Portal de Periódicos da CAPES

Genome Sequence Resources of Klebsiella michiganensis AKKL-001, Which Causes Bacterial Blight of Mulberry

2022; American Phytopathological Society; Volume: 35; Issue: 4 Linguagem: Inglês

10.1094/mpmi-09-21-0222-a

1943-7706

Longhui Luo, Yuxin Huang, Jiping Liu,

Genomics and Phylogenetic Studies

HomeMolecular Plant-Microbe Interactions®Vol. 35, No. 4Genome Sequence Resources of Klebsiella michiganensis AKKL-001, Which Causes Bacterial Blight of Mulberry PreviousNext RESOURCE ANNOUNCEMENT OPENOpen Access licenseGenome Sequence Resources of Klebsiella michiganensis AKKL-001, Which Causes Bacterial Blight of MulberryLonghui Luo, Yuxin Huang, and Jiping LiuLonghui Luohttps://orcid.org/0000-0002-1050-1031College of Animal Science, Regional Sericulture Training Center for Asia-Pacific, South China Agriculture University, Wushan Road, Guangzhou, Guangdong 510642, China, Yuxin HuangCollege of Animal Science, Regional Sericulture Training Center for Asia-Pacific, South China Agriculture University, Wushan Road, Guangzhou, Guangdong 510642, China, and Jiping Liu†Corresponding author: J. Liu; E-mail Address: liujiping@scau.edu.cnCollege of Animal Science, Regional Sericulture Training Center for Asia-Pacific, South China Agriculture University, Wushan Road, Guangzhou, Guangdong 510642, China AffiliationsAuthors and Affiliations Longhui Luo Yuxin Huang Jiping Liu † College of Animal Science, Regional Sericulture Training Center for Asia-Pacific, South China Agriculture University, Wushan Road, Guangzhou, Guangdong 510642, China Published Online:14 Mar 2022https://doi.org/10.1094/MPMI-09-21-0222-AAboutSectionsPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Genome AnnouncementKlebsiella michiganensis is a pathogenic bacterium related to mulberry (Morus alba L.) wilt disease. Here, we present the complete genome sequence of Klebsiella michiganensis AKKL-001, isolated from diseased mulberry in Guangxi, China. The complete genome sequence of K. michiganensis AKKL-001 was characterized by a 6,149,586-base circular chromosome with a 55.80% GC content. This genome will contribute to epidemiological and comparative genomic studies of genus Klebsiella. To our knowledge, this is the first genome announcement of a mulberry-associated bacterium from the genus Klebsiella.Mulberry (Morus alba L.) is a woody plant belonging to the family Moraceae and is widespread in Asia, Africa, and Europe and has diverse beneficial characters (Dhanyalakshmi and Nataraja 2018). Klebsiella spp. are a facultative aerobic/anaerobic bacteria with a wide geographical distribution (Bagley 1985), most of which are reported as conditional pathogens of humans and animals (Marques et al. 2019; Rodríguez-Medina et al. 2019). But for plants, Klebsiella spp. are mostly reported as nitrogen-fixing bacteria that are closely related to the healthy growth of plants (Chen et al. 2016; Lin et al. 2015). In recent years, reports in strains belonging to the Klebsiella genus and their interactions with plant diseases has increased (Fan et al. 2015; Huang et al. 2020). Strain AKKL-001 was isolated from surface-sterilized root tissues of diseased mulberry in China, on Luria-Bertani medium at 28°C (per liter of medium: 10 g of tryptone, 5 g of yeast extract, 10 g of NaCl) (Bertani 1951). Strain AKKL-001 was inoculated on mulberry seedlings under greenhouse conditions and showed similar wilting symptoms to those in the field. The complete genome of K. michiganensis AKKL-001 was sequenced and assembled, using Illumina reads, to gain detailed insight into the genomic features and pathogenic mechanism of the strain. A bacterial sample of K. michiganensis AKKL-001 has been deposited in the International Depositary Authority (Guangdong Microbial Culture Collection Center, Guangzhou, China), assigned accession number GDMCC 1.1603.High–molecular weight DNA was extracted from overnight bacterial cultures using