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. 2014 Jun 19;5(1):135–140. doi: 10.5598/imafungus.2014.05.01.13

IMA Genome-F 2: Ceratocystis manginecans, Ceratocystis moniliformis, Diplodia sapinea

Draft genome sequences of Diplodia sapinea, Ceratocystis manginecans, and Ceratocystis moniliformis

Magriet A van der Nest 1, Wubetu Bihon 1,2, Lieschen De Vos 1, Kershney Naidoo 1, Danielle Roodt 1, Enrico Rubagotti 4, Bernard Slippers 1, Emma T Steenkamp 3, P Markus Wilken 1, Andrea Wilson 1, Michael J Wingfield 1, Brenda D Wingfield 1,
PMCID: PMC4107891  PMID: 25083413

Abstract

The draft nuclear genomes of Diplodia sapinea, Ceratocystis moniliformis s. str., and C. manginecans are presented. Diplodia sapinea is an important shoot-blight and canker pathogen of Pinus spp., C. moniliformis is a saprobe associated with wounds on a wide range of woody angiosperms and C. manginecans is a serious wilt pathogen of mango and Acacia mangium. The genome size of D. sapinea is estimated at 36.97 Mb and contains 13 020 predicted genes. Ceratocystis moniliformis includes 25.43 Mb and is predicted to encode at least 6 832 genes. This is smaller than that reported for the mango wilt pathogen C. manginecans which is 31.71 Mb and is predicted to encode at least 7 494 genes. The latter is thus more similar to C. fimbriata s.str., the type species of the genus. The genome sequences presented here provide an important resource to resolve issues pertaining to the taxonomy, biology and evolution of these fungi.

Keywords: Diplodia pinea, Endophyte, Dothideomycetes, mango wilt, Ceratocystis fimbriata

Acknowledgments

These genome projects were financed by the University of Pretoria, the Department of Science and Technology (DST)/National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology, Genomics Research Institute (University of Pretoria) and Claude Leon Foundation, South Africa. The Improving Academic Qualifications (IAQ) NRF Sabbatical grant is also acknowledged for the substantial financial contribution towards the sequencing costs. This work is based on the research supported in part by a number of grants from the National Research Foundation of South Africa (includes Grant specific unique reference number (UID) 83924). The Grant holders acknowledge that opinions, findings and conclusions or recommendations expressed in any publication generated by the NRF supported research are that of the author(s), and that the NRF accepts no liability whatsoever in this regard.

