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Abstract

Single nucleotide polymorphisms (SNPs) are becoming increasingly popular markers for studying a variety of biological phenomena. This paper describes the development and analysis of a set of SNP markers for the basidiomycete fungus . is a gourmet mycorrhizal mushroom primarily associated with pine forests. However, little is known about its genetics and genomic variation, including SNP variation. To identify and analyse SNPs in , a genomic library was constructed and >72 000 nt were analysed from >200 random clones. Primers from 20 sequenced fragments were then designed to amplify and sequence >10 000 bp sequences from the original strain, from which the genomic library was constructed, as well as another strain from >350 km away; both strains were from south-western China. These two strains had similar intra-strain SNP frequencies (1.104 and 1.278 % per nucleotide, respectively). The combined analysis revealed that 14 of the 20 examined fragments contained SNPs, ranging from two to 47 per fragment, and yielding a total of 178 SNPs out of the 10 428 sequenced nucleotides (an SNP frequency of 1.707 %). Among the 178 SNPs, one site had three alternative nucleotides, while the remaining 177 had two each, with 148 transitions and 29 transversions, resulting in a combined transition to transversion ratio of 5.1. In addition, the haplotype phases of all SNPs within individual fragments for both strains were determined. Phylogenetic analyses of these haplotypes revealed three kinds of haplotype relationship, including haplotype sharing both within and between strains. Furthermore, a subset of the SNPs detectable by restriction enzyme digests was screened for its distribution among 31 additional wild strains from five distinct locations in south-western China. The implications of these SNPs and haplotypes for our understanding of the genetics, population history, ecology and evolution of this important mushroom species are discussed.

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2007-07-01
2019-10-23
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References

