Biology subjects

Sonti, R. V.

Publications and source records attributed to Sonti, R. V..

15 recordsLinked to original sources

bioRxiv2026

Genome Assembly of the Iconic Samba Mahsuri Delineates Locus-specific Population Structure within Indica Rice

High-quality reference genomes enable detailed analysis of structural variation and its consequences for genome organization in crops. Here, we present a chromosome-scale genome assembly of Oryza sativa cv. Samba Mahsuri (SM), an elite Indian mega rice variety cultivated for its grain and cooking quality. Using PacBio HiFi sequencing in combination with Illumina reads and Bionano optical mapping, we generated a [~]395 Mb assembly (SMv1.0) with 97.7% BUSCO completeness. A robust annotation framework identified 31,138 evidence-guided protein-coding gene models alongside 59,152 ab initio predictions. Comparative genomic analyses revealed extensive macrosynteny with established rice reference genomes, while uncovering pronounced locus-specific sequence and structural polymorphisms. Notably, a complex inversion-match-inversion (IMI) configuration on chromosome 6 differentiates SM from the japonica reference Nipponbare, but not from the indica reference R498. Population-scale analyses of 533 cultivated and 4 wild rice accessions demonstrate that genetic variation within the IMI region produces a markedly sharper and more coherent population structure than is observed in flanking regions or genome-wide, including tight subpopulation-based clustering and segregation of alternative IMI configurations within indica rice. Together, these results establish SMv1.0 as a robust chromosome-scale reference genome sequence for rice and demonstrate how large structural polymorphisms can shape locus-specific patterns of relatedness that diverge from genome-wide ancestry. Significance StatementWe present a high-quality chromosome-scale genome sequence of the elite Indian rice variety Samba Mahsuri (SM), which, to the best of our knowledge, represents the first chromosome-scale reference genome from Indian rice germplasm assembled using a map-based method. Using this reference to analyze population-scale genotyping data from 533 cultivated and four wild rice accessions reveals markedly tighter population clustering within a megabase-scale inversion (IMI) region, than at the whole-genome scale, along with a pronounced split within indica rice that is independent of genome-wide ancestry.

plant biology↗

bioRxiv2025

Omics-driven Identification of Candidate Genes and SNP markers in a Major QTL Controlling Early Heading in Rice

Precise control of heading date is essential for optimizing regional adaptability, enhancing climate resilience, and maximizing grain yield in rice, making it a key breeding target. The SM93 rice line exhibits a 7-10-day earlier heading than the elite Indian variety, Samba Mahsuri (SM). F2 populations derived from a cross of SM with SM93 were phenotyped for heading date across three successive kharif (rainy) seasons (2019-2021), revealing consistent early heading and notable transgressive segregation. Initial QTL-seq analysis identified a high-confidence QTL on Chr3, qDTH3, strongly associated with days to heading (DTH). KASP assays and association mapping were subsequently performed to refine the QTL, narrowing it down to a 2.53 Mb region, explaining [~]25% of the trait. SNP markers closely linked to heading were identified. Transcriptomic analysis revealed significant differential regulation of genes within qDTH3 and upregulation of the MADS- box network in SM93 during panicle initiation, suggesting their role in promoting early heading. Our integrative strategy led to the identification of candidate genes within qDTH3, associated with heading date, phytohormone regulation, and protein turnover, include the transcription factors, OsMADS34/PAP2 (Os03g0753100), OsZHD11 (Os03g0718500), HSFA2A (Os03g0745000), OsH3 (Os03g0727200), OSH1/Oskn1 (Os03g0727000), a histidine kinase, HK4 (Os03g0717700), and a Serine carboxypeptidase, OsSCP19 (Os03g0730400). Our findings provide SNP markers in and around these genes, as potentially valuable tools for breeding early-maturing rice varieties with improved adaptability. HIGHLIGHTThis study on the SM93 rice line identifies a major QTL for early heading and describes genes and SNP markers that are closely linked to this trait, which can be used in trait advancement. By fine-tuning heading date, we can help rice varieties better withstand temperature extremes, drought, and other climate-related stresses, making it a key target for genetic improvement and breeding strategies.

plant biology↗

bioRxiv2025

A novel allele of Mitogen Activated Protein Kinase 6 is linked to disease resistance and constitutive immunity in rice.