REFERENCES

  1. Al Adawi A, Barnes I, Khan I, Al Subhi A, Al Jahwari A, Deadman M, Wingfield B, Wingfield M. (2013) Ceratocystis manginecans associated with a serious wilt disease of two native legume trees in Oman and Pakistan. Australasian Plant Pathology 42: 179–193 [Google Scholar]
  2. Al Adawi A, Deadman M, Al Rawahi A, Al Maqbali Y, Al Jahwari A, Al Saadi B, Al Amri I, Wingfield M. (2006) Aetiology and causal agents of mango sudden decline disease in the Sultanate of Oman. European Journal of Plant Pathology 116: 247–254 [Google Scholar]
  3. Al-Sadi AM, Al-Ouweisi FA, Al-Shariani NK, Al Adawi AO, Kaplan EJ, Deadman ML. (2010) Histological changes in mango seedlings following infection with Ceratocystis manginecans, the cause of mango decline. Journal of Phytopathology 158: 738–743 [Google Scholar]
  4. Baker CJ, Harrington TC, Krauss U, Alfenas AC. (2003) Genetic variability and host specialization in the Latin American clade of Ceratocystis fimbriata. Phytopathology 93: 1274–1284 [DOI] [PubMed] [Google Scholar]
  5. Barnes I, Roux J, Wingfield B, O’Neill M, Wingfield M. (2003) Ceratocystis fimbriata infecting Eucalyptus grandis in Uruguay. Australasian Plant Pathology 32: 361–366 [Google Scholar]
  6. Bihon W, Slippers B, Burgess T, Wingfield MJ, Wingfield BD. (2012) Diverse sources of infection and cryptic recombination revealed in South African Diplodia pinea populations. Fungal Biology 116: 112–120 [DOI] [PubMed] [Google Scholar]
  7. Bihon W, Wingfield MJ, Slippers B, Duong TA, Wingfield BD. (2014) MAT gene idiomorphs suggest a heterothallic sexual cycle in a predominantly asexual and important pine pathogen. Fungal Genetics and Biology 62: 55–61 [DOI] [PubMed] [Google Scholar]
  8. Blanco-Ulate B, Rolshausen P, Cantua D. (2013) Draft Genome Sequence of Neofusicoccum parvum Isolate UCR-NP2, a Fungal Vascular Pathogen Associated with Grapevine Cankers. Genome Announcements 1(3):e00339-13; doi:10.1128/genomeA.00339-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. (2011) Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27: 578–579 [DOI] [PubMed] [Google Scholar]
  10. Boetzer M, Pirovano W. (2012) Toward almost closed genomes with GapFiller. Genome Biology 13: R56. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Burgess TI, Wingfield MJ, Wingfield BD. (2004) Global distribution of Diplodia pinea genotypes revealed using simple sequence repeat (SSR) markers. Australasian Plant Pathology 33: 513–519 [Google Scholar]
  12. Cuomo CA, Güldener U, Xu J-R, Trail F, Turgeon BG.et al. (2007) The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science 317: 1400–1402 [DOI] [PubMed] [Google Scholar]
  13. Espagne E, Lespinet O, Malagnac F, Da Silva C, Jaillon O.et al. (2008) The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biology 9: R77. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Haridas S, Wang Y, Lim L, Massoumi Alamouti S, Jackman S.et al. (2013) The genome and transcriptome of the pine saprophyte Ophiostoma piceae, and a comparison with the bark beetle-associated pine pathogen Grosmannia clavigera. BMC Genomics 14: 373. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Heath RN, Wingfield MJ, Wingfield BD, Meke G, Mbaga A, Roux J. (2009) Ceratocystis species on Acacia mearnsii and Eucalyptus spp. in Eastern and Southern Africa including six new species. Pretoria: University of Pretoria Press [Google Scholar]
  16. Hunt J. (1956) Taxonomy of the genus Ceratocystis. Lloydia 19: 1–58 [Google Scholar]
  17. Kamgan Nkuekam GK, Wingfield MJ, Roux J. (2013) Ceratocystis species, including two new taxa, from Eucalyptus trees in South Africa. Australasian Plant Pathology 42: 283–311 [Google Scholar]
  18. Kamgan Nkuekam N, Jacobs K, De Beer Z, Wingfield M, Roux J. (2008) Ceratocystis and Ophiostoma species including three new taxa, associated with wounds on native South African trees. Fungal Diversity 29: 37–59 [Google Scholar]
  19. Kile G. (1993) Plant diseases caused by species of Ceratocystis sensu stricto and Chalara. In: Ceratocystis and Ophiostoma: taxonomy, ecology and pathogenicity (Wingfield MJ, Seifert KA, Webber JF, eds): 173–183 St Paul, MN: APS Press [Google Scholar]
  20. Kirisits T. (2004) Fungal associates of European bark beetles with special emphasis on the ophiostomatoid fungi. In: Bark and wood boring insects in living trees in Europe, a synthesis (Lieutier F, Day KR, Battisti A., Grégoire JC, Evans HF, eds): 181–123 Dordrecht: Kluwer Academic Publishers [Google Scholar]
  21. Kirisits T, Konrad H, Wingfield MJ, Chhetri DB. (2013) Ophiostomatoid fungi associated with the Eastern Himalayan spruce bark beetle, Ips schmutzenhoferi, in Bhutan and their pathogenicity to Picea spinulosa and Pinus wallichiana. In: The Ophiostomatoid Fungi: expanding frontiers (Seifert KA, de Beer ZW, Wingfield MJ, eds): 99–112 [CBS Biodiversity Series no. 12.] Utrecht: CBS-KNAW Fungal Biodiversity Centre [Google Scholar]
  22. Krings U, Berger R. (1998) Biotechnological production of flavours and fragrances. Applied Microbiology and Biotechnology 49: 1–8 [DOI] [PubMed] [Google Scholar]
  23. Parra G, Bradnam K, Korf I. (2007) CEGMA: A pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23: 1061–1067 [DOI] [PubMed] [Google Scholar]
  24. Phillips AJL, Alves A, Abdollahzadeh J, Slippers B, Wingfield MJ, Groenewald JZ, Crous PW. (2013) The Botryosphaeriaceae: genera and species known from culture. Studies in Mycology 76: 51–167 [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Poussio GB, Kazmi MR, Akem C, Fateh FS. (2010) First record of Ceratocystis fimbriata associated with shisham (Dalbergia sissoo) decline in Pakistan. Australasian Plant Disease Notes 5: 63–65 [Google Scholar]
