Single-nucleotide polymorphism discovery in Leptographium longiclavatum, a mountain pine beetle-associated symbiotic fungus, using whole-genome resequencing

Molecular Ecology Resources

Volumn 14, Issue 2, 2014, Pages 401-410

  Ojeda, Dario I ^a   Dhillon, Braham ^a   Tsui, Clement K M ^a   Hamelin, Richard C ^a,b  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b LAURENTIAN FORESTRY CENTRE   (Canada)

Author keywords

Bark beetle; Bioinformatics; Blue stain fungi; Next generation sequencing; Ophiostomatoid fungi; Sequenom Iplex Gold Assay

Indexed keywords

FUNGAL DNA;

ANIMAL; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; FUNGAL GENOME; GENETICS; GENOTYPING TECHNIQUE; ISOLATION AND PURIFICATION; MICROBIOLOGICAL EXAMINATION; MICROBIOLOGY; MOLECULAR GENETICS; OPHIOSTOMATALES; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM; WEEVIL;

ANIMALS; DNA, FUNGAL; GENOME, FUNGAL; GENOTYPING TECHNIQUES; MOLECULAR SEQUENCE DATA; MYCOLOGICAL TYPING TECHNIQUES; OPHIOSTOMATALES; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; WEEVILS;

EID: 84894249639     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12191     Document Type: Article

References (54)