Bacterial Blight (BB) is the most serious bacterial disease of rice. Usage of resistant cultivars has been a successful strategy in controlling BB. However, constant selection pressure causes the evolution of hypervirulent pathogenic strains that break down resistance, thus necessitating additional sources of resistance. An induced-mutant line derived from the elite rice cultivar Samba Mahsuri was identified to exhibit broad-spectrum resistance to BB. Using next-generation gene mapping approaches, we identified a genomic interval in chromosome 6 to be linked to BB resistance. Analysis of the SNPs in the locus and subsequent linkage analysis indicated that a missense SNP located in the second exon of the Mitogen-Activated Protein Kinase 6 (OsMAPK6) could be the causal mutation. A detailed examination of OsMAPK6 gene sequences in over 4000 rice genomes revealed that the mutant allele identified in this study is novel to rice germplasm. The candidate SNP causes the substitution of an invariant Serine residue with a Proline residue (S84P), thus likely affecting the protein function. Global transcriptome, metabolome, biochemical, and molecular analyses suggested that BB42 exhibit constitutive immunity. On the mechanistic front, the mutation seems to result in diminished brassinosteroid signaling in BB42. Taken together, we report a novel allele of a highly conserved MAPK gene and provide evidence for its possible association with constitutive immunity and disease resistance in rice.

plant biology↗

bioRxiv2024

Xanthomonas oryzae pv. oryzae type-III effector TAL9b targets a broadly conserved disease susceptibility locus to promote pathogenesis in rice

Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight of rice, translocates multiple Transcription Activator-Like Effectors (TALEs) into rice cells. The TALEs localize to the host cell nucleus, where they bind to the DNA in a sequence-specific manner and enhance gene expression to promote disease susceptibility. Xoo strain PXO99A encodes nineteen TALEs, but the host targets of all these TALEs have not been defined. A meta-analysis of rice transcriptome profiles revealed a gene annotated as flavonol synthase/flavanone-3 hydroxylase (henceforth OsS5H/FNS-03g) to be highly induced upon Xoo infection. Further analyses revealed that this gene is induced by PXO99A using TAL9b, a broadly conserved TALE of Xoo. Disruption of tal9b rendered PXO99A less virulent. OsS5H/FNS-03g functionally complemented its Arabidopsis homologue AtDMR6, a well-studied disease susceptibility locus. Biochemical analyses suggested that OsS5H/FNS-03g is a bifunctional protein with Salicylic Acid 5 Hydroxylase (S5H) and Flavone Synthase-I (FNS-I) activities. Further, an exogenous application of apigenin on rice leaves, the flavone that is enzymatically produced by OsS5H/FNS-03g, promoted virulence of PXO99A tal9b-. Overall, our study suggests that OsS5H/FNS-03g is a bifunctional enzyme and its product apigenin is potentially involved in promoting Xoo virulence.

plant biology↗

bioRxiv2024

Xanthomonas protegens sp. nov., a rice seed-associated probiotic and taxonomic outlier species of Xanthomonas sontii

