Abstract:Plasmids in 39 strains of Erwinia stewartii were examined by agarose gel electrophoresis. Most virulent strains had from 11 to 13 plasmids ranging in molecular mass from 2.8 to 210 megadaltons and contained plasmids of 210, 70, 49, 43, 29.5, 16.8, 8.8, and 2.8 megadaltons. Plasmids in strains SW2 and SS104 were characterized by both electron microscopy and agarose gel electrophoresis and may be useful as convenient references for sizing plasmids by electrophoresis. Specific size classes of plasmids could not b… Show more
“…A particular feature of Pnst subsp. stewartii strains is their ability to maintain large numbers of plasmids, with between eleven and thirteen plasmids, ranging in size from 4 to 320 kb, have previously been identified in 39 virulent strains by gel electrophoresis ( Coplin et al, 1981 ). It was postulated that up to 25% of the total Pnst subsp.…”
Section: Resultsmentioning
confidence: 99%
“…It was postulated that up to 25% of the total Pnst subsp. stewartii genomic DNA content may be plasmid-borne ( Coplin et al, 1981 ). Using available sequences for Pnst subsp.…”
Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart’s wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes, has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis. While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.
“…A particular feature of Pnst subsp. stewartii strains is their ability to maintain large numbers of plasmids, with between eleven and thirteen plasmids, ranging in size from 4 to 320 kb, have previously been identified in 39 virulent strains by gel electrophoresis ( Coplin et al, 1981 ). It was postulated that up to 25% of the total Pnst subsp.…”
Section: Resultsmentioning
confidence: 99%
“…It was postulated that up to 25% of the total Pnst subsp. stewartii genomic DNA content may be plasmid-borne ( Coplin et al, 1981 ). Using available sequences for Pnst subsp.…”
Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart’s wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes, has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis. While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.
“…Erwinia stewartii SW2, 13 mass characterized plasmids. [ 42 ] Plasmids pGMTE pGEMT-easy, AmpR Promega Corp. (Madison, WI, USA) pBluescript II SK(+) Phagemid, pUC derivative, AmpR Stratagene (La Jolla, CA, USA) pLAFR3 Tra − Mob+, RK2 replicon, tetR [ 45 ] Primers SPCF33–1-F 5’-GCACGTTCTTCTTGGAAGCA-3’ This study SPCF33–1-R 5’-CCTGGATGAAGTAGTGCAAT-3’ SPCF64–1-F 5’-CACTCAACGAGTCCCAGCTT-3’ This study SPCF64–1-R 5’-GTAATCAGGGCGTGCAGGCG-3’ J-pthA1 5′- CTTCAACTCAAACGCCGGAC-3’ [ 23 ] J-pthA2 5′- CATCGCGCTGTTCGGGAG-3′ Fig. 1 Total genomic and plasmid extractions of strains were subjected to electrophoresis ( a ) and probed with pthA probe (using primer pthAF/R DIG as the probe), Xc-A306-p33 and Xc-A306-p64 plasmid specific probes by Southern hybridization ( b , c and d , respectively).…”
Section: Resultsmentioning
confidence: 99%
“…Plasmids of Pantoea stewartii SW2 (syn. Erwinia stewartii see Table 1 ) were used as molecular size markers [ 42 ].…”
BackgroundXanthomonas citri, a causal agent of citrus canker, has been a well-studied model system due to recent availability of whole genome sequences of multiple strains from different geographical regions. Major limitations in our understanding of the evolution of pathogenicity factors in X. citri strains sequenced by short-read sequencing methods have been tracking plasmid reshuffling among strains due to inability to accurately assign reads to plasmids, and analyzing repeat regions among strains. X. citri harbors major pathogenicity determinants, including variable DNA-binding repeat region containing Transcription Activator-like Effectors (TALEs) on plasmids. The long-read sequencing method, PacBio, has allowed the ability to obtain complete and accurate sequences of TALEs in xanthomonads. We recently sequenced Xanthomonas citri str. Xc-03-1638-1-1, a copper tolerant A group strain isolated from grapefruit in 2003 from Argentina using PacBio RS II chemistry. We analyzed plasmid profiles, copy number and location of TALEs in complete genome sequences of X. citri strains.ResultsWe utilized the power of long reads obtained by PacBio sequencing to enable assembly of a complete genome sequence of strain Xc-03-1638-1-1, including sequences of two plasmids, 249 kb (plasmid harboring copper resistance genes) and 99 kb (pathogenicity plasmid containing TALEs). The pathogenicity plasmid in this strain is a hybrid plasmid containing four TALEs. Due to the intriguing nature of this pathogenicity plasmid with Tn3-like transposon association, repetitive elements and multiple putative sites for origins of replication, we might expect alternative structures of this plasmid in nature, illustrating the strong adaptive potential of X. citri strains. Analysis of the pathogenicity plasmid among completely sequenced X. citri strains, coupled with Southern hybridization of the pathogenicity plasmids, revealed clues to rearrangements of plasmids and resulting reshuffling of TALEs among strains.ConclusionsWe demonstrate in this study the importance of long-read sequencing for obtaining intact sequences of TALEs and plasmids, as well as for identifying rearrangement events including plasmid reshuffling. Rearrangement events, such as the hybrid plasmid in this case, could be a frequent phenomenon in the evolution of X. citri strains, although so far it is undetected due to the inability to obtain complete plasmid sequences with short-read sequencing methods.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4408-9) contains supplementary material, which is available to authorized users.
“…Bacteria can contain more than one plasmid, since some of them can be lost during division. For instance, Pantoea stewartii can harbor up to 13 different plasmids [ 39 ]. Although bacteria usually transfer plasmids within their population [ 40 ], horizontal transfer of genetic information remains quite common in the prokaryotic world.…”
Section: The Most Significant Phytopathogensmentioning
In recent years, there has been an increase in the number of diseases caused by bacterial, fungal, and viral infections. Infections affect plants at different stages of agricultural production. Depending on weather conditions and the phytosanitary condition of crops, the prevalence of diseases can reach 7080% of the total plant population, and the yield can decrease in some cases down to 8098%. Plants have innate cellular immunity, but specific phytopathogens have an ability to evade that immunity. This article examined phytopathogens of viral, fungal, and bacterial nature and explored the concepts of modern plant protection, methods of chemical, biological, and agrotechnical control, as well as modern methods used for identifying phytopathogens.
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