Genome Sequence Resources of Pseudomonas syringae Strains Isolated from Sweet Cherry Orchards in Chile
2022; American Phytopathological Society; Volume: 35; Issue: 10 Linguagem: Inglês
10.1094/mpmi-04-22-0092-a
ISSN1943-7706
AutoresFrancisco Correa, M. Francisca Beltrán, Paz Millas, Zoe Moreno, Patricio Hinrichsen, Pablo Meza, Boris Sagredo,
Tópico(s)Plant Pathogens and Fungal Diseases
ResumoHomeMolecular Plant-Microbe Interactions®Vol. 35, No. 10Genome Sequence Resources of Pseudomonas syringae Strains Isolated from Sweet Cherry Orchards in Chile PreviousNext RESOURCE ANNOUNCEMENT OPENOpen Access licenseGenome Sequence Resources of Pseudomonas syringae Strains Isolated from Sweet Cherry Orchards in ChileFrancisco Correa, M. Francisca Beltrán, Paz Millas, Zoe Moreno, Patricio Hinrichsen, Pablo Meza, and Boris SagredoFrancisco CorreaInstituto de Investigaciones Agropecuarias (INIA), INIA Rayentué. Avenida Salamanca s/n, Rengo, Chile, M. Francisca BeltránInstituto de Investigaciones Agropecuarias (INIA), INIA Rayentué. Avenida Salamanca s/n, Rengo, ChilePrograma de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago, Chile, Paz MillasInstituto de Investigaciones Agropecuarias (INIA), INIA Quilamapu. Avenida Vicente Méndez 515, Chillán, Chile, Zoe MorenoInstituto de Investigaciones Agropecuarias (INIA), INIA Rayentué. Avenida Salamanca s/n, Rengo, Chile, Patricio HinrichsenInstituto de Investigaciones Agropecuarias (INIA), INIA La Platina. Avenida Santa Rosa 11610, La Pintana, Santiago, Chile, Pablo MezaInstituto de Investigaciones Agropecuarias (INIA), INIA La Platina. Avenida Santa Rosa 11610, La Pintana, Santiago, Chile, and Boris Sagredo†Corresponding author: B. Sagredo; E-mail Address: bsagredo@inia.clhttp://orcid.org/0000-0002-3277-7477Instituto de Investigaciones Agropecuarias (INIA), INIA Rayentué. Avenida Salamanca s/n, Rengo, ChileAffiliationsAuthors and Affiliations Francisco Correa1 M. Francisca Beltrán1 2 Paz Millas3 Zoe Moreno1 Patricio Hinrichsen4 Pablo Meza4 Boris Sagredo1 † 1Instituto de Investigaciones Agropecuarias (INIA), INIA Rayentué. Avenida Salamanca s/n, Rengo, Chile 2Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago, Chile 3Instituto de Investigaciones Agropecuarias (INIA), INIA Quilamapu. Avenida Vicente Méndez 515, Chillán, Chile 4Instituto de Investigaciones Agropecuarias (INIA), INIA La Platina. Avenida Santa Rosa 11610, La Pintana, Santiago, Chile Published Online:29 Sep 2022https://doi.org/10.1094/MPMI-04-22-0092-AAboutSectionsView articlePDFSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat View articleResource AnnouncementBacterial canker is an important disease on cherry trees (Prunus avium L.), caused by species of the Pseudomonas syringae complex. This pathogen is commonly found in plant tissues, being present in several niches, on and within the host at various stages of the disease cycle. The pathogen has the ability to kill both young and older trees. With poor control, cherry tree losses of up to 40% in young plants and 10 to 20% in commercial orchards can be reached (Lemus et al. 2019). This situation is critical in a country such as Chile, where the reported area planted with cherry production has risen to approximately 49,000 ha in 2021 (The Office of Agricultural Studies and Policies and The Natural Resources Information Center, Santiago, Chile), by far the most important producer and exporter from the Southern hemisphere.Bacterial samples were collected from commercial sweet cherry (Prunus avium L.) orchards from six cherry-growing regions in Chile. Samples were isolated from symptomatic tissues such as cankerous wood, leaf lesions, and necrotic cherry fruits and asymptomatic tissues such as leaf wash and macerated buds. Collected samples were grown on Difco Pseudomonas agar F (Becton, Dickinson and Company, Sparks, MD, U.S.A.) at 26°C and were checked for fluorescence. The DNA of 31 P. syringae