Rice seed microbiota play a vital role throughout their growth and developmental stages. Xanthomonas sontii is known as an abundant, core-vertically transmitted rice seed endophyte with probiotic properties. Studies reveal a less explored world of non-pathogenic Xanthomonas (NPX) species like X. sontii and X. indica that are associated with healthy rice seeds. The present study reports the isolation, biochemical characterization, and in-depth taxonogenomic evidence for a third NPX species, X. protegens, from rice seeds, a taxonomic outlier of X. sontii. It also highlights the importance of using multiple taxonogenomic indices to identify taxonomic outlier species. Similar to the other two NPX species, the new member species is also non-pathogenic and provides in vivo protection to rice plants from Xanthomonas oryzae pv. oryzae upon leaf clip inoculation. The pangenome investigation suggested a set of unique genes to the novel species that might be important in adaptation to rice plants and differentiate it from other NPX species. The study will allow the design of markers for the identification of these NPX members, targeted culturomics of a particular NPX species and in the discovery of other novel NPX species from healthy rice seed microbiome for further exploitation in rice health.

evolutionary biology↗

bioRxiv2023

Multiomics-assisted characterization of rice-Yellow Stem Borer interaction provides genomic and mechanistic insights into stem borer tolerance in rice

Yellow stem borer (YSB), Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae), is a major pest of rice in India, that can lead to 20-60% loss in rice production. Effective management of YSB infestation is challenged by the non-availability of adequate source of resistance and poor understanding of resistance mechanisms, thus necessitating studies for generating resources to breed YSB resistant rice and to understand rice-YSB interaction. In this study, by using bulk-segregant analysis in combination with next-generation sequencing, Quantitative Trait Loci (QTL) intervals in five rice chromosomes were mapped that could be associated with YSB tolerance at vegetative phase in a highly tolerant rice line named SM92. Further, multiple SNP markers that showed significant association with YSB tolerance in rice chromosomes 1, 5, 10, and 12 were developed. RNA-sequencing of the susceptible and tolerant lines revealed multiple genes present in the candidate QTL intervals to be differentially regulated upon YSB infestation. Comparative transcriptome analysis revealed a putative candidate gene that was predicted to encode an alpha-amylase inhibitor. Analysis of the transcriptome and metabolite profiles further revealed a possible link between phenylpropanoid metabolism and YSB tolerance. Taken together, our study provides insights on rice-YSB interaction at genomic, transcriptomic and metabolomic level, thereby facilitating the understanding of tolerance mechanism. Importantly, a promising breeding line and markers for YSB tolerance have been developed that can potentially aid in marker-assisted breeding of YSB resistance among elite rice cultivars. SIGNIFICANCE STATEMENTGlobal rice production is threatened by various pests, among which stem borers pose serious challenges. Hence, understanding the molecular intricacies of rice-stem borer interaction is necessary for effective pest management. Here, we used a multi-omics approach to unravel the mechanisms that might help rice combat yellow stem borer infestation, thus providing insights and scope for developing YSB tolerant rice varieties. To facilitate the latter, we developed markers that co-segregate with tolerance.

plant biology↗

bioRxiv2023

Phase variation in LPS O-antigen biosynthetic gene cluster of the rice pathogen Xanthomonas oryzaepv. oryzae

Bacteria respond to environmental cues in different ways. Phase variation is one such adaptation where heritable and reversible changes in DNA aid bacteria to alter the expression of specific genes. The bacterial plant pathogen Xanthomonas oryzae pv. oryzae (Xoo) causes the serious bacterial blight disease of rice. The mucoid phenotype of Xoo colonies is attributed to the secreted exopolysaccharide (EPS), xanthan gum. Spontaneous non-mucoid variants of Xoo which are deficient in EPS production and virulence were observed to accumulate in long-term stationary phase cultures. This phenomenon was termed stationary phase variation and variant colonies as stationary phase variants (SPV). Several but not all of these SPVs have been earlier described to carry spontaneous insertions of endogenous insertion sequence elements in the gum operon which encodes genes involved in EPS biosynthesis. In this study, we show that a number of SPVs harbour variations in the lipopolysaccharide (LPS) outer antigen (O-antigen) biosynthetic gene cluster. The data revealed that the vast majority of variations are due to either insertion of endogenous insertion sequence (IS) elements or slipped strand mispairing (SSM). Also, it was observed that many of these SPVs exhibited reversion to wild type mucoid phenotype via restoration of the wild type genotype. The results indicate that the phenomenon of phase variation is occurring in the LPS O-antigen biosynthetic gene cluster of Xoo.