  26. Rokas A, Williams BL, King N, Carroll SB. (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798–804 [DOI] [PubMed] [Google Scholar]
  27. Roux J, van Wyk M, Hatting H, Wingfield M. (2004) Ceratocystis species infecting stem wounds on Eucalyptus grandis in South Africa. Plant Pathology 53: 414–421 [Google Scholar]
  28. Roux J, Wingfield M. (2009) Ceratocystis species: Emerging pathogens of non-native plantation Eucalyptus and Acacia species. Southern Forests 71: 115–120 [Google Scholar]
  29. Roux J, Wingfield M, Bouillet JP, Wingfield B, Alfenas A. (2000) A serious new wilt disease of Eucalyptus caused by Ceratocystis fimbriata in Central Africa. Forest Pathology 30: 175–184 [Google Scholar]
  30. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol Ý (2009) ABySS: A parallel assembler for short read sequence data. Genome Research 19: 1117–1123 [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Smith H, Wingfield MJ, de Wet J, Coutinho TA. (2000) Genotypic diversity of Sphaeropsis sapinea from South Africa and Northern Sumatra. Plant Disease 84: 139–142 [DOI] [PubMed] [Google Scholar]
  32. Stanke M, Tzvetkova A, Morgenstem B. (2006) AUGUSTUS at EGASP: using EST, protein and genomic aligenments for improved gene prediction in the human genome. Genome Biology 7 (Suppl. 1): S11.1–S11.8 [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Stanosz GR, Blodgett JT, Smith DR, Kruger EL. (2001) Water stress and Sphaeropsis sapinea as a latent pathogen of red pine seedlings. New Phytologist 149: 531–538 [DOI] [PubMed] [Google Scholar]
  34. Stanosz GR, Smith DR, Leisso R. (2007) Diplodia shoot blight and asymptomatic persistence of Diplodia pinea on or in stems of jack pine nursery seedlings. Forest Pathology 37: 145–154 [Google Scholar]
  35. Swart WJ, Wingfield MJ. (1991) Biology and control of Sphaeropsis sapinea on Pinus species in South Africa. Plant Disease 75: 761–766 [Google Scholar]
  36. Tarigan M, Roux J, van Wyk M, Tjahjono B, Wingfield M J. (2011) A new wilt and die-back disease of Acacia mangium associated with Ceratocystis manginecans and C. acaciivora sp. nov. in Indonesia. South African Journal of Botany 77: 292–304 [Google Scholar]
  37. Tarigan M, Roux J, Wingfield MJ, van Wyk M, Tjahjono B. (2010) Three new Ceratocystis spp. in the Ceratocystis moniliformis complex from wounds on Acacia mangium and A. crassicarpa. Mycoscience 51: 53–67 [Google Scholar]
  38. Upadhyay HP. (1981) A Monograph of Ceratocystis and Ceratocystiopsis. Athens, GA: University of Georgia Press [Google Scholar]
  39. van Wyk M, Al Adawi AO, Khan IA, Deadman ML, Al Jahwari AA, Wingfield BD, Ploetz R, Wingfield MJ. (2007) Ceratocystis manginecans sp. nov., causal agent of a destructive mango wilt disease in Oman and Pakistan. Fungal Diversity 27: 213–230 [Google Scholar]
  40. van Wyk M, Roux J, Barnes I, Wingfield BD, Chhetri DB, Kirisits T, Wingfield MJ. (2004) Ceratocystis bhutanensis sp. nov., associated with the bark beetle Ips schmutzenhoferi on Picea spinulosa in Bhutan. Studies in Mycology 50: 365–379 [Google Scholar]
  41. van Wyk M, Roux J, Barnes I, Wingfield BD, Wingfield MJ. (2006) Molecular phylogeny of the Ceratocystis moniliformis complex and description of C. tribiliformis sp. nov. Fungal Diversity 21: 181–201 [Google Scholar]
  42. van Wyk N, Trollope KM, Steenkamp ET, Wingfield BD, Volschenk H. (2013) Identification of the gene for beta-Fructofuranosidase from Ceratocystis moniliformis CMW 10134 and characterization of the enzyme expressed in Saccharomyces cerevisiae. BMC Biotechnology 13: 100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Vandamme EJ, Soetaert W. (2002) Bioflavours and fragrances via fermentation and biocatalysis. Journal of Chemical Technology and Biotechnology 77: 1323–1332 [Google Scholar]
  44. Wall DP, Tonellato PJ. (2012) The future of genomics in pathology. F1000 medicine reports, 4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Webster RK, Butler EE. (1967) A morphological and biological concept of the species Ceratocystis fimbriata. Canandian Journal of Botany 45: 1457–1467 [Google Scholar]
  46. Wiemann P, Sieber CM, von Bargen KW, Studt L, Niehaus EM.et al. (2013) Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites. PLoS Pathogen 9: e1003475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Wilken PM, Steenkamp ET, De Beer ZW, Wingfield MJ, Wingfield BD. (2013) Draft nuclear genome sequence for the plant pathogen, Ceratocystis fimbriata. IMA Fungus 4: 357–358 [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Wingfield BD, van Wyk M, Roos H, Wingfield MJ. (2013) Ceratocystis: emerging evidence for discrete generic boundaries. In: The Ophiostomatoid Fungi: expanding frontiers (Seifert KA, de Beer ZW, Wingfield MJ, eds): 57–64 [CBS Biodiversity Series no. 12.] Utrecht: CBS-KNAW Fungal Biodiversity Centre [Google Scholar]
  49. Yuan Z-Q, Mohammed C. (2002) Ceratocystis moniliformopsis sp. nov., an early coloniser of Eucalyptus obliqua logs in Tasmania, Australia. Australian Systematic Botany 15: 125–133 [Google Scholar]
  50. Zerbino DR, Birney E. (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18: 821–829 [DOI] [PMC free article] [PubMed] [Google Scholar]
IMA Fungus. 2014 Jun 19;5(1):135–136.