1. Abbott CL, Gilmore SR, Lewis CT et al. (2012) Development of a SNP genetic marker system based on variation in microsatellite flanking regions of Phytophthora infestans. Canadian Journal of Plant Pathology, 32, 440-457.
2. Alamouti SM, Wang V, Diguistini S et al. (2011) Gene genealogies reveal cryptic species and host preferences for the pine fungal pathogen Grosmannia clavigera. Molecular Ecology, 20, 2581-2602.
3. Ben-Ari G, Zenvirth D, Sherman A et al. (2005) Application of SNPs for assessing biodiversity and phylogeny among yeast strains. Heredity, 95, 493-501.
4. Bouakaze C, Keyser C, Gonzalez A et al. (2011) MALDI-TOF MS-based SNP genotyping assay using the iPLEX Gold technology for identification of Mycobacterium tuberculosis complex species and lineages. Journal of Clinical Microbiology, 49, 3292-3299.
5. Broders KD, Woeste KE, San Miguel PJ, Westerman RP, Boland GJ (2011) Discovery of single-nucleotide polymorphisms (SNPs) in the uncharacterized genome of the ascomycete Ophiognomonia clavigignenti-juglandacearum from 454 sequence data. Molecular Ecology Resources, 11, 693-702.
6. Buggs R, Chamala S, Wu W et al. (2010) Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping. Molecular Ecology, 19(Suppl 1), 132-146.
7. Bundock PC, Eliott FG, Ablett G et al. (2009) Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. Plant Biotechnology Journal, 7, 347-354.
8. Carroll AL, Taylor SW Régnière J, Safranyik L(2004) Effects of climate change on range expansion by the mountain pine beetle in British Columbia. In: Mountain Pine Beetle Symposium: Challenges and Solutions (eds Shore TL, Brooks JE & Stone JE), pp. 223-232. Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, Information Report BC-X-399.
9. Cingolani P, Platts A, Wang L et al. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin), 6, 80-92.
10. Cullingham CI, Cooke JEK, Dang S et al. (2011) Mountain pine beetle host-range expansion threatens the boreal forest. Molecular Ecology, 20, 2157-2171.
11. Cuomo CA, Güldener U, Xu J-R et al. (2007) The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science, 317, 1400-1402.
12. De La Giroday H-MC, Carroll AL, Aukema BH (2012) Breach of the northern Rocky Mountain geoclimatic barrier: initiation of range expansion by the mountain pine beetle. Journal of Biogeography, 39, 1112-1123.
13. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Research, 27, 4636-4641.
14. DiGuistini S, Wang Y, Liao NY et al. (2011) Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen. Proceedings of the National Academy of Sciences of the United States of America, 108, 2504-2509.
15. Drummond AJ, Ashton B, Buxton S et al. (2010) Geneious pro v4.7. Available from www.geneious.com.
16. Ehrich M, Böcker S, Van Den Boom D (2005) Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS. Nucleic Acids Research, 33, e38.
17. Everett MV, Grau ED, Seeb JE (2011) Short reads and nonmodel species: exploring the complexities of next-generation sequence assembly and SNP discovery in the absence of a reference genome. Molecular Ecology Resources, 11, 93-108.
18. Fournier A, Widmer F, Enkerli J (2010) Development of a single-nucleotide polymorphism (SNP) assay for genotyping of Pandora neoaphidis. Fungal Biology, 114, 498-506.
19. Fu Y, Peterson GW (2011) Developing genomic resources in two Linum species via 454 pyrosequencing and genomic reduction. Molecular Ecology Resources, 12, 492-500.
20. Gabriel S, Ziaugra L, Tabbaa D (2009) SNP genotyping using the Sequenom MassARRAY iPLEX platform. In: Current Protocols in Human Genetics (eds Haines JL, Korf BR & Morton CC et al.), vol. 60, pp. 2.12.1-2.12.16. John Wiley & Sons, Inc., Massachusetts.
21. Garvin MR, Saitoh K, Gharrett AJ (2010) Application of single nucleotide polymorphisms to non-model species: a technical review. Molecular Ecology Resources, 10, 915-934.
22. Geraldes A, Pang J, Thiessen N et al. (2011) SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Molecular Ecology Resources, 11(Suppl 1), 81-92.
23. Hesse-Orce U, DiGuistini S, Keeling CI et al. (2010) Gene discovery for the bark beetle-vectored fungal tree pathogen Grosmannia clavigera. BMC Genomics, 11, 536.
24. Ho DW, Yiu WC, Yap MK et al. (2011) Genotyping performance assessment of whole genome amplified DNA with respect to multiplexing level of assay and its period of storage. PLoS ONE, 6, e26119.
25. James PMA, Coltman DW, Murray BW, Hamelin RC, Sperling FAH (2011) Spatial genetic structure of a symbiotic beetle-fungal system: toward multi-taxa integrated landscape genetics (S Joly, Ed, ). PLoS ONE, 6, e25359.
26. Kumar S, Banks TW, Cloutier S (2012) SNP discovery through next-generation sequencing and its applications. International Journal of Plant Genomics, 2012, 1-15.
27. Kurtz W, Dymond C, Stinson G et al. (2008) Mountain pine beetle and forest carbon feedback to climate change. Nature, 452, 987-990.