microbiology↗

bioRxiv2023

Comparative genomics-based insights into diversification and bio-protection function of Xanthomonas indica, a non-pathogenic species of rice

Xanthomonas species have been extensively studied as major and model pathogens of plants. However, there is an increasing recognition of the complex and large world of non-pathogenic species of Xanthomonas in the recent decades. One pathogenic Xanthomonas species has been known in rice for the last hundred years, yet in recent years, three non-pathogenic Xanthomonas (NPX) species have been reported. Thus, there is a need to understand the species-level diversity of NPXs like their pathogenic counterparts. In the present study, we report isolation and investigation into the genomic diversity of Xanthomonas indica, a newly discovered NPX species from rice. The study allowed us to establish the relationship of X. indica strains within clade I of Xanthomonads. All the strains formed a distinct but diverse clade compared to clades corresponding to other NPX species from rice and other hosts. X. indica lacks major virulence factors found in their pathogenic counterparts. Identification of highly diverse strains and open-pan genome indicates ongoing selection to acquire new functions for adaptation. X. indica also harbours large-scale interstrain variations in the lipopolysaccharide O-antigen biosynthetic gene cluster, which hints at the selection at this locus. Interestingly, all the diverse strains of X. indica were able to protect rice from bacterial leaf blight pathogen of rice upon leaf clip inoculation. Comparative genomics revealed the association of a RiPP, a metalloprotease and a bacterial-killing type IV secretion system conserved across its related member species, including X. sontii, in the clade I with in-vivo anti-pathogenic properties. Overall the study has provided novel evolutionary insights into an important NPX member species. The findings and genomic resources will allow further systematic molecular studies to understand its interaction with the host plant.

genomics↗

bioRxiv2022

Xanthomonas indica sp. nov., a non-pathogenic bacterium isolated from healthy rice (Oryza sativa) seeds from India

Two yellow pigmented bacterial strains were isolated from healthy rice seeds. The strains designated as PPL560T and PPL568 were identified as members of genus Xanthomonas based on analysis of biochemical and 16S rRNA gene sequence retrieved from whole genome sequence. Isolates formed a distinct monophyletic lineage with X. sontii and X. sacchari as the closest relatives in the phylogenetic tree based on core gene content shared by reported species in genus Xanthomonas. Pairwise ortho Average Nucleotide Identity and digital DNA-DNA hybridisation values calculated against other species of Xanthomonas were below their respective cut-offs. In planta studies revealed that PPL560T and PPL568 are non-pathogenic to rice plants upon leaf clip inoculation. Absence of type III secretion system related genes and effectors further supported their non-pathogenic status. Herein, we propose Xanthomonas indica sp. nov. as novel species of genus Xanthomonas with PPL560T=MTCC13185 as its type strain and PPL568 as another constituent member.

evolutionary biology↗

bioRxiv2021

Proteomic analysis of rice leaves following treatment of Xanthomonas oryzae pv. oryzae secreted cell wall degrading enzyme

Bacterial Blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases in various rice cultivating countries. Xoo secretes a mixture of plant cell wall degrading enzymes (CWDEs) such as cellulases, lipases, xylanases, and proteases to degrade different components of the plant cell wall. LipA; a lipase/esterase, is one such Xoo secreted CWDE and is an important virulence factor of Xoo. Treatment of rice tissue with purified LipA induces immune responses. In this study, a LC-MS based proteomics study was performed to identify the differentially expressed proteins (DEPs) in rice following LipA treatment. A total of 212 proteins were identified in control and 201 proteins in LipA treated samples. There were 151 proteins common between control and treatment. Fold change analysis of these common proteins through SIEVE identified 26 upregulated and 49 downregulated proteins by at least [≥]1.5 fold in the LipA treated sample. Pathway analysis indicated that many proteins related to redox regulation, photosynthesis, and translation are differentially expressed after LipA treatment. We also observed that some of the differentially expressed proteins contain translation regulatory elements that may regulate translation after LipA treatment. The comparison of proteomics data with previously performed transcriptome analysis indicated that different sets of genes and pathways are altered in both the analyses.