isolates was extracted from pure cultures using silica spin columns (Epoch Life Science Inc., Sugar Land, TX, U.S.A.). Libraries were prepared and complete genomes were sequenced using HiSeq with 150-bp paired ends for the sequencing provider GENEWIZ (New York). Raw data for each genome was checked using FASTQC (Andrews 2010) and was trimmed with BBDuk (available online). Each genome was then assembled using Unicycler v0.4.9 (Wick et al. 2017) and was annotated with the Prokaryotic Genome Annotation Pipeline v4.3 (Tatusova et al. 2014). The reads and genomes were uploaded to GenBank under the BioProject number PRJNA750090. The genomes of the 31 strains were sequenced with an average coverage of 300× and were assembled into 65 contigs, on average, with an average total length of 5.9 Mbp. Table 1 lists the genome assembly and annotation statistics. To examine the relatedness of strains, a phylogeny based on concatenated multilocus sequence typing (MLST) loci was carried out using the 31 genomes sequenced in this study and 34 genomes of strains representing the phylogenomic species of P. syringae proposed by Gomila et al. (2017) (Supplementary Table S1). All sequenced genomes were compared through average nucleotide identity (ANI), using a FastANI v1.33 (Jain et al. 2018) algorithm to compare with the closest complete genomes available from the National Center for Biotechnology Information database, assuming 95% ANI value as the threshold to demarcate species. The results are presented in Table 1. The P. syringae phylogeny based on concatenated MLST loci is presented in Figure 1. All strains are part of the Pseudomonas syringae group. Twenty-nine strains were separated in two clear clades of Pseudomonas syringae pv. syringae strains, the first clade of 20 strains groups with pss9097 isolated from Prunus avium (Hulin et al. 2018), the pssCFBP2118 strain from Prunus spp. (Ruinelli et al. 2019), the pssB301D strain from Pyrus communis (Ravindran et al. 2015), and the pssB728a strain from snap bean (Feil et al. 2005). The second P. syringae pv. syringae clade, with nine strains, groups with pssCFBP4215 isolated from Prunus spp. (Ruinelli et al. 2019). Strain PslA1M171 was grouped in a clade separate from P. syringae pv. syringae and the ANI value was 98.4% with strain lapsATCC10859, belonging to P. syringae pv. lapsa and isolated from infected wheat (Kong et al. 2016). Strain PsA1M246 was grouped with strain psUMAF0158, with ANI value of 99.2%. Strain psUMAF0158 causes apical necrosis of mango trees (Martínez-García et al. 2015).Table 1. Genome data and accession numbers of Pseudomonas syringae strains isolated from sweet cherryaSequencing run statisticsAssembly statisticsStrainGeographic origin, yearTaxonomic designationPrunus avium cultivar, tissueSRA accession numberNo. of readsRefSeq assembly accessionTotal sequence lengthBest ANI hit strain, ANI valuePssA1M3Chillán, Ñuble region, 2019P. syringae pv. syringaeLeaf washSRR1843574623,050,104GCF_022560185.15,936,545GCF_900235825.1, 99.04%PssA1M25Puerto Octay, Los Lagos region, 2017P. syringae pv. syringaeCankerous woodSRR1843574527,316,962GCF_022509985.16,069,567GCF_002905815.2, 99.99%PssA1M129Rengo, O'Higgins region, 2018P. syringae pv. syringaeCv. Lapins, macerated budsSRR1843573423,050,104GCF_022510065.15,874,805GCF_002905815.2, 98.93%PssA1M140San Fernando, O'Higgins region, 2018P. syringae pv. syringaeCv. Lapins, macerated budsSRR1843572321,997,703SAMN254098615,878,182GCF_900235825.1, 98.91%PssA1M163San Vicente, O'Higgins region, 2018P. syringae pv. syringaeCv. Lapins, macerated budsSRR1843572120,738,646GCF_022510045.15,935,443GCF_000988485.1, 98.95%PslA1M171Mallo, O'Higgins region, 2018P. syringae pv. lapsaCv. Stella, macerated budsSRR1843572029,797,105GCF_022510085.15,998,665GCF_001482725.1, 98.44%PssA1M197Angol, Araucanía region, 2018P. syringae pv. syringaeCherry fruitsSRR1843571927,063,818GCF_022510105.16,059,828GCF_900235825.1, 