution of 142 pigeonpea mini-core collections based on their reference-based assembly of the chloroplast genome. A total of 8921 SNPs were found, which were again filtered and finally 3871 non-synonymous SNPs were detected and used for diversity estimates. These 3871 SNPs were classified into 12 groups and were present in only 44 of the 125 genes, demonstrating the presence of a precise mechanism for maintaining the whole chloroplast genome throughout evolution. The Acetyl-CoA carboxylase D gene possesses the maximum number of SNPs (12.29%), but the Adenosine Tri-Phosphate synthatase cluster genes (atpA, atpB, atpE, atpF, atpH, and atpI) altogether bear 43.34% of the SNPs making them most diverse. Various diversity estimates, such as the number of effective alleles (1.013), Watterson's estimate (0.19), Tajima's D ( - 3.15), Shannon's information index (0.036), suggest the presence of less diversity in the cultivated gene pool of chloroplast genomes. The genetic relatedness estimates based on pairwise correlations were also in congruence with these diversity descriptors and indicate the prevalence of rare alleles in the accessions. Interestingly, no stratification was observed either through STRUCTURE, PCoA, or phylogenetic analysis, indicating the common origin of the chloroplast in all the accessions used, irrespective of their geographical distribution. Further 6194 Cleaved Amplified Polymorphic Sequences (CAPS) markers for 531 SNPs were developed and validated in a selected set of germplasm. Based on these results, we inferred that all of the cultivated gene pools of pigeonpea have a common origin for the chloroplast genome and they possess less diversity in protein-coding regions, indicating a stable and evolved plastid genome. At the same time, all diversity analysis indicates the occurrence of rare alleles, suggesting the suitability of the mini-core collection in future pigeonpea improvement programs. In addition, the development of chloroplast genome-based CAPS markers would have utility in pigeonpea breeding programs. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03785-8.
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The GRAS proteins are plant-specific transcription factors (TFs) that play a crucial role in various plant physiological processes, including tissue development and stress responses. To date, GRAS family has been comprehensively characterized in Arabidopsis, soybean, rice, chickpea and other plant species. To understand the structural and functional aspects of pigeonpea (C. cajan), we identified 60 putative GRAS (CcGRAS) genes from pigeonpea genome and further analysed their physicochemical properties, subcellular locations, evolutionary classification, exon-intron structures, conserved domains, gene duplication events and cis-promoter regions. Based on the sequence similarity, CcGRAS family was clustered into 9 subfamilies and the genes with a similar structure and motif distribution were clustered in the same group. The gene duplication studies revealed that these genes were derived from tandem and dispersed duplication events. The cis-promoter regulatory analysis of CcGRAS genes indicated the presence of three types of cis-acting elements including light-responsive, hormone-responsive and plant growth and development related. The expression profiling of CcGRAS genes revealed their tissue-specific functions and differential nature. Collectively, this study highlights relevant functional and regulatory elements of GRAS family in pigeonpea creating a significant resource for future functional studies. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03782-x.
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The complexities of a genome are underpinned to the vast expanses of the intergenic region, which constitutes â¼97-98% of the genome. This region is essentially composed of what is colloquially referred to as the "junk DNA" and is composed of various elements like transposons, repeats, pseudogenes, etc. The latter have long been considered as dead elements merely contributing to transcriptional noise in the genome. Many studies now describe the previously unknown regulatory functions of these genes. Recent advances in the Next-generation sequencing (NGS) technologies have allowed unprecedented access to these regions. With the availability of whole genome sequences of more than 788 different plant species in past 20 years, genome annotation has become feasible like never before. Different bioinformatic pipelines are available for the identification of pseudogenes. However, still little is known about their biological functions. The functional validation of these genes remains challenging and research in this area is still in infancy, particularly in plants. CRISPR/Cas-based genome editing could provide solutions to understand the biological roles of these genes by allowing creation of precise edits within these genes. The possibility of pseudogene reactivation or resurrection as has been demonstrated in a few studies might open new avenues of genetic manipulation to yield a desirable phenotype. This review aims at comprehensively summarizing the progress made with regards to the identification of pseudogenes and understanding their biological functions in plants.
