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Genome sequencing and analysis of Kloeckera apiculata strain 34-9, a biocontrol agent against postharvest pathogens in citrus

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Abstract

Kloeckera apiculata, as the anamorphic state of Hanseniaspora uvarum from the Ascomycota phylum, plays an important role in the inhibition of fungal diseases in plants and spontaneous wine fermentation. This study was performed to sequence and analyze the whole genome of K. apiculata strain 34-9; This analysis provides further genomic features and assists functional research. The complete genome was determined using an Illumina HiSeq 2000 system applying paired-end and mate-pair methods to construct four reads libraries. The data assembly of all the reads resulted in a total genome size of 8.1 Mb, including 106 contigs, which were assembled into 41 scaffolds with a 31.95 % G+C content and a 234X sequence coverage. The performance of the gene prediction and functional annotation revealed that 2724 of 3786 protein-coding genes matched the KOG database, and 1127 genes were classified into GO categories. Further genome features analyses found 1066 microsatellite sites, 71 tRNAs, 3 rRNAs and 3 microRNAs in the genomic DNA. A prediction of the metabolic pathways identified potentially crucial genes for explaining the phenylalanine pathway involved in biocontrol. Comparisons with the typical yeasts Lachancea thermotolerans, Kluyveromyces lactis and Saccharomyces cerevisiae revealed the particularity and difference of K. apiculata strain 34-9. The genome alignments among Hanseniaspora vineae T02/19AF, K. apiculata DSM 2768 and 34-9 indicated numerous homologous regions distributed over the genomes between strain DSM2768 and 34-9. A SSR analysis identified that mono- and tri- nucleotide repeat types were more abundant in all six types, likely affecting the evolution of K. apiculata.

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References

  • Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang HZ, Lopez R, Magrane M et al (2004) UniProt: the universal protein knowledgebase. Nucl Acids Res 32:115–119

    Article  Google Scholar 

  • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al (2000) Gene Ontology: tool for the unification of biology. Nat Genet 25:25–29

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aylor DL, Price EW, Carbone I (2006) SNAP: combine and Map modules for multilocus population genetic analysis. Bioinformatics 22:1399–1401

    Article  CAS  PubMed  Google Scholar 

  • Besemer J, Borodovsky M (2005) GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucl Acids Res 33:451–454

    Article  Google Scholar 

  • Bink FJ (2010) Molekulargenetische und physiologische Untersuchungen an der Weinhefe Kloeckera apiculata (Hanseniaspora uvarum). Germany: Universitat Osnabruck dissertation

  • Cabranes C, Mangas JJ, Blanco D (1997) Selection and biochemical characterisation of Saccharomyces cerevisiae and Kloeckera apiculata strains isolated from Spanish cider. J Inst Brewing 103:165–169

    Article  CAS  Google Scholar 

  • Cai GH, Leadbetter CW, Muehlbauer MF, Molnar TJ, Hillman BI (2013) Genome-wide microsatellite identification in the fungus Anisogramma anomala using illumina sequencing and genome assembly. PLoS ONE 8:82408

    Article  Google Scholar 

  • Caruso M, Capece A, Saizano G, Romano P (2002) Typing of Saccharomyces cerevisiae and Kloeckera apiculata strains from Aglianico wine. Lett Appl Microbiol 34:323–328

    Article  CAS  PubMed  Google Scholar 

  • Clemente-Jimenez JM, Mingorance-Cazoria L, Martinez-Rodriguez S, Las Heras-Vazquez FJ, Rodriguez-Vico F (2005) Influence of sequential yeast mixtures on wine fermentation. Int J Food Microbiol 98:301–308

    Article  CAS  PubMed  Google Scholar 

  • Consortium GO (2004) The Gene Ontology (GO) database and informatics resource. Nucl Acids Res 32:258–261

    Article  Google Scholar 

  • Consortium U (2014) Activities at the universal protein resource (UniProt). Nucl Acids Res 42:191–198

    Article  Google Scholar 

  • Darling AC, Mau B, Blattner FR, Perna NT (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14:1394–1403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5:11147

