Deep phylo-taxono-genomics (DEEPT genomics) reveals misclassification ofXanthomonasspecies complexes intoXylella, StenotrophomonasandPseudoxanthomonas
Abstract GenusXanthomonasencompasses specialized group of phytopathogenic bacteria with generaXylella, StenotrophomonasandPseudoxanthomonasbeing its closest relatives. While species of generaXanthomonasandXylellaare known as serious phytopathogens, members of other two genera are found in diverse habitats with metabolic versatility of biotechnological importance. Few species ofStenotrophomonasare multidrug resistant opportunistic nosocomial pathogens. In the present study, we report genomic resource of genusPseudoxanthomonasand 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 ofXanthomonas. The members ofPseudoxanthomonasare more diverse and ancestral and rest forming two mega species groups (MSGs) i.e.Xanthomonas Xylella(XX-MSG) andStenotrophomonas(S-MSG). Within XX-MSG, there are 3 species complexes i.e.,X. citricomplex (Xcc) member species are primarily pathogenic to dicots,X. hyacinthicomplex (Xhc) member species are primarily pathogenic to monocots andXanthomonas(Xylella)fastidosacomplex (Xfc) with diverse phytopathogenic potential. Interestingly,Xylellaseems to be a variantXanthomonaslineage or species complex that is sandwiched between Xcc and Xhc. LikeXylella, within S-MSG, we find a species complex of clinical originXanthomonas(Stenotrophomonas)maltophiliacomplex (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.Repositories Genome Submission Accession Number:MWIP00000000, PDWO00000000, PDWN00000000, PDWT00000000, PDWS00000000, PDWW00000000, PDWU00000000, PDWR00000000, PDWL00000000, PDWQ00000000, PDWM00000000, PDWP00000000, PDWV00000000, PDWK00000000 and QOVG00000000.
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Preprint| Erscheinungsjahr: |
2021 |
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| Erschienen: |
2021 |
| Enthalten in: |
bioRxiv.org - (2021) vom: 15. Dez. Zur Gesamtaufnahme - year:2021 |
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| Sprache: |
Englisch |
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| Beteiligte Personen: |
Bansal, Kanika [VerfasserIn] |
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| doi: |
10.1101/2020.02.04.933507 |
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| PPN (Katalog-ID): |
XBI000723444 |
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| 245 | 1 | 0 | |a Deep phylo-taxono-genomics (DEEPT genomics) reveals misclassification ofXanthomonasspecies complexes intoXylella, StenotrophomonasandPseudoxanthomonas |
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| 520 | |a Abstract GenusXanthomonasencompasses specialized group of phytopathogenic bacteria with generaXylella, StenotrophomonasandPseudoxanthomonasbeing its closest relatives. While species of generaXanthomonasandXylellaare known as serious phytopathogens, members of other two genera are found in diverse habitats with metabolic versatility of biotechnological importance. Few species ofStenotrophomonasare multidrug resistant opportunistic nosocomial pathogens. In the present study, we report genomic resource of genusPseudoxanthomonasand 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 ofXanthomonas. The members ofPseudoxanthomonasare more diverse and ancestral and rest forming two mega species groups (MSGs) i.e.Xanthomonas Xylella(XX-MSG) andStenotrophomonas(S-MSG). Within XX-MSG, there are 3 species complexes i.e.,X. citricomplex (Xcc) member species are primarily pathogenic to dicots,X. hyacinthicomplex (Xhc) member species are primarily pathogenic to monocots andXanthomonas(Xylella)fastidosacomplex (Xfc) with diverse phytopathogenic potential. Interestingly,Xylellaseems to be a variantXanthomonaslineage or species complex that is sandwiched between Xcc and Xhc. LikeXylella, within S-MSG, we find a species complex of clinical originXanthomonas(Stenotrophomonas)maltophiliacomplex (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.Repositories Genome Submission Accession Number:MWIP00000000, PDWO00000000, PDWN00000000, PDWT00000000, PDWS00000000, PDWW00000000, PDWU00000000, PDWR00000000, PDWL00000000, PDWQ00000000, PDWM00000000, PDWP00000000, PDWV00000000, PDWK00000000 and QOVG00000000 | ||
| 700 | 1 | |a Kumar, Sanjeet |e verfasserin |4 aut | |
| 700 | 1 | |a Kaur, Amandeep |e verfasserin |4 aut | |
| 700 | 1 | |a Sharma, Shikha |e verfasserin |4 aut | |
| 700 | 1 | |a Patil, Prashant |e verfasserin |4 aut | |
| 700 | 1 | |a Patil, Prabhu B. |e verfasserin |4 aut | |
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