28. Lee S, Kim J, Breuil C (2005) Leptographium longiclavatum sp. nov., a new species associated with mountain pine beetle, Dendroctonus ponderosae. Mycological Research, 109, 1162-1170.
29. Lee S, Kim J, Breuil C (2006a) Pathogenicity of Leptographium longiclavatum associated with Dendroctonus ponderosae to Pinus contorta. Canadian Journal of Forest Research, 36, 2864-2872.
30. Lee S, Kim J, Breuil C (2006b) Diversity of fungi associated with the mountain pine beetle, Dendroctonus ponderosae and infested lodgepole pines in British Columbia. Fungal Diversity, 22, 91-105.
31. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
32. Li H, Handsaker B, Wysoker A et al. (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-2079.
33. Lim YW, Alamouti SM, Kim JJ, Lee S, Breuil C (2004) Multigene phylogenies of Ophiostoma clavigerum and closely related species from bark beetle-attacked Pinus in North America. FEMS Microbiology Letters, 237, 89-96.
34. Majoros WH, Pertea M, Salzberg SL (2004) TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders. Bioinformatics, 20, 2878-2879.
35. ® Gold assay. (JK DiStefano, Ed, ). Methods in Molecular Biology (Clifton, N.J), 700, 61-76.
36. Neafsey DE, Barker BM, Sharpton TJ et al. (2010) Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Research, 20, 938-946.
37. Novaes E, Drost DR, Farmerie WG et al. (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics, 9, 312.
38. Ramos AM, Crooijmans RPMA, Affara NA et al. (2009) Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology (L Orban, Ed, ). PLoS ONE, 4, 13.
39. Rice AV, Thormann MN, Langor DW (2007) Virulence of, and interactions among, mountain pine beetle associated blue-stain fungi on two pine species and their hybrids in Alberta. Canadian Journal of Botany, 85, 316-323.
40. Roe AD, Rice AV, Bromilow SE, Cooke JEK, Sperling FAH (2010) Multilocus species identification and fungal DNA barcoding: insights from blue stain fungal symbionts of the mountain pine beetle. Molecular Ecology Resources, 10, 946-959.
41. Roe AD, James P, Rice AV, Cooke JEK, Sperling FAH (2011a) Spatial community structure of mountain pine beetle fungal symbionts across a latitudinal gradient. Microbial Ecology, 62, 347-360.
42. Roe AD, Rice AV, Coltman DW, Cooke JEK, Sperling FAH (2011b) Comparative phylogeography, genetic differentiation and contrasting reproductive models in three fungal symbionts of a multipartite bark beetle symbiosis. Molecular Ecology, 20, 584-600.
43. Sambaraju KR, Carroll AL, Zhu J et al. (2012) Climate change could alter the distribution of mountain pine beetle outbreaks in western Canada. Ecography, 35, 211-223.
44. Shi A, Chen P, Vierling R et al. (2011) Multiplex single nucleotide polymorphism (SNP) assay for detection of soybean mosaic virus resistance genes in soybean. Theoretical and Applied Genetics, 122, 445-457.
45. Simpson JT, Wong K, Jackman SD et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Research, 19, 1117-1123.
46. Solheim H, Krokene P (1998) Growth and virulence of mountain pine beetle associated blue-stain fungi, Ophiostoma clavigerum and Ophiostoma montium. Canadian Journal of Botany, 76, 561-566.
47. Syrmis MW, Moser RJ, Whiley DM et al. (2011) Comparison of a multiplexed MassARRAY system with real-time allele-specific PCR technology for genotyping of methicillin-resistant Staphylococcus aureus. Clinical Microbiology and Infection, 17, 1804-10.
48. Thomas E, Pakala S, Fedorova ND, Nierman WC, Cubeta MA (2012) Triallelic SNP-mediated genotyping of regenerated protoplasts of the heterokaryotic fungus Rhizoctonia solani. Journal of Biotechnology, 158, 144-150.
49. Tollenaere C, Susi H, Nokso-Koivisto J et al. (2012) SNP design from 454 sequencing of Podosphaera plantaginis transcriptome reveals a genetically diverse pathogen metapopulation with high levels of mixed- genotype infection. PLoS ONE, 7, e52492.
50. Trick M, Long Y, Meng J, Bancroft I (2009) Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnology Journal, 7, 334-346.
51. Tsui CKM, Roe AD, El-kassaby YA et al. (2012) Population structure and migration pattern of a conifer pathogen, Grosmannia clavigera, as influenced by its symbiont, the mountain pine beetle. Molecular Ecology, 21, 71-86.
52. Tsui CK-M, Diguistini S, Wang Y et al. (2013) Unequal recombination and evolution of the mating-Type (MAT) loci in the pathogenic fungus Grosmannia clavigera and relatives. G3, 3, 465-80.
53. Van Bers NEM, Van Oers K, Kerstens HHD et al. (2010) Genome-wide SNP detection in the great tit Parus major using high throughput sequencing. Molecular Ecology, 19(Suppl 1), 89-99.
54. Yamaoka Y, Hiratsuka Y, Maruyama PJ (1995) The ability of Ophiostoma clavigerum to kill mature lodgepole-pine trees. European Journal of Forest Pathology, 25, 401-404.