IMA Genome-F 2A

Draft genome sequence of the pine fungal pathogen Diplodia sapinea

INTRODUCTION

Diplodia sapinea, also known as Diplodia pinea or Sphaeropsis sapinea (Phillips et al. 2013), was first reported in France in 1842 as a saprobe on dead Pinus sylvestris. It has subsequently been reported from many countries of the world on Pinus species growing in their natural environment and where they are propagated as non-natives in commercially managed plantations (Swart et al. 1991, Burgess et al. 2004). This fungus exists as an endophyte in healthy tree tissues, but causes disease when trees are stressed (Swart et al. 1991, Stanosz et al. 2007, 2001).

No sexual morph has been reported for D. sapinea (Smith et al. 2000, Burgess et al. 2004). However, results of a population genetics study of the fungus considering the lack of linkage disequilibrium amongst alleles, as well as the generally high genotypic diversity, proposed that a cryptic sexual state probably exists for this fungus (Bihon et al. 2012). In support of this conclusion, a recent study of mating type loci showed various populations of D. sapinea contained the two mating type idiomorphs in more or less equal frequency, which is indicative of a heterothallic sexual cycle (Bihon et al. 2014).

The aim of this study was to produce a full genome sequence for an isolate of D. sapinea and to make this available for further study. Such studies could address aspects of the biology of the pathogen such as its selective pathogenicity on conifers, compared to most other Botryosphaeriales that infect angiosperms.

SEQUENCED STRAINS

USA: Wisconsin: isol. ex Pinus banksiana, June 1986, M. Palmer (CMW 190/CBS 117911; CBS H-21777 – dried cultures). – South Africa: Kwa-Zulu Natal: 7-Oaksisol. ex Pinus patula, Sept. 2008, W. Bihon (CMW 39103/CBS 138184; CBS H-21778– dried cultures).

NUCLEOTIDE SEQUENCE ACCESSION NUMBER

The Whole Genome Shotgun projects have been deposited at DBJ/EMBL/GenBank under the accessions AXCF00000000 and JHUM00000000. The version described in this paper is version AXCF01000000 and JHUM01000000 for strains CMW 190 and CMW 39103 respectively.