    Article  Google Scholar 

  • Dickinson JR, Salgado LE, Hewlins MJ (2003) The catabolism of amino acids to long chain and complex alcohols in Saccharomyces cerevisiae. J Biol Chem 278:8028–8034

    Article  CAS  PubMed  Google Scholar 

  • Dyrløv Bendtsen J, Nielsen H, Heijne GV, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340:783–795

    Article  Google Scholar 

  • Erten H (2002) Relations between elevated temperatures and fermentation behaviour of Kloeckera apiculata and Saccharomyces cerevisiae associated with winemaking in mixed cultures. World J Microb Biot 18:377–382

    Article  Google Scholar 

  • Farias ME, Manca de Nadra MC (2003) Flocculation and cell surface characterization of Kloeckera apiculata from wine. J Appl Microbiol 95:457–462

    Article  CAS  PubMed  Google Scholar 

  • Fromm DP, Sundaramurthy A, James Schuck P, Kino G, Moerner WE (2004) Gap-dependent optical coupling of single “bowtie” nanoantennas resonant in the visible. Nano Lett 4:957–961

    Article  CAS  Google Scholar 

  • Garcia-Martos P, Hernandez-Molina JM, Galan F, Ruiz-Henestrosa JR, Garcia-Agudo R, Palomo MJ, Mira J (1998) Isolation of Hanseniaspora uvarum (Kloeckera apiculata) in humans. Mycopathologia 144:73–75

    Article  PubMed  Google Scholar 

  • Gil JV, Mateo JJ, Jimenez M, Pastor A, Huerta T (1996) Aroma compounds in wine as influenced by apiculate yeasts. J Food Sci 61:1247–1250

    Article  CAS  Google Scholar 

  • Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M et al (1996) Life with 6000 genes. Science 274:546–567

    Article  CAS  PubMed  Google Scholar 

  • Guillamón JM, Sabate J, Barrio E, Cano J, Querol A (1998) Rapid identification of wine yeast species based on RFLP analysis of the ribosomal internal transcribed spacer (ITS) region. Arch Microbiol 169:387–392

    Article  PubMed  Google Scholar 

  • Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucl Acids Res 28:27–30

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucl Acids Res 32:277–280

    Article  Google Scholar 

  • Korres AM, Buss DS, Ventura JA, Fernandes PM (2011) Candida krusei and Kloeckera apis inhibit the causal agent of pineapple fusariosis, Fusarium guttiforme. Fungal Biol 115:1251–1258

    Article  PubMed  Google Scholar 

  • Krogh A, Larsson B, Von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567–580

    Article  CAS  PubMed  Google Scholar 

  • Lagesen K, Hallin P, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucl Acids Res 35:3100–3108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li W, Jaroszewski L, Godzik A (2001) Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 17:282–283

    Article  CAS  PubMed  Google Scholar 

  • Liu HM, Guo JH, Cheng YJ, Luo L, Liu P, Wang BQ, Deng BX, Long CA (2010) Control of gray mold of grape by Hanseniaspora uvarum and its effects on postharvest quality parameters. Ann Microbiol 60:31–35

    Article  Google Scholar 

  • Liu J, Sui Y, Wisniewski M, Droby S, Liu YS (2013) Review: utilization of antagonistic yeasts to manage postharvest fungal diseases of fruit. Int J Food Microbiol 167:153–160

    Article  PubMed  Google Scholar 

  • Liu P, Cheng YJ, Yang M, Liu YJ, Chen K, Long CA, Deng XX (2014a) Mechanisms of action for 2-phenylethanol isolated from Kloeckera apiculata in control of Penicillium molds of citrus fruits. BMC Microbiol 14:242

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu P, Fang JF, Chen K, Long CA, Cheng YJ (2014b) Phenylethanol promotes adhesion and biofilm formation of the antagonistic yeast Kloeckera apiculata for the control of blue mold on citrus. FEMS Yeast Res 14:536–546

