Insights from the Genome Sequence of Acidovorax citrulli M6, a Group I Strain of the Causal Agent of Bacterial Fruit Blotch of Cucurbits

Abstract

Acidovorax citrulli is a seedborne bacterium that causes bacterial fruit blotch of cucurbit plants including watermelon and melon. A. citrulli strains can be divided into two major groups based on DNA fingerprint analyses and biochemical properties. Group I strains have been generally isolated from non-watermelon cucurbits, while group II strains are closely associated with watermelon. In the present study, we report the genome sequence of M6, a group I model A. citrulli strain, isolated from melon. We used comparative genome analysis to investigate differences between the genome of strain M6 and the genome of the group II model strain AAC00-1. The draft genome sequence of A. citrulli M6 harbors 139 contigs, with an overall approximate size of 4.85 Mb. The genome of M6 is ∼500 Kb shorter than that of strain AAC00-1. Comparative analysis revealed that this size difference is mainly explained by eight fragments, ranging from ∼35–120 Kb and distributed throughout the AAC00-1 genome, which are absent in the M6 genome. In agreement with this finding, while AAC00-1 was found to possess 532 open reading frames (ORFs) that are absent in strain M6, only 123 ORFs in M6 were absent in AAC00-1. Most of these M6 ORFs are hypothetical proteins and most of them were also detected in two group I strains that were recently sequenced, tw6 and pslb65. Further analyses by PCR assays and coverage analyses with other A. citrulli strains support the notion that some of these fragments or significant portions of them are discriminative between groups I and II strains of A. citrulli. Moreover, GC content, effective number of codon values and cluster of orthologs’ analyses indicate that these fragments were introduced into group II strains by horizontal gene transfer events. Our study reports the genome sequence of a model group I strain of A. citrulli, one of the most important pathogens of cucurbits. It also provides the first comprehensive comparison at the genomic level between the two major groups of strains of this pathogen.

Characterization of Acidovorax citrulli strains isolated from solanaceous plants

“…Remarkably, the two strains carry the T3E gene Aave_2708 , which has been found to occur in all Group II strains, but not in all Group I strains tested so far (Eckshtain‐Levi et al ., 2014; Jiménez‐Guerrero et al ., 2020; Zhao et a l ., 2020). Lastly, further characterization by sequencing of the genomes of strains T1 and EP revealed high similarity to the genome of the Group II strain AAC00‐1, including the occurrence of most genomic regions that are considered to be genetic markers of Group II strains (Eckshtain‐Levi et al ., 2016). Altogether, these findings demonstrate that the two strains isolated from solanaceous plants are more closely related to A .…”

“…Comparative analyses between the genomes of the model strains M6 (Group I; NCBI accessions CP029373.1 and CP029374.1) and AAC00‐1 (Group II; NCBI accession NC_008752.1) revealed differences that may be associated with host preference (Eckshtain‐Levi et al ., 2016; Yang et al ., 2019). The M6 genome is shorter than that of AAC00‐1 and lacks eight fragments, ranging from 35 to 120 kb, that are distributed throughout the genome of AAC00‐1 (Eckshtain‐Levi et al ., 2016). Moreover, it appears that Group I genomes are shorter than Group II genomes, with the aforementioned differences reflecting genetic markers that distinguish between the two group of strains (Eckshtain‐Levi et al ., 2016).…”

“…The M6 genome is shorter than that of AAC00‐1 and lacks eight fragments, ranging from 35 to 120 kb, that are distributed throughout the genome of AAC00‐1 (Eckshtain‐Levi et al ., 2016). Moreover, it appears that Group I genomes are shorter than Group II genomes, with the aforementioned differences reflecting genetic markers that distinguish between the two group of strains (Eckshtain‐Levi et al ., 2016).…”

Show me your secret(ed) weapons: a multifaceted approach reveals a wide arsenal of type III‐secreted effectors in the cucurbit pathogenic bacterium Acidovorax citrulli and novel effectors in the Acidovorax genus

“…Acidovorax citrulli M6 is a group I strain that was isolated in 2002 from a BFB outbreak in melons (Burdman et al, 2005) and subsequently became a model group I strain for investigation of basic aspects of BFB. Its genome has been sequenced, first by Illumina MiSeq (Eckshtain-Levi et al, 2016) and more recently by PacBio (Yang et al, 2019), which allowed its complete closure.…”

Show me your secret(ed) weapons: a multifaceted approach reveals novel type III-secreted effectors of a plant pathogenic bacterium

“…Acidovorax citrulli M6 is a group I strain that was isolated in 2002 from a BFB outbreak of melons in Israel [5], and subsequently became a model group I strain for investigation of basic aspects of BFB. The A. citrulli M6 genome has been sequenced, first by Illumina MiSeq [8] and recently, by PacBio [9], which allowed its complete closure.…”