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Genoma , Seudogenes , Seudogenes/genéticaRESUMEN
To combat drought stress in rice, a major threat to global food security, three major quantitative trait loci for 'yield under drought stress' (qDTYs) were successfully exploited in the last decade. However, their molecular basis still remains unknown. To understand the role of secondary regulation by miRNA in drought stress response and their relation, if any, with the three qDTYs, the miRNA dynamics under drought stress was studied at booting stage in two drought tolerant (Sahbaghi Dhan and Vandana) and one drought sensitive (IR 20) cultivars. In total, 53 known and 40 novel differentially expressed (DE) miRNAs were identified. The primary drought responsive miRNAs were Osa-MIR2919, Osa-MIR3979, Osa-MIR159f, Osa-MIR156k, Osa-MIR528, Osa-MIR530, Osa-MIR2091, Osa-MIR531a, Osa-MIR531b as well as three novel ones. Sixty-one target genes that corresponded to 11 known and 4 novel DE miRNAs were found to be co-localized with the three qDTYs, out of the 1746 target genes identified. We could validate miRNA-mRNA expression under drought for nine known and three novel miRNAs in eight different rice genotypes showing varying degree of tolerance. From our study, Osa-MIR2919, Osa-MIR3979, Osa-MIR528, Osa-MIR2091-5p and Chr01_11911S14Astr and their target genes LOC_Os01g72000, LOC_Os01g66890, LOC_Os01g57990, LOC_Os01g56780, LOC_Os01g72834, LOC_Os01g61880 and LOC_Os01g72780 were identified as the most promising candidates for drought tolerance at booting stage. Of these, Osa-MIR2919 with 19 target genes in the qDTYs is being reported for the first time. It acts as a negative regulator of drought stress tolerance by modulating the cytokinin and brassinosteroid signalling pathway.
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MicroARNs , Oryza , Sequías , Oryza/genética , Sitios de Carácter Cuantitativo , Resistencia a la Sequía , MicroARNs/genéticaRESUMEN
Auxin Response Factors (ARF) are a family of transcription factors that mediate auxin signalling and regulate multiple biological processes. Their crucial role in increasing plant biomass/yield influenced this study, where a systematic analysis of ARF gene family was carried out to identify the key proteins controlling embryo/seed developmental pathways in pigeonpea. A genome-wide scan revealed the presence of 12 ARF genes in pigeonpea, distributed across the chromosomes 1, 3, 4, 8 and 11. Domain analysis of ARF proteins showed the presence of B3 DNA binding, AUX response, and IAA domains. Majority of them are of nuclear origin, and do not exhibit the level of genomic expansion as observed in Glycine max (51 members). The duplication events seem to range from 31.6 to 42.3 million years ago (mya). Promoter analysis revealed the presence of multiple cis-acting elements related to stress responses, hormone signalling and other development processes. The expression atlas data highlighted the expression of CcARF8 in hypocotyl, bud and flower whereas, CcARF7 expression was significantly high in pod. The real-time expression of CcARF2, CcARF3 and CcARF18 was highest in genotypes with high seed number indicating their key role in regulating embryo development and determining seed set in pigeonpea.