    Article  CAS  Google Scholar 

  • Long CA, Gao Y (2009) Kloeckera apiculata strain (34-9) to control Botrytis cinerea during the pre-and postharvest handling of strawberries. Ann Microbiol 59:77–81

    Article  Google Scholar 

  • Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res 25:955–964

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He SQ, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ et al (2003) CDD: a curated Entrez database of conserved domain alignments. Nucl Acids Res 31:383–387

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martin KJ, Rygiewicz PT (2005) Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts. BMC Microbiol 5:28

    Article  PubMed  PubMed Central  Google Scholar 

  • Medema MH, Blin K, Cimermancic P, Jager VD, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucl Acids Res 39:339–346

    Article  Google Scholar 

  • Medina K, Boido E, Dellacassa E, Carrau F (2012) Growth of non-Saccharomyces yeasts affects nutrient availability for Saccharomyces cerevisiae during wine fermentation. Int J Food Microbiol 157:245–250

    Article  CAS  PubMed  Google Scholar 

  • Moreira N, Mendes F, Guedes de Pinho P, Hogg T, Vasconcelos I (2008) Heavy sulphur compounds, higher alcohols and esters production profile of Hanseniaspora uvarum and Hanseniaspora guilliermondii grown as pure and mixed cultures in grape must. Int J Food Microbiol 124:231–238

    Article  CAS  PubMed  Google Scholar 

  • Pallmann CL, Brown JA, Olineka TL, Cocolin L, Mills DA, Bisson LF (2001) Use of WL medium to profile native flora fermentations. Am J Enol Viticult 52:198–203

    CAS  Google Scholar 

  • Plata C, Millan C, Mauricio JC, Ortega JM (2003) Formation of ethyl acetate and isoamyl acetate by various species of wine yeasts. Food Microbiol 20:217–224

    Article  CAS  Google Scholar 

  • Pramateftaki PV, Kouvelis VN, Lanaridis P, Typas MA (2006) The mitochondrial genome of the wine yeast Hanseniaspora uvarum: a unique genome organization among yeast/fungal counterparts. FEMS Yeast Res 6:77–90

    Article  CAS  PubMed  Google Scholar 

  • Price EW, Carbone I (2005) SNAP: workbench management tool for evolutionary population genetic analysis. Bioinformatics 21:402–404

    Article  CAS  PubMed  Google Scholar 

  • Price AL, Jones NC, Pevzner PA (2005) De novo identification of repeat families in large genomes. Bioinformatics 21:351–358

    Article  Google Scholar 

  • Radler F, Schmitt MJ, Meyer B (1990) Killer toxin of Hanseniaspora uvarum. Arch Microbiol 154:175–178

    Article  CAS  PubMed  Google Scholar 

  • Riedel T, Teshima H, Petersen J, Fiebig A, Davenport K, Daligault H, Erkkila T, Gu W, Munk C, Xu Y et al (2013) Genome sequence of the Leisingera aquimarina type strain (DSM 24565 T), a member of the marine Roseobacter clade rich in extrachromosomal elements. Stand Genom Sci 8:389

    Article  Google Scholar 

  • Ro DK, Douglas CJ (2004) Reconstitution of the entry point of plant phenylpropanoid metabolism in yeast (Saccharomyces cerevisiae) implications for control of metabolic flux into the phenylpropanoid pathway. J Biol Chem 279:2600–2607

    Article  CAS  PubMed  Google Scholar 

  • Romano P, Suzzi G, Comi G, Zironi R (1992) Higher alcohol and acetic acid production by apiculate wine yeasts. J Appl Bacteriol 73:126–130

    Article  CAS  Google Scholar 

  • Romano P, Suzzi G, Domizio P, Fatichenti F (1997) Secondary products formation as a tool for discriminating non-Saccharomyces wine strains. Anton Van Leeuw 71:239–242

    Article  CAS  Google Scholar 

  • Romano P, Fiore C, Paraggio M, Caruso M, Capece A (2003) Function of yeast species and strains in wine flavour. Int J Food Microbiol 86:169–180