a bacteria genomic DNA extraction kit (Sangon Biotech Co., Ltd.). DNA quantity was assessed using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific) and a Qubit 2.0 fluorometer (Life Technologies). DNA integrity was assessed using the quantitative PCR method and the Agilent 2100 BioAnalyzer system (Agilent). For paired-end sequencing, whole-genome DNA was used to prepare a DNA library with a 350-bp insert. Whole-genome sequencing was conducted with manufactured 2 × 150-bp alignment reads on an Illumina Hiseq4000 System by Science Corporation of Gene Technology Co., Ltd. The whole-genome sequencing approach resulted in 10,802,416 high-quality filtered reads with an average paired-end read length of 500 bp and 526-fold sequencing coverage, on average. Quality filtered reads were assembled using SPAdes, version 3.5.0 (Bankevich et al. 2012). The genome sequence data were uploaded to Similar Genome Finder Server (Davis et al. 2020) to determine the accurate and reliable taxonomic position. The genome was automatically annotated using the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline (Haft et al. 2018) and the RAST tool kit (Overbeek et al. 2014). Using gene ontology (GO) (Ashburner et al. 2000), Kyoto Encyclopedia of Genes and Genomes (KEGG) (Kanehisa et al. 2016), and Cluster of Orthologous Groups of proteins (COG) (Galperin et al. 2015) for gene function annotation. To identify virulence-associated genes, carbohydrate-active enzymes (CAZymes) were predicted by the CAZymes database (Cantarel et al. 2009). Secondary metabolism gene clusters were annotated using antiSMASH (Medema et al. 2011). Identification of genomic islands (GIs) was performed using the IslandViewer 4 platform and the SIGI-HMM, IslandPick, IslandPath-DIMOB, and Islander prediction methods (Bertelli et al. 2017). The CRISPR recognition tool (Bland et al. 2007) was used to predict CRISPRs in the genome.The complete genome of K. michiganensis AKKL-001 contained one circular 6,149,586-base circular chromosome with no plasmid. Comparative analysis of genome sequencing information and annotation results of AKKL-001 and its two closest strains of K. michiganensis can be found in Table 1. Strain AKKL-001 is most closely related to K. michiganensis F107 (NCBI accession number CP024643) isolated from human sputum, with which it shares 99.25% average nucleotide identity, by using OAT software (Lee et al. 2016). The G+C content was 55.80%, consisting of 5,581 coding genes, 87 transfer RNA genes, 25 ribosomal RNA genes, and eight noncoding RNA genes, and 91 pseudogenes were predicted as well. By using functional protein alignments, 5,023 proteins were assigned to the COG database, 1,269 proteins were assigned to GO terms, and 1,125 proteins were mapped to KEGG pathways. Compared with F107 and BD1007, AKKL-001 has more COG and KEGG genes (Table 1). The K. michiganensis AKKL-001 genome presents several genes related to plant disease, including genes for plant cell wall–degrading enzymes and genes involved in the biosynthesis of type I and type II secretion systems. Furthermore, it contains genes for nitrogen fixation. By using the IslandViewer 4 platform, CAZymes, and antiSMASH bacterial version, 86 GIs, 171 CAZymes, and 108 secondary metabolite–related synthetic genes were identified, respectively. The genomic information of K. michiganensis AKKL-001 will be important to clarify the virulence as well as for understanding the evolutionary history of Klebsiella genus.Table 1. Genome assembly statistics of Klebsiella michiganensis AKKL-001 and its two closest strainsParameterKlebsiella michiganensis strainAKKL-001 (this work)F107BD177HostMorus albaHomo sapiensBactrocera dorsalisNCBI accessionCP060111.1CP024643.1CP048108.1Genome size (bp)61,49,58661,52,54568,12,698Genome coverage526.0×79.8×100.0×GC content55.80%55.37%55.05%Contig(s)1 chromosome1 chromosome, 2 plasmid1 chromosome, 4 plasmidAverage nucleotide identity (%)NA99.25%97.90%Gene (Total)5,7926,0846,508Gene (coding)5,5815,6616,201Transfer RNA878685Ribosomal RNA252525Noncoding RNA81013Pseudogenes91302184Proteins with COG assignments502327713756Proteins with KEGG assignments112511021132Proteins with gene ontology assignments1269710830Nitrogen-fixation gene171717CRISPRs003Genomic islandsIslandPick423455SIGI-HMM311527IslandPath-DIMOB13015CAZymes functional classification and corresponding geneGlycoside hydrolase958487Glycosyl transferases444140Carbohydrate esterase101011Auxiliary activity656Polysaccharide lyase7108Carbohydrate-binding module988Secondary metabolites related synthetic genesHomoserine lactone0019Type I polyketide synthase28035Nonribosomal peptide synthetase604271Thiopeptide202020Ladderane0019N-acyl amino acid0064Table 1. Genome assembly statistics of Klebsiella michiganensis AKKL-001 and its two closest strainsView as image HTML Data AvailabilityThe genome sequence of Klebsiella michiganensis AKKL-001 has been deposited in NCBI GenBank in BioProject number PRJNA655785 under accession number CP060111.1. The original data have been deposited in the NCBI Sequence Read Archive under accession number SRX8904638.The author(s) declare no conflict of interest.Literature CitedAshburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., and Sherlock, G. 2000. Gene ontology: Tool for the unification of biology. Nat. Genet. 25:25-29. https://doi.org/10.1038/75556 Crossref, Medline, ISI, Google ScholarBagley, S. T. 1985. Habitat association of Klebsiella species. Infect. Control 6:52-58. https://doi.org/10.1017/S0195941700062603 Crossref, Medline, Google ScholarBankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., Pyshkin, A. V., Sirotkin, A. V., Vyahhi, N., Tesler, G., Alekseyev, M. A., and Pevzner, P. A. 2012. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19:455-477. https://doi.org/10.1089/cmb.2012.0021 Crossref, Medline, ISI, Google ScholarBertani, G. 1951. Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J. Bacteriol. 62:293-300. https://doi.org/10.1128/jb.62.3.293-300.1951 Crossref, Medline, ISI, Google ScholarBertelli, C., Laird, M. R., Williams, K. P., Simon Fraser University Research Computing Group, Lau, B. Y., Hoad, G., Winsor, G. L., and Brinkman, F. S. L. 2017. IslandViewer 4: Expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res. 45 (W1):W30-W35. https://doi.org/10.1093/nar/gkx343 Crossref, Medline, ISI, Google ScholarBland, C., Ramsey, T. L., Sabree, F., Lowe, M., Brown, K., Kyrpides, N. C., and Hugenholtz, P. 2007. CRISPR recognition tool (CRT): A tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 8:209. https://doi.org/10.1186/1471-2105-8-209 Crossref, Medline, ISI, Google ScholarCantarel, B. L., Coutinho, P. M., Rancurel, C., Bernard, T., Lombard, V., and Henrissat, B. 2009. The Carbohydrate-Active EnZymes database (CAZy): An expert resource for glycogenomics. Nucleic Acids Res. 37 (Database):D233-D238. https://doi.org/10.1093/nar/gkn663 Crossref, Medline, ISI, Google ScholarChen, M., Li, Y., Li, S., Tang, L., Zheng, J., and An, Q. 2016. Genomic identification of nitrogen-fixing Klebsiella variicola, K. pneumoniae and K. quasipneumoniae. J. Basic Microbiol. 56:78-84. https://doi.org/10.1002/jobm.201500415 Crossref, Medline, ISI, Google ScholarDavis, J. J., Wattam, A. R., Aziz, R. K., Brettin, T., Butler, R., Butler, R. M., Chlenski, P., Conrad, N., Dickerman, A., Dietrich, E. M., Gabbard, J. L., Gerdes, S., Guard, A., Kenyon, R. W., Machi, D., Mao, C., Murphy-Olson, D., Nguyen, M., Nordberg, E. K., Olsen, G. J., Olson, R. D., Overbeek, J. C., Overbeek, R., Parrello, B., Pusch, G. D., Shukla, M., Thomas, C., VanOeffelen, M., Vonstein, V., Warren, A. S., Xia, F., Xie, D., Yoo, H., and Stevens, R. 2020. The PATRIC bioinformatics resource center: Expanding data and analysis capabilities. Nucleic Acids Res. 48 (D1):D606-D612. Medline, ISI, Google ScholarDhanyalakshmi, K. H., and Nataraja, K. N. 2018. Mulberry (Morus spp.) has the features to treat as a potential perennial model system. Plant Signal. Behav. 