Complete assembly of the genome of an Acidovorax citrulli strain reveals a naturally occurring plasmid in this species

Rongzhi Yang; Diego Santos Garcia; Francisco Pérez Montaño; Gustavo Mateus Da Silva; Mei Zhao; Irene Jiménez Guerrero; Tally Rosenberg; Gong Chen; Inbar Plaschkes; Shai Morin; Ron Walcott; Saul Burdman

doi:10.3389/fmicb.2019.01400

Complete assembly of the genome of an Acidovorax citrulli strain reveals a naturally occurring plasmid in this species

Rongzhi Yang, Diego Santos Garcia, Francisco Pérez Montaño, Gustavo Mateus Da Silva, Mei Zhao, Irene Jiménez Guerrero, Tally Rosenberg, Gong Chen, Inbar Plaschkes, Shai Morin, Ron Walcott, Saul Burdman^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

10 Scopus citations

Abstract

Acidovorax citrulli is the causal agent of bacterial fruit blotch (BFB), a serious threat to cucurbit crop production worldwide. Based on genetic and phenotypic properties, A. citrulli strains are divided into two major groups: group I strains have been generally isolated from melon and other non-watermelon cucurbits, while group II strains are closely associated with watermelon. In a previous study, we reported the genome of the group I model strain, M6. At that time, the M6 genome was sequenced by MiSeq Illumina technology, with reads assembled into 139 contigs. Here, we report the assembly of the M6 genome following sequencing with PacBio technology. This approach not only allowed full assembly of the M6 genome, but it also revealed the occurrence of a ∼53 kb plasmid. The M6 plasmid, named pACM6, was further confirmed by plasmid extraction, Southern-blot analysis of restricted fragments and obtention of M6-derivative cured strains. pACM6 occurs at low copy numbers (average of ∼4.1 ± 1.3 chromosome equivalents) in A. citrulli M6 and contains 63 open reading frames (ORFs), most of which (55.6%) encoding hypothetical proteins. The plasmid contains several genes encoding type IV secretion components, and typical plasmid-borne genes involved in plasmid maintenance, replication and transfer. The plasmid also carries an operon encoding homologs of a Fic-VbhA toxin-antitoxin (TA) module. Transcriptome data from A. citrulli M6 revealed that, under the tested conditions, the genes encoding the components of this TA system are among the highest expressed genes in pACM6. Whether this TA module plays a role in pACM6 maintenance is still to be determined. Leaf infiltration and seed transmission assays revealed that, under tested conditions, the loss of pACM6 did not affect the virulence of A. citrulli M6. We also show that pACM6 or similar plasmids are present in several group I strains, but absent in all tested group II strains of A. citrulli.

Original language	American English
Article number	1400
Journal	Frontiers in Microbiology
Volume	10
Issue number	JUN
DOIs	https://doi.org/10.3389/fmicb.2019.01400
State	Published - 2019

Bibliographical note

Funding Information:
This work was supported by research grants 851/14 from the Israel Science Foundation (ISF) and IS-5023-17C from the United States-Israel Binational Agricultural Research and Development (BARD) Fund. RY was recipient of a Chinese government scholarship from the China Scholarship Council (CSC). DSG was recipient of a Golda Meir post-doctoral fellowship (Hebrew University). FPM was recipient of the José Castillejo grant of the Ministry of Education, Culture and Sport of the Spanish Government. GS was recipient of Lady Davis and Golda Meir post-doctoral fellowships (Hebrew University).

Publisher Copyright:
Copyright © 2019 Yang, Santos Garcia, Pérez Montaño, da Silva, Zhao, Jiménez Guerrero, Rosenberg, Chen, Plaschkes, Morin, Walcott and Burdman.

