Biology subjects

Patil, P. B.

Publications and source records attributed to Patil, P. B..

24 records · Page 2Linked to original sources

bioRxiv2020

Codon pattern reveals SARS-CoV-2 to be a monomorphic strain that emerged through recombination of replicase and envelope alleles of bat and pangolin origin

Viruses are dependent on the host tRNA pool, and an optimum codon usage pattern (CUP) is the driving force in its evolution. Systematic analysis of CUP of the coding sequences (CDS) of representative major pangolin lineages A and B of SARS-CoV-2 indicate a single transmission event of a codon-optimized virus from its source into humans. Here, no direct congruence could be detected in CUP of all CDS of SARS-CoV-2 with the non-human natural SARS viruses further reiterating its novelty. Several CDS show similar CUP with bat or pangolin, while others have distinct CUP pointing towards a possible hybrid nature of the virus. At the same time, phylogenetic diversity suggests the role of even silent mutations in its success by adapting to host tRNA pool. However, genomes of SARS-CoV-2 from primary infections are required to investigate the origins amongst the competing natural or lab leak theories.

microbiology↗

bioRxiv2020

Deep phylo-taxono-genomics (DEEPT genomics) reveals misclassification of Xanthomonas species complexes into Xylella, Stenotrophomonas and Pseudoxanthomonas

Genus Xanthomonas encompasses specialized group of phytopathogenic bacteria with genera Xylella, Stenotrophomonas and Pseudoxanthomonas being its closest relatives. While species of genera Xanthomonas and Xylella are known as serious phytopathogens, members of other two genera are found in diverse habitats with metabolic versatility of biotechnological importance. Few species of Stenotrophomonas are multidrug resistant opportunistic nosocomial pathogens. In the present study, we report genomic resource of genus Pseudoxanthomonas and further in-depth comparative studies with publically available genome resources of other three genera. Surprisingly, based on deep phylo-taxono-genomic or DEEPT criteria, all the four genera were found to be one genus and hence synonyms of Xanthomonas. The members of Pseudoxanthomonas are more diverse and ancestral and rest forming two mega species groups (MSGs) i.e. Xanthomonas Xylella (XX-MSG) and Stenotrophomonas (S-MSG). Within XX-MSG, there are 3 species complexes i.e., X. citri complex (Xcc) member species are primarily pathogenic to dicots, X. hyacinthi complex (Xhc) member species are primarily pathogenic to monocots and Xanthomonas (Xylella) fastidosa complex (Xfc) with diverse phytopathogenic potential. Interestingly, Xylella seems to be a variant Xanthomonas lineage or species complex that is sandwiched between Xcc and Xhc. Like Xylella, within S-MSG, we find a species complex of clinical origin Xanthomonas (Stenotrophomonas) maltophilia complex (Xmc). Comparative studies revealed selection and role of xanthomonadin pigment and xanthan gum in emergence of plant pathogenic XX-MSG. Pan genome analysis also revealed large set of unique genes with particular functions suited for plant/animal lifestyle responsible for emergence of variant Xfc and Xmc species complexes. Overall, our systematic and large scale genera based study has allowed us to understand the origin and to clarify the taxonomic breadth of genus of high importance in agriculture, medicine and industry. Such DEEPT genomics studies are also way forward to identify right markers or functions for diagnosis and drug development of any pathogenic bacteria. RepositoriesGenome Submission Accession Number: MWIP00000000, PDWO00000000, PDWN00000000, PDWT00000000, PDWS00000000, PDWW00000000, PDWU00000000, PDWR00000000, PDWL00000000, PDWQ00000000, PDWM00000000, PDWP00000000, PDWV00000000, PDWK00000000 and QOVG00000000

genomics↗

bioRxiv2019

Extreme phylogenomic diversity in non-pathogenic Xanthomonas strains associated with citrus

Xanthomonas are primarily known as a group of phytopathogens infecting diverse plants. Recent molecular studies reveal existence of novel species and strains of Xanthomonas that follow non-pathogenic (NPX) lifestyle. Presently, we report whole genome sequence of four NPX reported from Citrus sp. (NPXc). Taxonogenomic analysis revealed surprising diversity as each of the three isolates were found to be novel genomospecies that together form a Citri associated non-pathogenic Xanthomonas species complex (NPXc complex). Interestingly, this NPXc complex is related to another non-pathogenic species, X. sontii from rice (NPXr). On the other hand, the fourth NPXc isolate was found to be related to NPX isolates from walnut (NPXw), altogether they form a potential taxonomic outlier of pathogenic X. arboricola species. Interestingly, their pathogenic counterparts, X. citri and X. arboricola are known to cause similar symptoms in diverse fruit plants. Further, genomic investigation of well-characterized pathogenicity clusters in NPXc isolates revealed lifestyle specific gene content dynamics. Majorly, genes essential for virulence (T3SS, effectors, T6SS, biofilm cluster etc.) and adaptation (gum, rpf, iron uptake and utilization, T2SS (xps) and variable repertoire of cell wall degrading enzymes) could be depicted by comparative genomics of Xanthomonas community comprising of diverse lifestyle isolates. Overall, present analysis confers that non-pathogenic isolates of diverse host phylogenomically converge and are evolving in parallel to their pathogenic counterparts. Hence, there is a need to understand the world of NPX isolates from diverse and economically important hosts. Genomic knowledge and resource will be invaluable in both basic and applied research of genus Xanthomonas.

