Phylogenetic and pangenomic analyses of members of the family <i>Micrococcaceae</i> related to a plant-growth-promoting rhizobacterium isolated from the rhizosphere of potato (<i>Solanum tuberosum</i> L.)
We report the results of taxonomic studies on members of the family Micrococcaceae that, according to the 16S rRNA, internal transcribed spacer 1 (ITS1), average nucleotide identity (ANI), and average amino acid identity (AAI) tests, are related to Kocuria rosea strain RCAM04488, a plant-growth-prom...
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2024-05-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/4144 |
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| author | S. Yu. Shchyogolev G. L. Burygin L. A. Dykman L. Yu. Matora |
| author_facet | S. Yu. Shchyogolev G. L. Burygin L. A. Dykman L. Yu. Matora |
| author_sort | S. Yu. Shchyogolev |
| collection | DOAJ |
| description | We report the results of taxonomic studies on members of the family Micrococcaceae that, according to the 16S rRNA, internal transcribed spacer 1 (ITS1), average nucleotide identity (ANI), and average amino acid identity (AAI) tests, are related to Kocuria rosea strain RCAM04488, a plant-growth-promoting rhizobacterium (PGPR) isolated from the rhizosphere of potato (Solanum tuberosum L.). In these studies, we used whole-genome phylogenetic tests and pangenomic analysis. According to the ANI > 95 % criterion, several known members of K. salina, K. polaris, and K. rosea (including K. rosea type strain ATCC 186T) that are related most closely to isolate RCAM04488 in the ITS1 test should be assigned to the same species with appropriate strain verification. However, these strains were isolated from strongly contrasting ecological and geographical habitats, which could not but affect their genotypes and phenotypes and which should be taken into account in evaluation of their systematic position. This contradiction was resolved by a pangenomic analysis, which showed that the strains differed strongly in the number of accessory and strain-specific genes determining their individuality and possibly their potential for adaptation to different ecological niches. Similar results were obtained in a full-scale AAI test against the UniProt database (about 250 million records), by using the AAI-profiler program and the proteome of K. rosea strain ATCC 186T as a query. According to the AAI > 65 % criterion, members of the genus Arthrobacter and several other genera belonging to the class Actinomycetes, with a very wide geographical and ecological range of sources of isolation, should be placed into the same genus as Kocuria. Within the paradigm with vertically inherited phylogenetic markers, this could be regarded as a signal for their following taxonomic reclassification. An important factor in this case may be the detailing of the gene composition of the strains and the taxonomic ratios resulting from analysis of the pangenomes of the corresponding clades. |
| format | Article |
| id | doaj-art-0089a4f785664039aceee8030d027f03 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2024-05-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-0089a4f785664039aceee8030d027f032025-02-01T09:58:13ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592024-05-0128330831610.18699/vjgb-24-351465Phylogenetic and pangenomic analyses of members of the family <i>Micrococcaceae</i> related to a plant-growth-promoting rhizobacterium isolated from the rhizosphere of potato (<i>Solanum tuberosum</i> L.)S. Yu. Shchyogolev0G. L. Burygin1L. A. Dykman2L. Yu. Matora3Institute of Biochemistry and Physiology of Plants and Microorganisms – Subdivision of the Saratov Federal Scientific Centre of the Russian Academy of SciencesInstitute of Biochemistry and Physiology of Plants and Microorganisms – Subdivision of the Saratov Federal Scientific Centre of the Russian Academy of Sciences; Saratov State Vavilov Agrarian UniversityInstitute of Biochemistry and Physiology of Plants and Microorganisms – Subdivision of the Saratov Federal Scientific Centre of the Russian Academy of SciencesInstitute of Biochemistry and Physiology of Plants and Microorganisms – Subdivision of the Saratov Federal Scientific Centre of the Russian Academy of SciencesWe report