Keywords

Acidovorax citrulli
Bacterial fruit blotch
Plasmid
SMRT sequencing
Toxin-antitoxin system

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10.3389/fmicb.2019.01400

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Yang, R., Garcia, D. S., Montaño, F. P., Da Silva, G. M., Zhao, M., Guerrero, I. J., Rosenberg, T., Chen, G., Plaschkes, I., Morin, S., Walcott, R., & Burdman, S. (2019). Complete assembly of the genome of an Acidovorax citrulli strain reveals a naturally occurring plasmid in this species. Frontiers in Microbiology, 10(JUN), Article 1400. https://doi.org/10.3389/fmicb.2019.01400

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abstract = "Acidovorax citrulli is the causal agent of bacterial fruit blotch (BFB), a serious threat to cucurbit crop production worldwide. Based on genetic and phenotypic properties, A. citrulli strains are divided into two major groups: group I strains have been generally isolated from melon and other non-watermelon cucurbits, while group II strains are closely associated with watermelon. In a previous study, we reported the genome of the group I model strain, M6. At that time, the M6 genome was sequenced by MiSeq Illumina technology, with reads assembled into 139 contigs. Here, we report the assembly of the M6 genome following sequencing with PacBio technology. This approach not only allowed full assembly of the M6 genome, but it also revealed the occurrence of a ∼53 kb plasmid. The M6 plasmid, named pACM6, was further confirmed by plasmid extraction, Southern-blot analysis of restricted fragments and obtention of M6-derivative cured strains. pACM6 occurs at low copy numbers (average of ∼4.1 ± 1.3 chromosome equivalents) in A. citrulli M6 and contains 63 open reading frames (ORFs), most of which (55.6%) encoding hypothetical proteins. The plasmid contains several genes encoding type IV secretion components, and typical plasmid-borne genes involved in plasmid maintenance, replication and transfer. The plasmid also carries an operon encoding homologs of a Fic-VbhA toxin-antitoxin (TA) module. Transcriptome data from A. citrulli M6 revealed that, under the tested conditions, the genes encoding the components of this TA system are among the highest expressed genes in pACM6. Whether this TA module plays a role in pACM6 maintenance is still to be determined. Leaf infiltration and seed transmission assays revealed that, under tested conditions, the loss of pACM6 did not affect the virulence of A. citrulli M6. We also show that pACM6 or similar plasmids are present in several group I strains, but absent in all tested group II strains of A. citrulli.",

keywords = "Acidovorax citrulli, Bacterial fruit blotch, Plasmid, SMRT sequencing, Toxin-antitoxin system",

author = "Rongzhi Yang and Garcia, {Diego Santos} and Monta{\~n}o, {Francisco P{\'e}rez} and {Da Silva}, {Gustavo Mateus} and Mei Zhao and Guerrero, {Irene Jim{\'e}nez} and Tally Rosenberg and Gong Chen and Inbar Plaschkes and Shai Morin and Ron Walcott and Saul Burdman",

note = "Funding Information: This work was supported by research grants 851/14 from the Israel Science Foundation (ISF) and IS-5023-17C from the United States-Israel Binational Agricultural Research and Development (BARD) Fund. RY was recipient of a Chinese government scholarship from the China Scholarship Council (CSC). DSG was recipient of a Golda Meir post-doctoral fellowship (Hebrew University). FPM was recipient of the Jos{\'e} Castillejo grant of the Ministry of Education, Culture and Sport of the Spanish Government. GS was recipient of Lady Davis and Golda Meir post-doctoral fellowships (Hebrew University). Publisher Copyright: Copyright {\textcopyright} 2019 Yang, Santos Garcia, P{\'e}rez Monta{\~n}o, da Silva, Zhao, Jim{\'e}nez Guerrero, Rosenberg, Chen, Plaschkes, Morin, Walcott and Burdman.",

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T1 - Complete assembly of the genome of an Acidovorax citrulli strain reveals a naturally occurring plasmid in this species

AU - Yang, Rongzhi

AU - Garcia, Diego Santos

AU - Montaño, Francisco Pérez

AU - Da Silva, Gustavo Mateus

AU - Zhao, Mei

AU - Guerrero, Irene Jiménez

AU - Rosenberg, Tally

AU - Chen, Gong

AU - Plaschkes, Inbar

AU - Morin, Shai

AU - Walcott, Ron

AU - Burdman, Saul

N1 - Funding Information: This work was supported by research grants 851/14 from the Israel Science Foundation (ISF) and IS-5023-17C from the United States-Israel Binational Agricultural Research and Development (BARD) Fund. RY was recipient of a Chinese government scholarship from the China Scholarship Council (CSC). DSG was recipient of a Golda Meir post-doctoral fellowship (Hebrew University). FPM was recipient of the José Castillejo grant of the Ministry of Education, Culture and Sport of the Spanish Government. GS was recipient of Lady Davis and Golda Meir post-doctoral fellowships (Hebrew University). Publisher Copyright: Copyright © 2019 Yang, Santos Garcia, Pérez Montaño, da Silva, Zhao, Jiménez Guerrero, Rosenberg, Chen, Plaschkes, Morin, Walcott and Burdman.

