James T Tambong, Renlin Xu, Maria Constanza Fleitas, Randy Kutcher
{"title":"通过对半透明黄单胞菌复合体的分类基因组学分析，描述了谷类黄单胞菌(Xanthomonas cerealis sp. nov.)和禾谷黄单胞菌(Xanthomonas graminis sp. nov.)。","authors":"James T Tambong, Renlin Xu, Maria Constanza Fleitas, Randy Kutcher","doi":"10.1099/ijsem.0.006523","DOIUrl":null,"url":null,"abstract":"<p><p>The pathovar-based taxonomy of the <i>Xanthomonas translucens</i> group is very confusing due to an overlap of plant host ranges and level of host specificity. Here, whole-genome sequence-based parameters (digital DNA-DNA hybridization and blast-based average nucleotide identity), phylogenomic, biochemical and phenotypical data were used to taxonomically analyse the 11 known pathovars of the <i>X. translucens</i> complex. This polyphasic approach taxonomically assigned the 11 pathovars of <i>X. translucens</i> complex into three distinct species, two of which are new: <i>X. translucens</i>, <i>X. cerealis</i> sp. nov. and <i>X. graminis</i> sp. nov. <i>X. translucens</i> consists of three pathovars: pv. <i>translucens</i> (=pv. <i>hordei</i>), pv. <i>pistaciae</i> strain A ICMP 16316<sup>PT</sup> and pv. <i>undulosa</i> (=pv. <i>secalis</i>). <i>X. cerealis</i> sp. nov. encompasses the pv. <i>cerealis</i> strain LMG 679<sup>PT</sup> and pv. <i>pistaciae</i> strain B ICMP 16317<sup>PT</sup> with genome similarity of 92.7% (dDDH) and 99.0% (ANIb) suggesting taxonomically similar genotypes. The other new species, <i>X. graminis</i> sp. nov., consists of the remaining five designated pathovars (pv. <i>graminis</i>, pv. <i>arrhenatheri,</i> pv. <i>poae</i>, pv. <i>phleipratensis</i> and pv. <i>phlei</i>) with highly variable dDDH and ANIb values ranging from 74.5 to 93.0% and from 96.7 to 99.2%, respectively, an indication of a very divergent taxonomic group. Only strains of pvs. <i>phlei</i> and <i>phleipratensis</i> showed the highest genomic similarities of 93.0% (dDDH) and 99.2% (ANIb), suggesting synonymic pathovars as both infect the same plant hosts. The dDDH and ANI data were corroborated by phylogenomics clustering. The fatty acid contents were similar but the type strain of <i>X. graminis</i> sp. nov. exhibited 20% less C<sub>15 : 0</sub> iso and 40% more C<sub>17 : 0</sub> iso fatty acids than the other species. Based on phenotypic, biochemical and whole-genome sequence data, we propose two new species, <i>Xanthomonas cerealis</i> sp. nov. and <i>Xanthomonas graminis</i> sp. nov. with type strains LMG 679<sup>T</sup> (=NCPPB 1944<sup>T</sup>) and LMG 726<sup>T</sup> (=NCPPB 2700<sup>T</sup>), respectively.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"74 9","pages":""},"PeriodicalIF":2.0000,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Taxonogenomic analysis of the <i>Xanthomonas translucens</i> complex leads to the descriptions of <i>Xanthomonas cerealis</i> sp. nov. and <i>Xanthomonas graminis</i> sp. nov.\",\"authors\":\"James T Tambong, Renlin Xu, Maria Constanza Fleitas, Randy Kutcher\",\"doi\":\"10.1099/ijsem.0.006523\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The pathovar-based taxonomy of the <i>Xanthomonas translucens</i> group is very confusing due to an overlap of plant host ranges and level of host specificity. Here, whole-genome sequence-based parameters (digital DNA-DNA hybridization and blast-based average nucleotide identity), phylogenomic, biochemical and phenotypical data were used to taxonomically analyse the 11 known pathovars of the <i>X. translucens</i> complex. This polyphasic approach taxonomically assigned the 11 pathovars of <i>X. translucens</i> complex into three distinct species, two of which are new: <i>X. translucens</i>, <i>X. cerealis</i> sp. nov. and <i>X. graminis</i> sp. nov. <i>X. translucens</i> consists of three pathovars: pv. <i>translucens</i> (=pv. <i>hordei</i>), pv. <i>pistaciae</i> strain A ICMP 16316<sup>PT</sup> and pv. <i>undulosa</i> (=pv. <i>secalis</i>). <i>X. cerealis</i> sp. nov. encompasses the pv. <i>cerealis</i> strain LMG 679<sup>PT</sup> and pv. <i>pistaciae</i> strain B ICMP 16317<sup>PT</sup> with genome similarity of 92.7% (dDDH) and 99.0% (ANIb) suggesting taxonomically similar genotypes. The other new species, <i>X. graminis</i> sp. nov., consists of the remaining five designated pathovars (pv. <i>graminis</i>, pv. <i>arrhenatheri,</i> pv. <i>poae</i>, pv. <i>phleipratensis</i> and pv. <i>phlei</i>) with highly variable dDDH and ANIb values ranging from 74.5 to 93.0% and from 96.7 to 99.2%, respectively, an indication of a very divergent taxonomic