Complete Genome Sequence of Sequevar 14M Ralstonia solanacearum Strain HA4-1 Reveals Novel Type III Effectors Acquired Through Horizontal Gene Transfer

Abstract

Ralstonia solanacearum , which causes bacterial wilt in a broad range of plants, is considered a “species complex” due to its significant genetic diversity. Recently, we have isolated a new R. solanacearum strain HA4-1 from Hong’an county in Hubei province of China and identified it being phylotype I, sequevar 14M (phylotype I-14M). Interestingly, we found that it can cause various disease symptoms among different potato genotypes and display different pathogenic behavior compared to a phylogenetically related strain, GMI1000. To dissect the pathogenic mechanisms of HA4-1, we sequenced its whole genome by combined sequencing technologies including Illumina HiSeq2000, PacBio RS II, and BAC-end sequencing. Genome assembly results revealed the presence of a conventional chromosome, a megaplasmid as well as a 143 kb plasmid in HA4-1. Comparative genome analysis between HA4-1 and GMI1000 shows high conservation of the general virulence factors such as secretion systems, motility, exopolysaccharides (EPS), and key regulatory factors, but significant variation in the repertoire and structure of type III effectors, which could be the determinants of their differential pathogenesis in certain potato species or genotypes. We have identified two novel type III effectors that were probably acquired through horizontal gene transfer (HGT). These novel R. solanacearum effectors display homology to several YopJ and XopAC family members. We named them as RipBR and RipBS. Notably, the copy of RipBR on the plasmid is a pseudogene, while the other on the megaplasmid is normal. For RipBS, there are three copies located in the megaplasmid and plasmid, respectively. Our results have not only enriched the genome information on R. solanacearum species complex by sequencing the first sequevar 14M strain and the largest plasmid reported in R. solanacearum to date but also revealed the variation in the repertoire of type III effectors. This will greatly contribute to the future studies on the pathogenic evolution, host adaptation, and interaction between R. solanacearum and potato.

Complete genome sequence analysis of the peanut pathogen Ralstonia solanacearum strain Rs-P.362200

“…Since the whole-genome sequencing of the first R. solanacearum strain, GMI1000, in 2002 [12], molecular biology and microbial whole-genome sequencing techniques have been considerably improved, and an increasing number of strains have been sequenced. Although R. solanacearum was found on peanuts in 1930s, it was not until 2019 that Tan first released the strains isolated from peanuts [17].…”

“…In addition to EPS, R. solanacearum exhibits many other virulence factors, such as effectors, type 4 fimbriae and polycarboxylate siderophore staphyloferrin B [15,16]. Type III effector proteins (T3Es) account for a considerable fraction of the many virulence factors, and current research on these proteins is more extensive than that on other virulence factors [17]. R. solanacearum uses syringe-like type III secretion system to inject T3Es into plant cells, interfering with the life activities of the host.…”

“…To date, the genome assemblies and annotations of 164 R. solanacearum strains have been released in the NCBI database (https://www.ncbi.nlm.nih.gov/genome/browse/ #!/prokaryotes/490/). HA4-1 is the first strain of R. solanacearum isolated from peanut and sequenced in 2019 [17]. Although increasing numbers of strains have been sequenced, more genomic sequences are still needed to fully analyze the species.…”

Avanços na identificação, variabilidade e genômica comparativa de Ralstonia solanacearum ecotipo moko no Brasil

“…Ralstonia solanacearum é considerada um complexo de espécies que apresentam variação na gama de hospedeiros, origem geográfica, patogenicidade e propriedades fisiológicas (DENNY 2006) No entanto, devido à variabilidade das espécies, o sistema hierárquico de classificação, subdividido em filotipos, sequevares, clados e clones, tem permanecido na identificação dos isolados (SANTIAGO et al 2016;LIU et al 2017a;TAN et al 2019;PROK-CHORCHIK et al 2020), assim como a designação do complexo R. solanacearum (CELLIER et al 2017;LANDRY et al 2020;GOPALAN-NAIR et al 2020;LEE et al 2020).…”

“…Na região amazônica é considerada como um fator limitante para a produção de banana (COE-LHO NETTO et al 2004). Em 1987, foi constatado no estado de Sergipe, no baixo São Francisco, plantas com sintomas de Moko nos cachos, com podridão seca de coloração parda, e escurecimento da região central do pseudocaule, mas que não apresentavam os sintomas de murcha (TALAMINI et al 2010). Esses sintomas indicaram a existência de uma variante do quadro sintomatológico de Moko, sendo denominado a partir de 2014 de síndrome Sergipe (Sergipe facies) (ALBUQUERQUE et al 2014).…”