PY - 2019

Y1 - 2019

N2 - Acidovorax citrulli is the causal agent of bacterial fruit blotch (BFB), a serious threat to cucurbit crop production worldwide. Based on genetic and phenotypic properties, A. citrulli strains are divided into two major groups: group I strains have been generally isolated from melon and other non-watermelon cucurbits, while group II strains are closely associated with watermelon. In a previous study, we reported the genome of the group I model strain, M6. At that time, the M6 genome was sequenced by MiSeq Illumina technology, with reads assembled into 139 contigs. Here, we report the assembly of the M6 genome following sequencing with PacBio technology. This approach not only allowed full assembly of the M6 genome, but it also revealed the occurrence of a ∼53 kb plasmid. The M6 plasmid, named pACM6, was further confirmed by plasmid extraction, Southern-blot analysis of restricted fragments and obtention of M6-derivative cured strains. pACM6 occurs at low copy numbers (average of ∼4.1 ± 1.3 chromosome equivalents) in A. citrulli M6 and contains 63 open reading frames (ORFs), most of which (55.6%) encoding hypothetical proteins. The plasmid contains several genes encoding type IV secretion components, and typical plasmid-borne genes involved in plasmid maintenance, replication and transfer. The plasmid also carries an operon encoding homologs of a Fic-VbhA toxin-antitoxin (TA) module. Transcriptome data from A. citrulli M6 revealed that, under the tested conditions, the genes encoding the components of this TA system are among the highest expressed genes in pACM6. Whether this TA module plays a role in pACM6 maintenance is still to be determined. Leaf infiltration and seed transmission assays revealed that, under tested conditions, the loss of pACM6 did not affect the virulence of A. citrulli M6. We also show that pACM6 or similar plasmids are present in several group I strains, but absent in all tested group II strains of A. citrulli.

AB - Acidovorax citrulli is the causal agent of bacterial fruit blotch (BFB), a serious threat to cucurbit crop production worldwide. Based on genetic and phenotypic properties, A. citrulli strains are divided into two major groups: group I strains have been generally isolated from melon and other non-watermelon cucurbits, while group II strains are closely associated with watermelon. In a previous study, we reported the genome of the group I model strain, M6. At that time, the M6 genome was sequenced by MiSeq Illumina technology, with reads assembled into 139 contigs. Here, we report the assembly of the M6 genome following sequencing with PacBio technology. This approach not only allowed full assembly of the M6 genome, but it also revealed the occurrence of a ∼53 kb plasmid. The M6 plasmid, named pACM6, was further confirmed by plasmid extraction, Southern-blot analysis of restricted fragments and obtention of M6-derivative cured strains. pACM6 occurs at low copy numbers (average of ∼4.1 ± 1.3 chromosome equivalents) in A. citrulli M6 and contains 63 open reading frames (ORFs), most of which (55.6%) encoding hypothetical proteins. The plasmid contains several genes encoding type IV secretion components, and typical plasmid-borne genes involved in plasmid maintenance, replication and transfer. The plasmid also carries an operon encoding homologs of a Fic-VbhA toxin-antitoxin (TA) module. Transcriptome data from A. citrulli M6 revealed that, under the tested conditions, the genes encoding the components of this TA system are among the highest expressed genes in pACM6. Whether this TA module plays a role in pACM6 maintenance is still to be determined. Leaf infiltration and seed transmission assays revealed that, under tested conditions, the loss of pACM6 did not affect the virulence of A. citrulli M6. We also show that pACM6 or similar plasmids are present in several group I strains, but absent in all tested group II strains of A. citrulli.

KW - Acidovorax citrulli

KW - Bacterial fruit blotch

KW - Plasmid

KW - SMRT sequencing

KW - Toxin-antitoxin system

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DO - 10.3389/fmicb.2019.01400

M3 - Article

AN - SCOPUS:85069049441

SN - 1664-302X

VL - 10

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

IS - JUN

M1 - 1400

ER -

Complete assembly of the genome of an Acidovorax citrulli strain reveals a naturally occurring plasmid in this species

Abstract

Bibliographical note

Keywords

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