13:e1491267. https://doi.org/10.1080/15592324.2018.1491267 Medline, ISI, Google ScholarFan, H. C., Zeng, L., and Yang, P. W. 2015. First report of banana soft rot caused by Klebsiella variicola in China. Plant Dis. 100:517. Link, ISI, Google ScholarGalperin, M. Y., Makarova, K. S., Wolf, Y. I., and Koonin, E. V. 2015. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 43 (D1):D261-D269. https://doi.org/10.1093/nar/gku1223 Crossref, Medline, ISI, Google ScholarHaft, D. H., DiCuccio, M., Badretdin, A., Brover, V., Chetvernin, V., O'Neill, K., Li, W., Chitsaz, F., Derbyshire, M. K., Gonzales, N. R., Gwadz, M., Lu, F., Marchler, G. H., Song, J. S., Thanki, N., Yamashita, R. A., Zheng, C., Thibaud-Nissen, F., Geer, L. Y., Marchler-Bauer, A., and Pruitt, K. D. 2018. RefSeq: An update on prokaryotic genome annotation and curation. Nucleic Acids Res. 46 (D1):D851-D860. https://doi.org/10.1093/nar/gkx1068 Crossref, Medline, ISI, Google ScholarHuang, M., He, P., Munir, S., Wu, Y., Li, X., He, P., and He, Y. 2020. Ecology and etiology of bacterial top rot in maize caused by Klebsiella pneumoniae KpC4. Microb. Pathog. 139:103906. https://doi.org/10.1016/j.micpath.2019.103906 Crossref, Medline, ISI, Google ScholarKanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M. 2016. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44 (D1):D457-D462. https://doi.org/10.1093/nar/gkv1070 Crossref, Medline, ISI, Google ScholarLee, I., Ouk Kim, Y., Park, S. C., and Chun, J. 2016. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int. J. Syst. Evol. Microbiol. 66:1100-1103. https://doi.org/10.1099/ijsem.0.000760 Crossref, Medline, ISI, Google ScholarLin, L., Wei, C., Chen, M., Wang, H., Li, Y., Li, Y., Yang, L., and An, Q. 2015. Complete genome sequence of endophytic nitrogen-fixing Klebsiella variicola strain DX120E. Stand. Genomic Sci. 10:22. https://doi.org/10.1186/s40793-015-0004-2 Crossref, Medline, ISI, Google ScholarMarques, C., Menezes, J., Belas, A., Aboim, C., Cavaco-Silva, P., Trigueiro, G., Telo Gama, L., and Pomba, C. 2019. Klebsiella pneumoniae causing urinary tract infections in companion animals and humans: Population structure, antimicrobial resistance and virulence genes. J. Antimicrob. Chemother. 74:594-602. https://doi.org/10.1093/jac/dky499 Crossref, Medline, ISI, Google ScholarMedema, M.H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M.A., Weber, T., Takano, E. and Breitling, R. 2011. antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res. 39:W339-W346. Crossref, Medline, ISI, Google ScholarOverbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T., Edwards, R. A., Gerdes, S., Parrello, B., Shukla, M., Vonstein, V., Wattam, A. R., Xia, F., and Stevens, R. 2014. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res. 42 (D1):D206-D214. https://doi.org/10.1093/nar/gkt1226 Crossref, Medline, ISI, Google ScholarRodríguez-Medina, N., Barrios-Camacho, H., Duran-Bedolla, J., and Garza-Ramos, U. 2019. Klebsiella variicola: An emerging pathogen in humans. Emerg. Microbes Infect. 8:973-988. https://doi.org/10.1080/22221751.2019.1634981 Crossref, Medline, ISI, Google ScholarFunding: Funding was provided by China Agriculture Research System of MOF and MARA (CARS-18-ZJ0304).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. 4 April 2022ISSN:0894-0282e-ISSN:1943-7706 Download Metrics Downloaded 706 times Article History Issue Date: 12 Apr 2022Published: 14 Mar 2022Accepted: 8 Jan 2022 Pages: 349-351 InformationCopyright © 2022 The Author(s).This is an open access article distributed under the CC BY-NC-ND 4.0 International license.FundingChina Agriculture Research System of MOF and MARAGrant/Award Number: CARS-18-ZJ0304Keywordsbacterial pathogensgenomeKlebsiella michiganensismulberry bacterial wiltThe author(s) declare no conflict of interest.PDF download