the results of taxonomic studies on members of the family Micrococcaceae that, according to the 16S rRNA, internal transcribed spacer 1 (ITS1), average nucleotide identity (ANI), and average amino acid identity (AAI) tests, are related to Kocuria rosea strain RCAM04488, a plant-growth-promoting rhizobacterium (PGPR) isolated from the rhizosphere of potato (Solanum tuberosum L.). In these studies, we used whole-genome phylogenetic tests and pangenomic analysis. According to the ANI > 95 % criterion, several known members of K. salina, K. polaris, and K. rosea (including K. rosea type strain ATCC 186T) that are related most closely to isolate RCAM04488 in the ITS1 test should be assigned to the same species with appropriate strain verification. However, these strains were isolated from strongly contrasting ecological and geographical habitats, which could not but affect their genotypes and phenotypes and which should be taken into account in evaluation of their systematic position. This contradiction was resolved by a pangenomic analysis, which showed that the strains differed strongly in the number of accessory and strain-specific genes determining their individuality and possibly their potential for adaptation to different ecological niches. Similar results were obtained in a full-scale AAI test against the UniProt database (about 250 million records), by using the AAI-profiler program and the proteome of K. rosea strain ATCC 186T as a query. According to the AAI > 65 % criterion, members of the genus Arthrobacter and several other genera belonging to the class Actinomycetes, with a very wide geographical and ecological range of sources of isolation, should be placed into the same genus as Kocuria. Within the paradigm with vertically inherited phylogenetic markers, this could be regarded as a signal for their following taxonomic reclassification. An important factor in this case may be the detailing of the gene composition of the strains and the taxonomic ratios resulting from analysis of the pangenomes of the corresponding clades.https://vavilov.elpub.ru/jour/article/view/4144<i>arthrobacterkocuriamicrococcaceae</i>pangenomepgprphylogenetic analysisstrain verification<i>solanum tuberosum</i> l. |
| spellingShingle | S. Yu. Shchyogolev G. L. Burygin L. A. Dykman L. Yu. Matora Phylogenetic and pangenomic analyses of members of the family <i>Micrococcaceae</i> related to a plant-growth-promoting rhizobacterium isolated from the rhizosphere of potato (<i>Solanum tuberosum</i> L.) Вавиловский журнал генетики и селекции <i>arthrobacter kocuria micrococcaceae</i> pangenome pgpr phylogenetic analysis strain verification <i>solanum tuberosum</i> l. |
| title | Phylogenetic and pangenomic analyses of members of the family <i>Micrococcaceae</i> related to a plant-growth-promoting rhizobacterium isolated from the rhizosphere of potato (<i>Solanum tuberosum</i> L.) |
| title_full | Phylogenetic and pangenomic analyses of members of the family <i>Micrococcaceae</i> related to a plant-growth-promoting rhizobacterium isolated from the rhizosphere of potato (<i>Solanum tuberosum</i> L.) |
| title_fullStr | Phylogenetic and pangenomic analyses of members of the family <i>Micrococcaceae</i> related to a plant-growth-promoting rhizobacterium isolated from the rhizosphere of potato (<i>Solanum tuberosum</i> L.) |
| title_full_unstemmed | Phylogenetic and pangenomic analyses of members of the family <i>Micrococcaceae</i> related to a plant-growth-promoting rhizobacterium isolated from the rhizosphere of potato (<i>Solanum tuberosum</i> L.) |
| title_short | Phylogenetic and pangenomic analyses of members of the family <i>Micrococcaceae</i> related to a plant-growth-promoting rhizobacterium isolated from the rhizosphere of potato (<i>Solanum tuberosum</i> L.) |
| title_sort | phylogenetic and pangenomic analyses of members of the family i micrococcaceae i related to a plant growth promoting rhizobacterium isolated from the rhizosphere of potato i solanum tuberosum i l |
| topic | <i>arthrobacter kocuria micrococcaceae</i> pangenome pgpr phylogenetic analysis strain verification <i>solanum tuberosum</i> l. |
| url | https://vavilov.elpub.ru/jour/article/view/4144 |
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