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Ácidos Indolacéticos , Familia de Multigenes , Ácidos Indolacéticos/metabolismo , Expresión Génica , Semillas , Evolución Molecular , Proteínas de Plantas/química , Filogenia , Regulación de la Expresión Génica de las PlantasRESUMEN
Amino acid transporters (AATs), besides, being a crucial component for nutrient partitioning system are also vital for growth and development of the plants and stress resilience. In order to understand the role of AAT genes in seed quality proteins, a comprehensive analysis of AAT gene family was carried out in chickpea leading to identification of 109 AAT genes, representing 10 subfamilies with random distribution across the chickpea genome. Several important stress responsive cis-regulatory elements like Myb, ABRE, ERE were detected in the promoter region of these CaAAT genes. Most of the genes belonging to the same sub-families shared the intron-exon distribution pattern owing to their conserved nature. Random distribution of these CaAAT genes was observed on plasma membrane, vacuolar membrane, Endoplasmic reticulum and Golgi membranes, which may be associated to distinct biochemical pathways. In total 92 out 109 CaAAT genes arise as result of duplication, among which segmental duplication was more prominent over tandem duplication. As expected, the phylogenetic tree was divided into 2 major clades, and further sub-divided into different sub-families. Among the 109 CaAAT genes, 25 were found to be interacting with 25 miRNAs, many miRNAs like miR156, miR159 and miR164 were interacting only with single AAT genes. Tissues specific expression pattern of many CaAAT genes was observed like CaAAP7 and CaAVT18 in nodules, CaAAP17, CaAVT5 and CaCAT9 in vegetative tissues while CaCAT10 and CaAAP23 in seed related tissues as per the expression analysis. Mature seed transcriptome data revealed that genotypes having high protein content (ICC 8397, ICC 13461) showed low CaAATs expression as compared to the genotypes having low protein content (FG 212, BG 3054). Amino acid profiling of these genotypes revealed a significant difference in amount of essential and non-essential amino acids, probably due to differential expression of CaAATs. Thus, the present study provides insights into the biological role of AAT genes in chickpea, which will facilitate their functional characterization and role in various developmental stages, stress responses and involvement in nutritional quality enhancement.
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Cicer , MicroARNs , Cicer/genética , Cicer/metabolismo , Filogenia , Proteínas de Plantas/química , Semillas , Sistemas de Transporte de Aminoácidos/genética , MicroARNs/metabolismo , Regulación de la Expresión Génica de las PlantasRESUMEN
Cluster bean (Cyamopsis tetragonoloba (L.) Taub 2n = 14, is commonly known as Guar. Apart from being a vegetable crop, it is an abundant source of a natural hetero-polysaccharide called guar gum or galactomannan. Here, we are reporting a chromosome-scale reference genome assembly of a popular cluster bean cultivar RGC-936, by combining sequencing data from Illumina, 10X Genomics, Oxford Nanopore technologies. An initial assembly of 1580 scaffolds with an N50 value of 7.12 Mb was generated and these scaffolds were anchored to a high density SNP linkage map. Finally, a genome assembly of 550.31 Mb (94% of the estimated genome size of ~ 580 Mb (through flow cytometry) with 58 scaffolds was obtained, including 7 super scaffolds with a very high N50 value of 78.27 Mb. Phylogenetic analysis using single copy orthologs among 12 angiosperms showed that cluster bean shared a common ancestor with other legumes 80.6 MYA. No evidence of recent whole genome duplication event in cluster bean was found in our analysis. Further comparative transcriptomics analyses revealed pod-specific up-regulation of genes encoding enzymes involved in galactomannan biosynthesis. The high-quality chromosome-scale cluster bean genome assembly will facilitate understanding of the molecular basis of galactomannan biosynthesis and aid in genomics-assisted improvement of cluster bean.
Asunto(s)
Cyamopsis , Cyamopsis/genética , Filogenia , Genoma , Verduras/genética , CromosomasRESUMEN
BACKGROUND: Crop improvement for tolerance to various biotic and abiotic stress factors necessitates understanding the key gene regulatory mechanisms. One such mechanism of gene regulation involves changes in cytosine methylation at the gene body and flanking regulatory sequences. The present study was undertaken to identify genes which might be potential targets of drought-induced DNA methylation in chickpea. METHODS AND RESULTS: Two chickpea genotypes, which contrast for drought tolerance, were subjected to drought stress conditions and their differential response was studied by analysing different morpho-physiological traits. Utilizing the in-house, high throughput sequencing data, the SQUAMOSA promoter-binding (SBP) protein-like (SPL) transcription factor genes were identified to be differentially methylated and expressed amongst the two genotypes, in response to drought stress. The methylation status of one of these genes was examined and validated through bisulfite PCR (BS-PCR). The identified genes could be possible homologs to known epialleles and can therefore serve as potential epialleles which can be utilized for crop improvement in chickpea. CONCLUSION: The SPL TF genes are potential targets of epigenetic regulation in response to drought stress in chickpea. Since these are TFs, they might play important roles in controlling the expression of other genes, thus contributing to differential drought response of the two genotypes.