Abstract
Documenting the role of novel mutation versus homologous recombination in bacterial evolution, and especially in the invasion of new hosts, is central to understanding the long-term dynamics of pathogenic bacteria. We used multilocus sequence typing (MLST) to study this issue in Xylella fastidiosa subsp. pauca from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS). All 55 citrus isolates typed (plus one coffee isolate) defined three similar sequence types (STs) dominated by ST11 (85%), while the remaining 22 coffee isolates defined two STs, mainly ST16 (74%). This low level of variation masked unusually large allelic differences (>1% divergence with no intermediates) at five loci (leuA, petC, malF, cysG, and holC). We developed an introgression test to detect whether these large differences were due to introgression via homologous recombination from another X. fastidiosa subspecies. Using additional sequencing around these loci, we established that the seven randomly chosen MLST targets contained seven regions of introgression totaling 2,172 bp of 4,161 bp (52%), only 409 bp (10%) of which were detected by other recombination tests. This high level of introgression suggests the hypothesis that X. fastidiosa subsp. pauca became pathogenic on citrus and coffee (crops cultivated in Brazil for several hundred years) only recently after it gained genetic variation via intersubspecific recombination, facilitating a switch from native hosts. A candidate donor is the subspecies infecting plum in the region since 1935 (possibly X. fastidiosa subsp. multiplex). This hypothesis predicts that nonrecombinant native X. fastidiosa subsp. pauca (not yet isolated) does not cause disease in citrus or coffee.
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Claims 6
Claim · model-written summary
The 55 citrus isolates of Xylella fastidiosa subsp. pauca defined three similar sequence types dominated by ST11 (85%).
- Material
- 55 citrus isolatese1
- Interactor
- Xylella fastidiosa subsp. pauca
Xylella fastidiosa subsp. paucae0pathogen - Outcome
- sequence typese1
- Value
- 85%e1
- Qualifier
- dominated by ST11e1
CitrusOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We used multilocus sequence typing (MLST) to study this issue in Xylella fastidiosa subsp. pauca from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS)”
e1“All 55 citrus isolates typed (plus one coffee isolate) defined three similar sequence types (STs) dominated by ST11 (85%)”
Claim · model-written summary
The 22 coffee isolates of Xylella fastidiosa subsp. pauca defined two sequence types, mainly ST16 (74%).
- Material
- 22 coffee isolatese2
- Interactor
- Xylella fastidiosa subsp. paucaXylella fastidiosa subsp. paucae0pathogen
- Outcome
- STse2
- Value
- 74%e2
- Qualifier
- mainly ST16e2
CoffeaOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We used multilocus sequence typing (MLST) to study this issue in Xylella fastidiosa subsp. pauca from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS)”
e2“the remaining 22 coffee isolates defined two STs, mainly ST16 (74%)”
Claim · model-written summary
Allelic differences at five loci in Xylella fastidiosa subsp. pauca isolates were unusually large, above 1% divergence with no intermediates.
- Interactor
- Xylella fastidiosa subsp. paucaXylella fastidiosa subsp. paucae0pathogen
- Gene
- leuA, petC, malF, cysG, and holCe3
- Outcome
- allelic differencese3
- Value
- >1% divergencee3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We used multilocus sequence typing (MLST) to study this issue in Xylella fastidiosa subsp. pauca from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS)”
e3“This low level of variation masked unusually large allelic differences (>1% divergence with no intermediates) at five loci (leuA, petC, malF, cysG, and holC)”
Claim · model-written summary
The introgression test found seven regions of introgression covering 52% of the 4,161 bp sequenced at the MLST targets.
- Interactor
- Xylella fastidiosa subsp. paucaXylella fastidiosa subsp. paucae0pathogen
- Outcome
- regions of introgressione4
- Value
- 52%e4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We used multilocus sequence typing (MLST) to study this issue in Xylella fastidiosa subsp. pauca from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS)”
e4“the seven randomly chosen MLST targets contained seven regions of introgression totaling 2,172 bp of 4,161 bp (52%)”
Claim · model-written summary
Only 10% of the introgressed sequence was detected by other recombination tests.
- Interactor
- Xylella fastidiosa subsp. paucaXylella fastidiosa subsp. paucae0pathogen
- Outcome
- of which were detected by other recombination testse5
- Value
- 10%e5
- Comparator
- other recombination testse5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We used multilocus sequence typing (MLST) to study this issue in Xylella fastidiosa subsp. pauca from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS)”
e5“only 409 bp (10%) of which were detected by other recombination tests”
Claim · model-written summary
High introgression suggests that the subspecies became pathogenic on citrus and coffee only recently, after gaining variation via intersubspecific recombination.
- Interactor
- Xylella fastidiosa subsp. paucaXylella fastidiosa subsp. paucae0pathogen
- Outcome
- became pathogenic on citrus and coffeee6
- Qualifier
- via intersubspecific recombinatione6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We used multilocus sequence typing (MLST) to study this issue in Xylella fastidiosa subsp. pauca from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS)”
e6“This high level of introgression suggests the hypothesis that X. fastidiosa subsp. pauca became pathogenic on citrus and coffee (crops cultivated in Brazil for several hundred years) only recently after it gained genetic variation via intersubspecific recombination, facilitating a switch from native hosts”