    Article  CAS  PubMed  Google Scholar 

  • Schuller D, Alves H, Dequin S, Casal M (2005) Ecological survey of Saccharomyces cerevisiae strains from vineyards in the Vinho Verde Region of Portugal. FEMS Microbiol Ecol 51:167–177

    Article  CAS  PubMed  Google Scholar 

  • Smit AF, Hubley R, Green P (1996) RepeatMasker Open-3.0

  • Sosa OA, Manca de Nadra MC, Farias ME (2008a) Behaviour of Kloeckera apiculata flocculent strain in coculture with Saccharomyces cerevisiae. Food Technol Biotech 46:413–418

    CAS  Google Scholar 

  • Sosa OA, Manca de Nadra MC, Farias ME (2008b) Modification by glucose of the flocculent phenotype of a Kloeckera apiculata wine strain. J Ind Microbiol Biot 35:851–857

    Article  CAS  Google Scholar 

  • Stanke M, Morgenstern B (2005) AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucl Acids Res 33:465–467

    Article  Google Scholar 

  • Stanke M, Steinkamp R, Waack S, Morgenstern B (2004) AUGUSTUS: a web server for gene finding in eukaryotes. Nucl Acids Res 32:309–312

    Article  Google Scholar 

  • Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN et al (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41

    Article  PubMed  PubMed Central  Google Scholar 

  • Tóth G, Gáspári Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10:967–981

    Article  PubMed  PubMed Central  Google Scholar 

  • Vezzi F, Narzisi G, Mishra B (2012) Reevaluating assembly evaluations with feature response curves: GAGE and assemblathons. PLoS ONE 7:52210

    Article  Google Scholar 

  • Wolfe KH (2006) Comparative genomics and genome evolution in yeasts. Philos Trans R Soc B 361:403–412

    Article  CAS  Google Scholar 

  • Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S et al (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415:871–880

    Article  CAS  PubMed  Google Scholar 

  • Zaluga J, Stragier P, Baeyen S, Haegeman A, Van Vaerenbergh J, Maes M, De Vos P (2014) Comparative genome analysis of pathogenic and non-pathogenic Clavibacter strains reveals adaptations to their lifestyle. BMC Genom 15:392

    Article  Google Scholar 

  • Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou W, Hu YY, Sui ZH, Fu F (2013) Genome survey sequencing and genetic background characterization of Gracilariopsis lemaneiformis (Rhodophyta) Based on next-generation sequencing. PLoS ONE 8:69909

    Article  Google Scholar 

  • Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20:176–183

    Article  CAS  PubMed  Google Scholar 

  • Zohre DE, Erten H (2002) The influence of Kloeckera apiculata and Candida pulcherrima yeasts on wine fermentation. Process Biochem 38:319–324

    Article  CAS  Google Scholar 

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Acknowledgments

This work was financially supported by the National Basic Research Program of China (973 program; no: 2013CB127100), the Fundamental Research Funds for the Central Universities (Program no. 2662016PY114) and the National Natural Science Foundation of China (Grant no. 31672205).

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Authors and Affiliations

  1. Key Laboratory of Horticultural Plant Biology of the Ministry of Education, National Centre of Citrus Breeding, Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China

    Kai Chen, Feng Zheng & Chao-an Long

  2. Institute of Pomology and Tea, Hubei Academy of Agricultural Sciences, Wuhan, People’s Republic of China

    Xiaoping Yang

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  1. Kai Chen
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  2. Xiaoping Yang
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  3. Feng Zheng
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Correspondence to Chao-an Long.

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Chen K, Yang XP, Zheng F, and Long CA declares that they have no conflict of interest.

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This article does not contain any studies with human subjects or animals performed by any of the authors.

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This Whole Genome Sequencing project has been deposited at DDBJ/EMBL/GenBank under the accession JPPO00000000. The version described in this paper is version JPPO02000000.

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Chen, K., Yang, X., Zheng, F. et al. Genome sequencing and analysis of Kloeckera apiculata strain 34-9, a biocontrol agent against postharvest pathogens in citrus. Genes Genom 39, 87–99 (2017). https://doi.org/10.1007/s13258-016-0475-6

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