group. Only strains of pvs. <i>phlei</i> and <i>phleipratensis</i> showed the highest genomic similarities of 93.0% (dDDH) and 99.2% (ANIb), suggesting synonymic pathovars as both infect the same plant hosts. The dDDH and ANI data were corroborated by phylogenomics clustering. The fatty acid contents were similar but the type strain of <i>X. graminis</i> sp. nov. exhibited 20% less C<sub>15 : 0</sub> iso and 40% more C<sub>17 : 0</sub> iso fatty acids than the other species. Based on phenotypic, biochemical and whole-genome sequence data, we propose two new species, <i>Xanthomonas cerealis</i> sp. nov. and <i>Xanthomonas graminis</i> sp. nov. with type strains LMG 679<sup>T</sup> (=NCPPB 1944<sup>T</sup>) and LMG 726<sup>T</sup> (=NCPPB 2700<sup>T</sup>), respectively.</p>\",\"PeriodicalId\":14390,\"journal\":{\"name\":\"International journal of systematic and evolutionary microbiology\",\"volume\":\"74 9\",\"pages\":\"\"},\"PeriodicalIF\":2.0000,\"publicationDate\":\"2024-09-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"International journal of systematic and evolutionary microbiology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1099/ijsem.0.006523\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"International journal of systematic and evolutionary microbiology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1099/ijsem.0.006523","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"MICROBIOLOGY","Score":null,"Total":0}
Taxonogenomic analysis of the Xanthomonas translucens complex leads to the descriptions of Xanthomonas cerealis sp. nov. and Xanthomonas graminis sp. nov.
The pathovar-based taxonomy of the Xanthomonas translucens group is very confusing due to an overlap of plant host ranges and level of host specificity. Here, whole-genome sequence-based parameters (digital DNA-DNA hybridization and blast-based average nucleotide identity), phylogenomic, biochemical and phenotypical data were used to taxonomically analyse the 11 known pathovars of the X. translucens complex. This polyphasic approach taxonomically assigned the 11 pathovars of X. translucens complex into three distinct species, two of which are new: X. translucens, X. cerealis sp. nov. and X. graminis sp. nov. X. translucens consists of three pathovars: pv. translucens (=pv. hordei), pv. pistaciae strain A ICMP 16316PT and pv. undulosa (=pv. secalis). X. cerealis sp. nov. encompasses the pv. cerealis strain LMG 679PT and pv. pistaciae strain B ICMP 16317PT with genome similarity of 92.7% (dDDH) and 99.0% (ANIb) suggesting taxonomically similar genotypes. The other new species, X. graminis sp. nov., consists of the remaining five designated pathovars (pv. graminis, pv. arrhenatheri, pv. poae, pv. phleipratensis and pv. phlei) with highly variable dDDH and ANIb values ranging from 74.5 to 93.0% and from 96.7 to 99.2%, respectively, an indication of a very divergent taxonomic group. Only strains of pvs. phlei and phleipratensis showed the highest genomic similarities of 93.0% (dDDH) and 99.2% (ANIb), suggesting synonymic pathovars as both infect the same plant hosts. The dDDH and ANI data were corroborated by phylogenomics clustering. The fatty acid contents were similar but the type strain of X. graminis sp. nov. exhibited 20% less C15 : 0 iso and 40% more C17 : 0 iso fatty acids than the other species. Based on phenotypic, biochemical and whole-genome sequence data, we propose two new species, Xanthomonas cerealis sp. nov. and Xanthomonas graminis sp. nov. with type strains LMG 679T (=NCPPB 1944T) and LMG 726T (=NCPPB 2700T), respectively.
期刊介绍：
Published by the Microbiology Society and owned by the International Committee on Systematics of Prokaryotes (ICSP), a committee of the Bacteriology and Applied Microbiology Division of the International Union of Microbiological Societies, International Journal of Systematic and Evolutionary Microbiology is the leading forum for the publication of novel microbial taxa and the ICSP’s official journal of record for prokaryotic names.
The journal welcomes high-quality research on all aspects of microbial evolution, phylogenetics and systematics, encouraging submissions on all prokaryotes, yeasts, microfungi, protozoa and microalgae across the full breadth of systematics including:
Identification, characterisation and culture preservation
Microbial evolution and biodiversity
Molecular environmental work with strong taxonomic or evolutionary content
Nomenclature
Taxonomy and phylogenetics.
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