  1. Ayoub, M.-J., Legras, J.-L., Saliba, R. & Gaillardin, C. ( 2006; ). Application of multi locus sequence typing to the analysis of the biodiversity of indigenous Saccharomyces cerevisiae wine yeasts from Lebanon. J Appl Microbiol 100, 699–711.[CrossRef]
    [Google Scholar]
  2. Brumfield, R. T., Beerli, P., Nickerson, D. A. & Edwards, S. V. ( 2003; ). The utility of single nucleotide polymorphisms in inference of population history. Trends Ecol Evol 18, 249–256.[CrossRef]
    [Google Scholar]
  3. Chapela, I. H. & Garbelotto, M. ( 2004; ). Phylogeography and evolution in matsutake and close allies inferred by analyses of ITS sequences and AFLPs. Mycologia 96, 730–741.[CrossRef]
    [Google Scholar]
  4. Fundyga, R. E., Kuykendall, R. J., Lee-Yang, W. & Lott, T. J. ( 2004; ). Evidence for aneuploidy and recombination in the human commensal yeast Candida parapsilosis. Infect Genet Evol 4, 37–43.[CrossRef]
    [Google Scholar]
  5. Gill, W. M., Guerin-Laguette, A., Lapeyrie, F. & Suzuki, K. ( 2000; ). Matsutake – morphological evidence of ectomycorrhizal formation between Tricholoma matsutake and host roots in a pure Pinus densiflora forest stand. New Phytol 147, 381–388.[CrossRef]
    [Google Scholar]
  6. Jones, T., Federspiel, N., Chibana, H., Dungan, J., Kalman, S., Magee, B. B., Newport, G., Thorstenson, R., Agabian, N. & other authors ( 2004; ). The diploid genome sequence of Candida albicans. Proc Natl Acad Sci U S A 101, 7329–7334.[CrossRef]
    [Google Scholar]
  7. Lan, L. & Xu, J. ( 2006; ). Multiple gene genealogical analyses suggest divergence and recent clonal dispersal in the opportunistic human pathogen Candida guilliermondii. Microbiology 152, 1539–1549.[CrossRef]
    [Google Scholar]
  8. Lian, C. L., Hogetsu, T., Matsushita, N., Guerin-Laguette, A., Suzuki, K. & Yamada, A. ( 2003; ). Development of microsatellite markers from an ectomycorrhizal fungus, Tricholoma matsutake, by an ISSR-suppression-PCR method. Mycorrhiza 13, 27–31.[CrossRef]
    [Google Scholar]
  9. Lian, C. L., Narimatsu, M., Nara, K. & Hogetsu, T. ( 2006; ). Tricholoma matsutake in a natural Pinus densiflora forest: correspondence between above- and below-ground genets, association with multiple host trees and alteration of existing ectomycorrhizal communities. New Phytol 171, 825–836.[CrossRef]
    [Google Scholar]
  10. Miller, R. D., Philips, M. S., Jo, I., Donaldson, M. A., Studebaker, J. F., Addleman, N., Alfisi, S. V., Ankener, W. M., Bhatti, H. A. & other authors ( 2005; ). High-density single-nucleotide polymorphism maps of the human genome. Genomics 86, 117–126.[CrossRef]
    [Google Scholar]
  11. Murata, H. & Babasaki, K. ( 2005; ). Intra- and inter-specific variations in the copy number of two types of retrotransposons from the ectomycorrhizal basidiomycete Tricholoma matsutake. Mycorrhiza 15, 381–386.[CrossRef]
    [Google Scholar]
  12. Murata, H. & Yamada, A. ( 2000; ). marY1, a member of the gypsy group of long terminal repeat retroelements from the ectomycorrhizal basidiomycete Tricholoma matsutake. Appl Environ Microbiol 66, 3642–3645.[CrossRef]
    [Google Scholar]
  13. Murata, H., Miyazaki, Y. & Yamada, A. ( 2001; ). marY2N, a LINE-like non-long terminal repeat (non-LTR) retroelement from the ectomycorrhizal homobasidiomycete Tricholoma matsutake. Biosci Biotechnol Biochem 65, 2301–2305.[CrossRef]
    [Google Scholar]
  14. Murata, H., Babasaki, K. & Yamada, A. ( 2005; ). Highly polymorphic DNA markers to specify strains of the ectomycorrhizal basidiomycete Tricholoma matsutake based on σmarY1, the long terminal repeat of gypsy-type retroelement marY1. Mycorrhiza 15, 179–186.[CrossRef]
    [Google Scholar]
  15. Nakayama, K. & Nakanishi, J. ( 2004; ). Tricholoma matsutake in Xichang, Sichuan and Chuxioug, Yunnan, China. In Abstracts of the 48th Annual Meeting of the Mycological Society of Japan, p. 45.
  16. Redhead, S. A. ( 1997; ). The pine mushroom industry in Canada and the United States: why it exists and where it is going. In Mycology in Sustainable Development, pp. 15–54. Edited by M. A. Palm & I. H. Chapela. Boone, NC: Parkway Publishers.
  17. Swofford, D. L. ( 2004; ). PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods). Sunderland, MA: Sinaur Associates.
  18. Tominaga, Y. ( 1978; ). Tricholoma matsutake. In The Biology and Cultivation of Edible Mushrooms, pp. 683–697. Edited by S. T. Chang & W. A. Hayes. London: Academic Press.
  19. Wang, Y., Hall, I. R. & Evans, L. A. ( 1997; ). Ectomycorrhizal fungi with edible fruiting bodies. I. Tricholoma matsutake and related fungi. Econ Bot 51, 311–327.[CrossRef]
    [Google Scholar]
  20. Welch, D. M. & Meselson, M. ( 2000; ). Evidence for the evolution of bdelloid rotifers without sexual reproduction or genetic exchange. Science 288, 1211–1215.[CrossRef]
    [Google Scholar]
  21. Xu, J. ( 2006a; ). Extracting haplotypes from diploid organisms. Curr Issues Mol Biol 8, 113–122.
    [Google Scholar]
  22. Xu, J. ( 2006b; ). Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Mol Ecol 15, 1713–1731.[CrossRef]
    [Google Scholar]
  23. Xu, J., Mitchell, T. G. & Vilgalys, R. ( 1999; ). PCR-restriction fragment length polymorphism (RFLP) analyses reveal both extensive clonality and local genetic differences in Candida albicans. Mol Ecol 8, 59–73.[CrossRef]
    [Google Scholar]
  24. Xu, J., Ramos, A. R., Vilgalys, R. & Mitchell, T. G. ( 2000a; ). Clonal and spontaneous origins of fluconazole resistance in Candida albicans. J Clin Microbiol 38, 1214–1220.
    [Google Scholar]
  25. Xu, J., Vilgalys, R. & Mitchell, T. G. ( 2000b; ). Multiple gene genealogies reveal recent dispersion and hybridization in the human pathogenic fungus Cryptococcus neoformans. Mol Ecol 9, 1471–1481.[CrossRef]
    [Google Scholar]
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