plant biology↗

bioRxiv2021

A bacterial derived plant- mimicking cytokinin hormone regulates social behaviour in a rice pathogen

Many plant-associated bacteria produce plant- mimicking hormones which are involved in modulating host physiology. However, their function in modulating bacterial physiology has not been reported. Here we show that the XopQ protein, a type-III effector of the rice pathogen, Xanthomonas oryzae pv. oryzae (Xoo), is involved in cytokinin biosynthesis. Xoo produces and secretes an active form of cytokinin which enables the bacterium to maintain a planktonic lifestyle and promotes virulence. RNA-seq analysis indicates that the cytokinin produced by Xoo is required for the regulation of several genes which are involved in biofilm formation. We have also identified the Xoo isopentenyl transferase gene, which is involved in the cytokinin biosynthesis pathway and is required for maintaining planktonic behaviour and virulence. Furthermore, mutations in the predicted cytokinin receptor kinase (PcrK) and the downstream response regulator (PcrR) of Xoo phenocopy the cytokinin biosynthetic mutants, but are not complemented by supplementation with exogenous cytokinin. Cytokinin biosynthetic functions are encoded in a number of diverse bacterial genomes suggesting that cytokinin may be a widespread signalling molecule in the bacterial kingdom.

microbiology↗

bioRxiv2020

Repeated gain and loss of a single gene modulates the evolution of vascular pathogen lifestyles

Vascular pathogens travel long distances through host veins leading to life-threatening, systemic infections. In contrast, non-vascular pathogens remain restricted to infection sites, triggering localized symptom development. The contrasting features of vascular and non-vascular diseases suggest distinct etiologies, but the basis for each remains unclear. Here, we show that the hydrolase CbsA acts as a phenotypic switch between vascular and non-vascular plant pathogenesis. cbsA was enriched in genomes of vascular phytopathogenic bacteria in the Xanthomonadaceae family and absent in most non-vascular species. CbsA expression allowed non-vascular Xanthomonas to cause vascular blight while cbsA mutagenesis resulted in reduction of vascular or enhanced non-vascular symptom development. Phylogenetic hypothesis testing further revealed that cbsA was lost in multiple non-vascular lineages and more recently gained by some vascular subgroups, suggesting that vascular pathogenesis is ancestral. Our results overall demonstrate how the gain and loss of single loci can facilitate the evolution of complex ecological traits.

microbiology↗

bioRxiv2020

Interaction of the Xanthomonas effectors XopQ and XopX results in induction of rice immune responses

Xanthomonas oryzae pv. oryzae uses several type III secretion system (T3SS) effectors, namely XopN, XopQ, XopX, and XopZ, to suppress rice immune responses that are induced following treatment with cell wall degrading enzymes. Here we show that the T3SS secreted effector XopX interacts with two of the eight rice 14-3-3 proteins. Mutants of XopX that are defective in 14-3-3 binding are also defective in suppression of immune responses, suggesting that interaction with 14-3-3 proteins is required for suppression of host innate immunity. However, Agrobacterium mediated delivery of both XopX and XopQ into rice cells results in induction of rice immune responses. These immune responses are not observed when either protein is individually delivered into rice cells. XopQ-XopX induced rice immune responses are not observed in a XopX mutant that is defective in 14-3-3 binding. Yeast two-hybrid and BiFC assays indicate that XopQ and XopX interact with each other. In a screen for Xanthomonas effectors which can suppress XopQ-XopX induced rice immune responses, five effectors were identified, namely XopU, XopV, XopP, XopG and AvrBs2, which were able to do so. These results suggest a complex interplay of Xanthomonas T3SS effectors in suppression of pathogen triggered immunity and effector triggered immunity to promote virulence on rice. Significance statementThis work studies the role of the type III effector XopX in the suppression and induction of rice immune responses, by differential interaction with the 14-3-3 proteins, or with the type III effector XopQ respectively. We have also identified a subset of type III effectors which can suppress this form of immune responses.

