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.

doi:10.3389/fmicb.2023.1206094

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

Journal Article · Mon Jun 26 00:00:00 EDT 2023 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2023.1206094· OSTI ID:2470614

Batarseh, Tiffany N. ^[1]; Batarseh, Sarah N. ^[1]; Morales-Cruz, Abraham ^[2]; Gaut, Brandon S. ^[3]

University of California, Berkeley, CA (United States)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Univ. of California, Irvine, CA (United States)

‘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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2470614

Journal Information:: Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Vol. 14; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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

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