genomics↗

bioRxiv2019

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

Three yellow pigmented, Gram negative, aerobic, rod shaped, motile bacterial strains designated as PPL1, PPL2 and PPL3 were isolated from healthy basmati rice seeds. Phenotypic, biochemical and 16S rRNA gene sequence analysis assigned these strains to the genus Xanthomonas. The 16S rRNA gene sequence was having 99.59% similarity with X. sacchari CFBP4641T. However, whole genome based phylogenomic analysis revealed that these strains formed a distinct monophyletic clade with X. sacchari CFBP4641T as their closest neighbour. Taxonogenomic studies based on average nucleotide identity (orthoANI) and digital DNA-DNA hybridization (dDDH) values of these strains with type strains (or representative strains) of different Xanthomonas species including X. sacchari showed below recommended threshold values of ANI (<96%) and dDDH (70%) for species delineation. Furthermore, at the whole genome level, PPL1 and PPL2 were found to be clonal, while PPL3 was not a clonal, but belonging to the same species. Our in planta pathogenicity studies revealed that the strains PPL1, PPL2 and PPL3 are non-pathogenic to rice plants. Hence, based on the present study, they form a novel lineage and species associated with rice seeds for which the name Xanthomonas sontii sp. nov. is proposed. The type strain for the X. sontii sp. nov. is PPL1T (CFBP8688T = ICMP23426T = MTCC12491T) and strains PPL2 (CFBP8689 = ICMP23427 = MTCC12492) and PPL3 (CFBP8690 =ICMP23428 = MTCC12492) as other strains of the species.

evolutionary biology↗

bioRxiv2019

Extreme genome selection towards complete antimicrobial resistance in a nosocomial strain of Stenotrophomonas maltophilia complex

We report first complete genome sequence and analysis of an extreme drug resistance (XDR) nosocomial Stenotrophomonas maltophilia that is resistant to the mainstream drugs i.e. trimethoprim/sulfamethoxazole (TMP/SXT) and levofloxacin. Taxonogenomic analysis revealed it to be a novel genomospecies of the Stenotrophomonas maltophilia complex (Smc). Comprehensive genomic investigation revealed fourteen dynamic regions (DRs) exclusive to SM866, consisting of diverse antibiotic resistance genes, efflux pumps, heavy metal resistance, various transcriptional regulators etc. Further, resistome analysis of Smc clearly depicted SM866 to be an enriched strain, having diversified resistome consisting of sul1 and sul2 genes. Interestingly, SM866 does not have any plasmid but it harbors two diverse super-integrons of chromosomal origin. Apart from genes for sulfonamide resistance (sul1 and sul2), both of these integrons harbor an array of antibiotic resistance genes linked to ISCR (IS91-like elements common regions) elements. These integrons also harbor genes encoding resistance to commonly used disinfectants like quaternary ammonium compounds and heavy metals like mercury. Hence, isolation of a novel strain belonging to a novel sequence type (ST) and genomospecies with diverse array of resistance from a tertiary care unit of India indicates extent and nature of selection pressure driving XDRs in hospital settings. There is an urgent need to employ complete genome based investigation using emerging technologies for tracking emergence of XDR at the global level and designing strategies of sanitization and antibiotic regime.\n\nImpact StatementThe hospital settings in India have one of the highest usage of antimicrobials and heavy patient load. Our finding of a novel clinical isolate of S. maltophilia complex with two super-integrons harbouring array of antibiotic resistance genes along with antimicrobials resistance genes indicates the extent and the nature of selection pressures in action. Further, the presence of ISCR type of transposable elements on both integrons not only indicates its propensity to transfer resistome but also their chromosomal origin suggests possibilities for further genomic/phenotypic complexities. Such complex cassettes and strain are potential threat to global health care. Hence, there is an urgent need to employ cost-effective long read technologies to keep vigilance on novel and extreme antimicrobial resistance pathogens in populous countries. There is also need for surveillance for usage of antimicrobials for hygiene and linked/rapid co-evolution of extreme drug resistance in nosocomial pathogens. Our finding of the chromosomal encoding XDR will shed a light on the need of hour to understand the evolution of an opportunistic nosocomial pathogen belonging to S. maltophilia.\n\nRepositoriesComplete genome sequence of Stenotrophomonas maltophilia SM866: CP031058

genomics↗

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↗