molecular biology↗

bioRxiv2019

The dual function receptor kinase, OsWAKL21.2, is involved in elaboration of lipaseA/esterase induced immune responses in rice

Plant pathogens secrete cell wall degrading enzymes (CWDEs) to degrade various components of the plant cell wall. Plants sense this cell wall damage as a mark of infection and induce immune responses. Little is known about the plant functions that are involved in the elaboration of cell wall damage-induced immune responses. Transcriptome analysis revealed that a rice receptor kinase, WALL-ASSOCIATED KINASE-LIKE 21 (OsWAKL21.2), is upregulated following treatment with either Xanthomonas oryzae pv. oryzae (Xoo, a bacterial pathogen) or lipaseA/esterase (LipA: a CWDE of Xoo). Downregulation of OsWAKL21.2 attenuates LipA mediated immune responses. Overexpression of OsWAKL21.2 in rice mimics LipA treatment mediated induction of immune responses and enhanced expression of defence related genes, indicating it could be involved in the perception of LipA induced cell wall damage in rice. OsWAKL21.2 is a dual function kinase having in-vitro kinase and guanylate cyclase (GC) activities. Ectopic expression of OsWAKL21.2 in Arabidopsis also activates plant immune responses. Interestingly, OsWAKL21.2 needs kinase activity to activate rice immune responses while in Arabidopsis it needs GC activity. Our study reveals a novel receptor kinase involved in elaboration of cell wall damage induced rice immune responses that can activate similar immune responses in two different species via two different mechanisms.\n\nOne sentence SummaryA novel rice receptor WAKL21 that sense cell wall damage caused by Xanthomonas secreted cell wall degrading enzyme to induce immune responses.

plant biology↗

bioRxiv2018

Biofilm forming capabilities and protein secretion systems distinguish ecologically diverse lineages of Xanthomonas from rice

Xanthomonas oryzae is a devastating pathogen of rice worldwide, however, X. sontii and X. maliensis are its non-pathogenic counterparts from the same host. So far, these non-pathogenic isolates were overlooked due to their less economic importance and lack of genomic information. We have carried out detailed ecological and evolutionary study focusing on diverse lifestyles of these strains. Phylogenomic analysis revealed two major lineages corresponding to X. sontii (ML-I) and X. oryzae (ML-II) species. Interestingly, one of the non-pathogenic Xanthomonas strains belonging to X. maliensis is intermediary to both the major lineages/species suggesting on-going diversification and selection. Accordingly, pangenome analysis revealed large number of lifestyle specific genes with atypical GC content indicating role of horizontal gene transfer in genome diversification. Our comprehensive comparative genomic investigation of major lineages has revealed that impact of recombination is more for X. sontii as compared to X. oryzae. Acquisition of type III secretion system and its effectome along with a type VI secretion system also seem to have played a major role in the pathogenic lineage. Other known key pathogenicity clusters or genes like biofilm forming cluster, cellobiohydrolase and non-fimbrial adhesin (yapH) are exclusive to pathogenic lineage. However, commonality of loci encoding exopolysacharide, rpf signalling molecule, iron-uptake, xanthomonadin pigment, etc. suggests their essentiality in host adaptation. Overall, this study reveals evolutionary history of pathogenic and non-pathogenic strains and will further open up a new avenue for better management of pathogenic strains for sustainable cultivation of a major staple food crop.

evolutionary biology↗