METHODS

DNA from single spore cultures of two strains of Diplodia sapinea (CMW190/CBS117911 and CMW39103) was extracted and sequenced using Illumina: HiSeq and MiSeq genome analyser at Agricultural Research Council (ARC) and Inqaba biotech, Pretoria, South Africa, respectively. Reads received were subjected to the necessary sequence quality analysis and those of less than 30 bases were trimmed. Reads were assembled into a draft genome using CLC Genomic de novo assembler 6.0 (CLC bio, Aarhus, Denmark). Completeness of the genome was estimated using the Core Eukaryotic Genes Mapping Approach (CEGMA) analysis (Parra et al. 2007). Gene prediction from the genome was done using AUGUSTUS (Stanke et al. 2006).

RESULTS AND DISCUSSION

The final assembly of isolate CMW190/CBS117911 consisted of 2194 contigs with N50 contig size of 37659 and that of CMW39103 had 4102 contigs with N50 of 38230 bases. Maximum contig size was 265719 bases. Contigs of ≥ 200 bases were submitted to the genome database of NCBI. The output from the CEGMA (Parra et al. 2007) pipeline analysis indicated that the genome sequence was estimated to be >95.6 % complete by mapping to the more conserved set of 248 Core Eukaryotic Genes (CEGs). Putative gene prediction using AUGUSTUS (Stanke et al. 2006) identified 13020 open reading frames (ORFs).

The estimated genome size of Diplodia sapinea was 36.97 Mb, which is smaller than the genome of most closely related sequenced species, Botryosphaeria dothidea (43.50 Mb) and Neofusicoccum parvum (42.50 Mb). It contains fewer genes compared to B. dothidea (14999) but higher than that of N. parvum (10470) (http://genome.jgi-psf.org/Botdo1/Botdo1.info.html; Blanco-Ulate et al. 2013). Diplodia sapinea has similar genome size to Fusarium graminearum (36.1 Mb), but with a greater number of genes (11640) (Cuomo et al. 2007). The genome sequence of D. sapinea species has already made the characterisation of the MAT locus possible (Bihon et al. 2014) and access to this genome will no doubt facilitate further research on this important tree pathogen.

Authors: W. Bihon, M.J. Wingfield, Bernard Slippers, and B.D. Wingfield

IMA Fungus. 2014 Jun 19;5(1):136–137.

IMA Genome-F 2B

Draft nuclear genome sequence for the sapstain fungus Ceratocystis moniliformis

INTRODUCTION

The Ceratocystis moniliformis complex defines one of several monophyletic assemblages in the genus Ceratocystis sensu lato (Yuan & Mohammed 2002, van Wyk et al. 2006, Kamgan Nkuekam et al. 2008, 2013, Tarigan et al. 2010, 2011). Members of this complex produce hat-shaped ascospores from ascomata with spiny bases and have disc-like structures at the bases of their ascomatal necks (Hunt 1956, Upadhyay 1981, van Wyk et al. 2004, 2006). These fungi are relatively fast-growing and produce strong fruity aromas and enzymes that could be industrially relevant. These include invertases that catalyse sucrose biotransformation (van Wyk et al. 2013) and various terpenes with fruity or floral odours that are used for large-scale production of bioflavours (Krings & Berger 1998, Vandamme & Soetaert 2002).

Species in the C. moniliformis complex are found on the surfaces of freshly wounded woody plants, especially trees (Kile 1993, Roux et al. 2004, Tarigan et al. 2010). Interestingly this group of fungi are all saprobes (Kile 1993, Yuan & Mohammed 2002, Tarigan et al. 2010), unlike species in the C. fimbriata complex which includes serious pathogens of economically important plants (Roux et al. 2000, Baker et al. 2003, Barnes et al. 2003, van Wyk et al. 2007, Heath et al. 2009). In some cases, species in the C. moniliformis complex cause sapstain that can result in economic losses as they lower the value of timber (van Wyk et al. 2006). Ceratocystis species are known to be transported to the wounded surfaces by insects such as sap-feeding beetles (Coleoptera: Nitidulidae) (Kirisits 2004). One species, C. bhutanensis, is also associated with a bark beetle (Ips schmutzenhoferi) on Picea spinulosa in Bhutan, but it does not appear to be a pathogen (van Wyk et al. 2004, Kirisits et al. 2013).

