Introduction: microbial local adaptation: insights from natural populations, genomics and experimental evolution

Giraud, Tatiana; Koskella, Britt; Laine, Anna‐Liisa

doi:10.1111/mec.14091

Cited by 25 publications

(30 citation statements)

References 56 publications

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“…We were able to investigate homologous recombination in the core/softcore genome of the 72 X. fastidiosa genomes. Recombination contributed more to genetic diversity than mutation, with an overall r/m value of 2.259, a relatively high value compared to that of other bacteria (29). Our r/m value at the species level was slightly lower than previous estimations made by Scally et al (3), which were based on 10 genes.…”

Section: Discussioncontrasting

confidence: 72%

“…Recombination is believed to play a major role in pathogen evolution, as bacteria acquire novel alleles or genes that may lead to host range expansion, increments in virulence, or adaptation to new ecological niches (28)(29)(30). For this pathogen, individual nucleotides have been estimated to be three times more likely to change due to recombination than due to point mutation, based on 10 genetic loci and a relatively small sample size (3).…”

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confidence: 99%

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Genomic Diversity and Recombination among Xylella fastidiosa Subspecies

Vanhove

Retchless

Sicard

et al. 2019

Appl Environ Microbiol

114

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Xylella fastidiosa is an economically important bacterial plant pathogen. With insights gained from 72 genomes, this study investigated differences among the three main subspecies, which have allopatric origins: X. fastidiosa subsp. fastidiosa, multiplex, and pauca. The origin of recombinogenic X. fastidiosa subsp. morus and sandyi was also assessed. The evolutionary rate of the 622 genes of the species core genome was estimated at the scale of an X. fastidiosa subsp. pauca subclade (7.62 ϫ 10 Ϫ7 substitutions per site per year), which was subsequently used to estimate divergence time for the subspecies and introduction events. The study characterized genes present in the accessory genome of each of the three subspecies and investigated the core genome to detect genes potentially under positive selection. Recombination is recognized to be the major driver of diversity in X. fastidiosa, potentially facilitating shifts to novel plant hosts. The relative effect of recombination in comparison to point mutation was calculated (r/m ϭ 2.259). Evidence of recombination was uncovered in the core genome alignment; X. fastidiosa subsp. fastidiosa in the United States was less prone to recombination, with an average of 3.22 of the 622 core genes identified as recombining regions, whereas a specific clade of X. fastidiosa subsp. multiplex was found to have on average 9.60 recombining genes, 93.2% of which originated from X. fastidiosa subsp. fastidiosa. Interestingly, for X. fastidiosa subsp. morus, which was initially thought to be the outcome of genome-wide recombination between X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. multiplex, intersubspecies homologous recombination levels reached 15.30% in the core genome. Finally, there is evidence of X. fastidiosa subsp. pauca strains from citrus containing genetic elements acquired from strains infecting coffee plants as well as genetic elements from both X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. multiplex. In summary, our data provide new insights into the evolution and epidemiology of this plant pathogen. IMPORTANCE Xylella fastidiosa is an important vector-borne plant pathogen. We used a set of 72 genomes that constitutes the largest assembled data set for this bacterial species so far to investigate genetic relationships and the impact of recombination on phylogenetic clades and to compare genome content at the subspecies level, and we used a molecular dating approach to infer the evolutionary rate of X. fastidiosa. The results demonstrate that recombination is important in shaping the genomes of X. fastidiosa and that each of the main subspecies is under different selective pressures. We hope insights from this study will improve our understanding of X. fastidiosa evolution and biology.

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Section: Discussioncontrasting

confidence: 72%

mentioning

confidence: 99%

Genomic Diversity and Recombination among Xylella fastidiosa Subspecies

Vanhove

Retchless

Sicard

et al. 2019

Appl Environ Microbiol

114

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“…Fungi are interesting eukaryotic models for adaptive divergence studies, with their small genomes, easy access to the haploid phase and experimental tractability for in vitro experiments (Giraud et al, 2017; Gladieux et al, 2014). Many fungi are used as food sources (Dupont et al, 2016) and some have been domesticated for food production.…”

Section: Introductionmentioning

confidence: 99%

Independent domestication events in the blue-cheese fungusPenicillium roqueforti

Dumas

Feurtey

Vega

et al. 2018

Preprint

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“…In pathogens, this means that species coexisting in sympatry in association with a common host species are likely to differ in other components of their ecological niches. The coexistence of multiple pathogens on the same crop species is in fact often associated with separation by time, resource use, abiotic conditions or geographical area (Fitt, Huang, van den Bosch, & West, ; Giraud, Koskella, & Laine, ). Closely related pathogens can also specialize on either the early or the late season part of a given plant life cycle (Hamelin, Bisson, Desprez‐Loustau, Fabre, & Mailleret, ; Mailleret, Castel, Montarry, & Hamelin, ).…”

Section: Introductionmentioning

confidence: 99%

Co‐occurrence among three divergent plant‐castrating fungi in the same Silene host species

et al. 2018

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The competitive exclusion principle postulates that different species can only coexist in sympatry if they occupy distinct ecological niches. The goal of this study was to understand the geographical distribution of three species of Microbotryum anther-smut fungi that are distantly related but infect the same host plants, the sister species Silene vulgaris and S. uniflora, in Western Europe. We used microsatellite markers to investigate pathogen distribution in relation to host specialization and ecological factors. Microbotryum violaceo-irregulare was only found on S. vulgaris at high elevations in the Alps. Microbotryum lagerheimii could be subdivided into two genetically differentiated clusters, one on S. uniflora in the UK and the second on S. vulgaris in the Alps and Pyrenees. The most abundant pathogen species, M. silenes-inflatae, could be subdivided into four genetic clusters, co-occurring in the Alps, the UK and the Pyrenees, and was found on both S. vulgaris and S. uniflora. All three fungal species had high levels of homozygosity, in agreement with the selfing mating system generally observed in anther-smut fungi. The three pathogen species and genetic clusters had large range overlaps, but occurred at sites with different elevations, temperatures and precipitation levels. The three Microbotryum species thus do not appear to be maintained by host specialization or geographic allopatry, but instead may occupy different ecological niches in terms of environmental conditions.

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Introduction: microbial local adaptation: insights from natural populations, genomics and experimental evolution

Cited by 25 publications

References 56 publications

Genomic Diversity and Recombination among Xylella fastidiosa Subspecies

Genomic Diversity and Recombination among Xylella fastidiosa Subspecies

Independent domestication events in the blue-cheese fungusPenicillium roqueforti

Co‐occurrence among three divergent plant‐castrating fungi in the same Silene host species

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