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Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history

‘Candidatus Liberibacter’ is a group of bacterial species that are obligate intracellular plant pathogens and cause Huanglongbing disease of citrus trees and Zebra Chip in potatoes. Here, we examined the extent of intra- and interspecific genetic diversity across the genus using comparative genomics...

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Autores principales: Batarseh, Tiffany N., Batarseh, Sarah N., Morales-Cruz, Abraham, Gaut, Brandon S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10330825/
https://www.ncbi.nlm.nih.gov/pubmed/37434713
http://dx.doi.org/10.3389/fmicb.2023.1206094
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author Batarseh, Tiffany N.
Batarseh, Sarah N.
Morales-Cruz, Abraham
Gaut, Brandon S.
author_facet Batarseh, Tiffany N.
Batarseh, Sarah N.
Morales-Cruz, Abraham
Gaut, Brandon S.
author_sort Batarseh, Tiffany N.
collection PubMed
description ‘Candidatus Liberibacter’ is a group of bacterial species that are obligate intracellular plant pathogens and cause Huanglongbing disease of citrus trees and Zebra Chip in potatoes. Here, we examined the extent of intra- and interspecific genetic diversity across the genus using comparative genomics. Our approach examined a wide set of Liberibacter genome sequences including five pathogenic species and one species not known to cause disease. By performing comparative genomics analyses, we sought to understand the evolutionary history of this genus and to identify genes or genome regions that may affect pathogenicity. With a set of 52 genomes, we performed comparative genomics, measured genome rearrangement, and completed statistical tests of positive selection. We explored markers of genetic diversity across the genus, such as average nucleotide identity across the whole genome. These analyses revealed the highest intraspecific diversity amongst the ‘Ca. Liberibacter solanacearum’ species, which also has the largest plant host range. We identified sets of core and accessory genes across the genus and within each species and measured the ratio of nonsynonymous to synonymous mutations (dN/dS) across genes. We identified ten genes with evidence of a history of positive selection in the Liberibacter genus, including genes in the Tad complex, which have been previously implicated as being highly divergent in the ‘Ca. L. capsica’ species based on high values of dN.
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spelling pubmed-103308252023-07-11 Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history Batarseh, Tiffany N. Batarseh, Sarah N. Morales-Cruz, Abraham Gaut, Brandon S. Front Microbiol Microbiology ‘Candidatus Liberibacter’ is a group of bacterial species that are obligate intracellular plant pathogens and cause Huanglongbing disease of citrus trees and Zebra Chip in potatoes. Here, we examined the extent of intra- and interspecific genetic diversity across the genus using comparative genomics. Our approach examined a wide set of Liberibacter genome sequences including five pathogenic species and one species not known to cause disease. By performing comparative genomics analyses, we sought to understand the evolutionary history of this genus and to identify genes or genome regions that may affect pathogenicity. With a set of 52 genomes, we performed comparative genomics, measured genome rearrangement, and completed statistical tests of positive selection. We explored markers of genetic diversity across the genus, such as average nucleotide identity across the whole genome. These analyses revealed the highest intraspecific diversity amongst the ‘Ca. Liberibacter solanacearum’ species, which also has the largest plant host range. We identified sets of core and accessory genes across the genus and within each species and measured the ratio of nonsynonymous to synonymous mutations (dN/dS) across genes. We identified ten genes with evidence of a history of positive selection in the Liberibacter genus, including genes in the Tad complex, which have been previously implicated as being highly divergent in the ‘Ca. L. capsica’ species based on high values of dN. Frontiers Media S.A. 2023-06-26 /pmc/articles/PMC10330825/ /pubmed/37434713 http://dx.doi.org/10.3389/fmicb.2023.1206094 Text en Copyright © 2023 Batarseh, Batarseh, Morales-Cruz and Gaut. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Batarseh, Tiffany N.
Batarseh, Sarah N.
Morales-Cruz, Abraham
Gaut, Brandon S.
Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history
title Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history
title_full Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history
title_fullStr Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history
title_full_unstemmed Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history
title_short Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history
title_sort comparative genomics of the liberibacter genus reveals widespread diversity in genomic content and positive selection history
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10330825/
https://www.ncbi.nlm.nih.gov/pubmed/37434713
http://dx.doi.org/10.3389/fmicb.2023.1206094
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