Overall, little is known regarding the biology of species in the C. moniliformis complex. The availability of the nuclear genome sequence for one of its members, C. moniliformis s.str., would improve our knowledge regarding the molecular processes underlying their ecology and potentially inform industrial applications for the production of biocompounds. Together with the publicly available genome sequences for other species of Ceratocystis, particularly the sweet potato pathogen C. fimbriata (Wilken et al. 2013) and the mango wilt pathogen C. manginecans, the C. moniliformis s.str. genome will also be a valuable resource for comparative genomics studies into the evolution and general biology of these important fungi.

SEQUENCED STRAIN

South Africa: Mpumalanga: Sabie, isol. ex Eucalyptus grandis, Apr. 2002, M. van Wyk (CMW 10134, CBS118127; CBS H-21775 – dried culture).

NUCLEOTIDE SEQUENCE ACCESSION NUMBER

The Whole Genome Shotgun project of the Ceratocystis moniliformis genome has been deposited at DDBJ/EMBL/GenBank under the accession no. JMSH00000000. The version described in this paper is version JMSH01000000.

METHODS

Genomic DNA was isolated and sequenced using the Genome Analyzer IIx platform (Illumina) at the Genome Centre, University of California at Davis (CA, USA). For this purpose, paired-end libraries with respective insert sizes of approximately 350 and 600 bases were used to produce reads with an average length of 100 bases. Poor-quality reads and/or terminal nucleotides were discarded using the software package CLC Genomics Workbench v. 6.0.1 (CLCbio, Aarhus, Denmark). The remaining reads were assembled using Abyss v. 1.3.7 with an optimized k-mer size of 91 (Simpson et al. 2009). Open reading frames (ORFs) were predicted using AUGUSTUS (Stanke et al. 2006) based on the gene models for Fusarium graminearum (http://bioinf.uni-greifswald.de/augustus), while genome completeness was evaluated using the Core Eukaryotic Genes Mapping Approach (CEGMA) pipeline (Parra et al. 2007).

RESULTS AND DISCUSSION

The draft nuclear genome of Ceratocystis moniliformis has an estimated size of 25 429 610 bases. A value of 191 280 was obtained for the N50 and a mean GC content of 48 %. The Abyss assembly generated 680 contigs, of which 365 were retained after filtering out contigs consisting of fewer than 500 nucleotides. This assembly was also predicted to encode 6 832 ORFs at a density of 269 ORFs/Mb. A CEGMA completeness score of at least 96.4 % were obtained for this version of the assembly.

Comparison of the C. moniliformis genome to those of C. fimbriata s.str. (Wilken et al. 2013) and C. manginecans showed differences in several key genome statistics. The C. moniliformis genome is 4.0 Mb smaller than the 29.4 Mb C. fimbriata s.str. genome, and 6.3 Mb smaller than the 31.7 Mb C. manginecans genome. Additionally, 533 and 761 fewer protein coding genes are predicted for the C. moniliformis genome than for C. fimbriata s.str. with its 7 266 predicted genes (Wilken et al. 2013) and C. manginecans with its 7 494 genes (see below), respectively. This is despite the fact that the three genomes are characterized by similar levels of completeness (i.e. 96.8 % for C. manginecans and 96.9 % for C. fimbriata s.str.). Although these genome differences for C. moniliformis could be linked to its non-pathogenic lifestyle (i.e. C. moniliformis is a saprophytic fungus that occurs on a wide range of woody hosts; van Wyk et al. 2006), further research is required for determining the significance of these differences in the overall biology of this group of fungi.

Authors: M.A. van der Nest, K. Naidoo, P.M. Wilken, E. Rubagotti, A. Wilson, L. De Vos, E.T. Steenkamp, M.J. Wingfield, and B.D. Wingfield

IMA Fungus. 2014 Jun 19;5(1):137–138.

IMA Genome-F 2C

Draft nuclear genome sequence for Ceratocystis manginecans, the causal agent of mango wilt disease

INTRODUCTION

The genus Ceratocystis (Ascomycota, Microscales) represents an important group of plant pathogens (Roux & Wingfield 2009). These fungi cause diseases on a wide range of root and tree crops, where they are associated with significant economic losses (Roux & Wingfield 2009). The mango (Mangifera indica) wilt pathogen, Ceratocystis manginecans, is a particularly virulent member of this genus that has devastated the mango industry in Oman and Pakistan (Al Adawi et al. 2006, 2013, van Wyk et al. 2007, Al-Sadi et al. 2010). This pathogen also threatens leguminous trees in Oman, Pakistan and Indonesia (Poussio et al. 2010, Tarigan et al. 2011, Al Adawi et al. 2013).