98.93%PssA1M198Longaví, Maule region, 2018P. syringae pv. syringaeCherry fruitsSRR1843571823,893,189GCF_022510135.16,063,609GCF_002905815.2, 99.99%PssA1M200Chillán, Ñuble region, 2019P. syringae pv. syringaeCv. Sweet heart, unknown tissueSRR1843571712,039,031GCF_022510125.15,966,328GCF_900235865.1, 99.13%PssA1M201Osorno, Los Lagos region, 2019P. syringae pv. syringaeCv. Regina, unknown tissueSRR1843571610,935,367GCF_022510165.16,080,657GCF_900235825.1, 98.99%PssA1M208Coihueco, Ñuble region, 2019P. syringae pv. syringaeUnknown tissueSRR1843574410,930,650GCF_022510185.16,138,117GCF_900235825.1, 98.9%PssA1M211Chillán, ñuble region, 2019P. syringae pv. syringaeUnknown tissueSRR1843574311,227,242GCF_022510205.15,967,373GCF_900235865.1, 99.13%PssA1M242Chillán, ñuble region, 2019P. syringae pv. syringaeUnknown tissueSRR1843574211,691,000GCF_022510225.15,967,123GCF_900235865.1, 99.14%PssA1M244Máfil, Los Ríos region, 2019P. syringae pv. syringaeCankerous woodSRR1843574111,332,862GCF_022510265.15,979,725GCF_900235825.1, 98.89%PsA1M246Máfil, Los Ríos region, 2019P. syringaeUnknown tissueSRR1843574011,788,011GCF_022513625.15,725,942GCF_001281365.1, 99.22%PssA1M249Retiro, Maule region, 2019P. syringae pv. syringaeCankerous woodSRR1843573914,571,089GCF_022513665.16,025,845GCF_002905815.2, 99.99%PssA1M250Río Negro, Los Lagos region, 2019P. syringae pv. syringaeLeaf washSRR1843573816,762,628GCF_022513725.15,982,456GCF_900235825.1, 98.89%PssA1M252Retiro, Maule region, 2020P. syringae pv. syringaeCankerous woodSRR1843573715,311,610GCF_022513685.16,058,564GCF_002905815.2, 99.99%PssA1M253Osorno, los Lagos region, 2020P. syringae pv. syringaeCankerous woodSRR1843573614,272,999GCF_022513735.16,064,702GCF_002905815.2, 99.99%PssA1M254Retiro, Maule region, 2020P. syringae pv. syringaeCankerous woodSRR1843573516,667,041GCF_022513705.16,021,939GCF_900235825.1, 98.92%PssA1M258Traiguén, Araucanía region, 2020P. syringae pv. syringaeCankerous woodSRR1843573313,418,107GCF_022513765.16,057,279GCF_002905815.2, 99.99%PssA1M259San Carlos, Ñuble region, 2020P. syringae pv. syringaeCankerous woodSRR1843573213,536,000GCF_022510285.16,058,593GCF_002905815.2, 99.99%PssA1M262Osorno, los Lagos region, 2020P. syringae pv. syringaeCankerous woodSRR1843573113,821,074GCF_022510235.16,049,736GCF_900235825.1, 98.97%PssA1M263Osorno, los Lagos region, 2020P. syringae pv. syringaeLeaf washSRR1843573010,552,710GCF_022510305.15,974,704GCF_900235825.1, 98.91%PssA1M265San Carlos, Ñuble region, 2020P. syringae pv. syringaeMacerated budsSRR1843572912,642,919GCF_022513785.15,930,445GCF_900235825.1, 99.04%PssA1M266San Carlos, Ñuble region, 2020P. syringae pv. syringaeMacerated budsSRR1843572813,418,590GCF_022513815.15,968,406GCF_900235865.1, 99.16%PssA1M271San Pablo, Los Lagos region, 2020P. syringae pv. syringaeMacerated budsSRR1843572712,123,912GCF_022513805.16,065,996GCF_002905815.2, 99.99%PssA1M273Máfil, Los Ríos region, 2020P. syringae pv. syringaeCankerous woodSRR1843572613,072,223GCF_022513845.15,967,256GCF_900235865.1, 99.15%PssA1M274Río Negro, Los Lagos region, 2020P. syringae pv. syringaeCankerous woodSRR1843572511,961,877GCF_022513865.16,025,696GCF_002905815.2, 99.99%PssA1M275Río Negro, Los Lagos region, 2020P. syringae pv. syringaeCankerous woodSRR1843572411,641,873GCF_022513885.15,970,511GCF_900235865.1, 99.15%PssA1M276San Pablo, Los Lagos region, 2020P. syringae pv. syringaeCankerous woodSRR1843572212,243,792GCF_022513905.16,028,954GCF_002905815.2, 99.99%aSRA = Short Read Archive, ANI = average nucleotide identity.Table 1. Genome data and accession numbers of Pseudomonas syringae strains isolated from sweet cherryaView as image HTML Fig. 1. Composite maximum-likelihood phylogenetic tree based on multilocus sequence typing (acnB, gapA, gltA, gyrB, pgi, and rpoD). The phylogenetic relationship between the 31 sequenced genomes (black dots) and reference Pseudomonas genomes (Supplementary Table S1) is shown. Symbols show the geographical origins of the isolates: white circle (○), Araucanía region; black circle (●), Ñuble region; white square (□), Los Ríos region; black square (■), Maule region; black diamond (◆), Los lagos region; and white diamond (◊), O'Higgins region. Bootstrap values (%) for 1,000 repetitions are given at the nodes.Download as PowerPointFurther analyses of these 31 genomes led to identification of genes related with bacterial pathogens. OrthoFinder version 2.5.2 (Emms and Kelly 2019) was used to identify orthologs. We focused the search on three gene groups typical of plant pathogens: i) syringomycin gene cluster, ii) syringopeptin gene cluster, and iii) type III secretion system (T3SS) genes (Supplementary Table S2). Briefly, syringopeptin and syringomycin (syr-syp) gene clusters function as virulence determinants in the plant-pathogen interaction. The syr-syp gene cluster appears to constitute a genomic island in P. syringae pv. syringae (Hacker and Kaper 2000; Scholz-Schroeder et al. 2003). Several genes were isolated and are involved in the production of syringomycin, including syrD, syrP, syrC, syrB1, syrB2, and syrE (Guenzi et al. 1998; Mo et al. 1991; Quigley and Gross 1994; Zhang et al. 1995). The genes encoding syringopeptin synthases A, B, and C (sypA, sypB, and sypC, respectively) are part of a gene cluster 73,800 bp in size (Scholz-Schroeder et al. 2003). The T3SS is a proteic needle-like structure used by bacterial pathogens to inject effectors into living host cells without entering them (Collmer et al. 2000). All P. syringae pv. syringae genomes encode a homolog of the RNA polymerase sigma factor (hrpL), which is a master regulator of the T3SS that interacts with a conserved "hrp box" motif, promoting expression of effectors and other virulence factors (Fouts et al. 2002). Effectors, such as the gene HopAA1, present in all strains, is known for specifically enhancing the epiphytic bacterial survival and growth in plants (Lee et al. 2012) and it functions as a chlorosis-promoting factor in P. syringae pv. tomato DC3000, producing speck lesions in host tomato (Munkvold et al. 2009).The draft genome sequences of this Chilean collection of Pseudomonas syringae strains isolated from sweet cherry expand our knowledge of bacterial pathogens and of the possible mechanisms associated with virulence and infection ability, keys for developing novel disease management strategies.Data and Strains AvailabilityThe draft genome sequences and corresponding read data has been deposited in the National Center for Biotechnology Information GenBank database under BioProject PRJNA750090. 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Bacteriol. 177:4009-4020. https://doi.org/10.1128/jb.177.14.4009-4020.1995 Crossref, Medline, ISI, Google ScholarFunding: This work was funded by Ministerio Agricultura de Chile Proyecto Nucleo P15-16, Gobierno Regional de O'Higgins FIC-R 30474707-0, and Agencia Nacional de Investigación y Desarrollo Anillo Regional ACTO190001.The author(s) declare no conflict of interest. Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.DetailsFiguresLiterature CitedRelated Vol. 35, No. 10 October 2022ISSN:0894-0282e-ISSN:1943-7706 Download Metrics Article History Issue Date: 8 Oct 2022Published: 29 Sep 2022Accepted: 13 Jun 2022 Pages: 933-937 InformationCopyright © 2022 The Author(s).This is an open access article distributed under the CC BY-NC-ND 4.0 International license.Funding Ministerio Agricultura de ChileGrant/Award Number: Proyecto Nucleo P15-16 Gobierno Regional de O'HigginsGrant/Award Number: FIC-R 30474707-0 Agencia Nacional de Investigación y DesarrolloGrant/Award Number: Anillo Regional ACTO190001 Keywordsbacterial canker pathogenPseudomonas syringaesweet cherryThe author(s) declare no conflict of interest.PDF download
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