Ceratocystis manginecans is a member of the C. fimbriata s.lat. species complex, which is an assemblage of morphologically similar and phylogenetically closely related species (Webster & Butler 1967, van Wyk et al. 2007, Wingfield et al. 2013). In this complex, C. manginecans is closely related to C. acaciivora, which is responsible for a debilitating canker and wilt disease of plantation-grown Acacia mangium in Indonesia (van Wyk et al. 2007, Tarigan et al. 2011). Although there is a need to refine the taxonomic position of some species in the complex (Wingfield et al. 2013), the close relationships among its members could indicate similar or shared mechanisms relating to their biology and role as pathogens. Elucidation of questions regarding their pathology and general biology would be facilitated by genome sequence comparisons (Rokas et al. 2003, Wall & Tonellato 2012). For this reason, the genome of the sweet potato pathogen, C. fimbriata was recently sequenced and shared publicly (Wilken et al. 2013). In this study we determined the genome sequence for C. manginecans, which will allow for comparisons between the two species, advancing studies on various aspects of the biology of species in this complex.

SEQUENCED STRAIN

Oman: Sohar area, isol. ex Prosopsis cineraria, Mar. 2005, A. O. Al Adawi (CBS 138185, CMW 17570; CBS H-21776 – dried).

NUCLEOTIDE SEQUENCE ACCESSION NUMBER

The Whole Genome Shotgun project of the Ceratocystis manginecans genome has been deposited at DDBJ/EMBL/GenBank under the accession number JJRZ00000000. The version described in this paper is version JJRZ01000000.

METHODS

All sequencing was performed on the Genome Analyzer IIx platform (Illumina) at the Genome Centre, University of California at Davis (CA, USA). Paired-end libraries with respective insert sizes of approximately 350 and 600 bases were used to produce read lengths of 100 bases. The software package CLC Genomics Workbench v. 6.0.1 (CLCbio, Aarhus, Denmark) was used to discard poor-quality reads and/or terminal nucleotides. The remaining reads were assembled using the Velvet de novo assembler (Zerbino & Birney 2008), with an optimised k-mer size of 71. The pre-assemblies were scaffolded using SSPACE v. 2.0 (Boetzer et al. 2011) and the gaps were reduced using GapFiller v. 2.2.1 (Boetzer & Pirovano 2012). Open Reading Frames (ORFs) were predicted using AUGUSTUS (Stanke et al. 2006) based on the gene models for Fusarium graminearum (http://bioinf.uni-greifswald.de/augustus), while genome completeness was evaluated using the Core Eukaryotic Genes Mapping Approach (CEGMA) pipeline (Parra et al. 2007).

RESULTS AND DISCUSSION

The Ceratocystsis manginecans draft genome had an estimated size of 31 706 104 DNA bases, a 22× average coverage, N50 contig size of 77 070 bases and a mean GC content of 47.9 %. The assembly generated 2 234 contigs, of which 980 were retained after filtering out contigs consisting of fewer than 500 nucleotides. The filtered assembly had a CEGMA completeness score of at least 96.4 % and was predicted to encoded 7 494 putative ORFs at a density of 236 ORFs/Mb.

The C. manginecans draft genome is similar in size than the genome of the sweet potato pathogen, C. fimbriata (29.4 Mb, 7 266 ORFs) (Wilken et al. 2013) and the wood-staining fungus Ophiostoma piceae (32.84 Mb, 8884 ORFs) (Haridas et al. 2013). However, the C. manginecans genome appears to be relatively small and harbours fewer genes than other species in Sordariomycetes. For example, the genomes of Podospora anserina (35.01 Mb, 10588 ORFs) (Espagne et al. 2008), Fusarium fujikuroi (43.83 Mb, 14813 ORFs) (Wiemann et al. 2013) and Cryphonectria parasitica (43.9 Mb, 11,184 ORFs) (http://genome.jgi.doe.gov/Crypa2/Crypa2.home.html) are much bigger in size and harbour more genes. The genome sequence information for C. manginecans will, therefore, increase our understanding of the biology, systematics and pathology of this group of globally important pathogens.

Authors: M.A. van der Nest, K. Naidoo, P.M. Wilken, E. Rubagotti, D. Roodt, L. De Vos, E.T. Steenkamp, M.J. Wingfield, and B.D. Wingfield


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