The Korean Journal of Mycology (한국균학회지)

The Korean Society of Mycology (한국균학회)
권호 표지
DOI QR코드

DOI QR Code

Genome-wide Single Nucleotide Polymorphism-based Assay for Phylogenetic Relationship of the Flammulina velutipes

팽이버섯(Flammulina velutipes)의 Genome-wide SNP (Single Nucleotide Polymorphism)에 의한 계통 분석

  • Woo, Sung-I (Mushroom Research Division, National Institute of Horticultural & Herbal Science, RDA) ;
  • Kim, Eun-Seon (Mushroom Research Division, National Institute of Horticultural & Herbal Science, RDA) ;
  • Han, Jae-Gu (Mushroom Research Division, National Institute of Horticultural & Herbal Science, RDA) ;
  • Jang, Kab Yeul (Mushroom Research Division, National Institute of Horticultural & Herbal Science, RDA) ;
  • Shin, Pyung-Gyun (Mushroom Research Division, National Institute of Horticultural & Herbal Science, RDA) ;
  • Oh, Youn-Lee (Mushroom Research Division, National Institute of Horticultural & Herbal Science, RDA) ;
  • Oh, Min Ji (Mushroom Research Division, National Institute of Horticultural & Herbal Science, RDA) ;
  • Jo, Sung-Hwan (SEEDERS) ;
  • Lee, Jeong-Hee (SEEDERS) ;
  • Kim, Kyung-Soo (Department of Applied Biology, Kangwon National University) ;
  • Kong, Won-Sik (Mushroom Research Division, National Institute of Horticultural & Herbal Science, RDA)
  • 우성이 (농촌진흥청 국립원예특작과학원 버섯과) ;
  • 김은선 (농촌진흥청 국립원예특작과학원 버섯과) ;
  • 한재구 (농촌진흥청 국립원예특작과학원 버섯과) ;
  • 장갑열 (농촌진흥청 국립원예특작과학원 버섯과) ;
  • 신평균 (농촌진흥청 국립원예특작과학원 버섯과) ;
  • 오연이 (농촌진흥청 국립원예특작과학원 버섯과) ;
  • 오민지 (농촌진흥청 국립원예특작과학원 버섯과) ;
  • 조성환 (씨더스) ;
  • 이정희 (씨더스) ;
  • 김경수 (강원대 응용생물학과) ;
  • 공원식 (농촌진흥청 국립원예특작과학원 버섯과)
  • Received : 2015.11.09
  • Accepted : 2015.12.16
  • Published : 2015.12.31
Download PDF
⟨ Previous Next ⟩

Abstract

Genome-wide reanalyzed data of 25 Flammulina strains were compared against the reference genome (KACC42780) to establish a genome-wide single nucleotide polymorphism (SNP). The rate of mapping differences between the strains reflected in the strain variation in its result. Genome-wide SNPs distribution divided into types of homozygous SNP and heterozygous SNP moreover all of the strains demonstrated a wide variation in all of the regions. In the further study of topological relationship between the collected strains, phylogenetic tree was separated into 3 major groups. Group I contained F. velutipes var. related strains of ASI 4062, 4148, 4195. Group 2 contained strains that are different species of ASI 4188 F. elastica, ASI 4190 F. fennae, and ASI 4194 F. rossica. The other 19 strains F. velutipes were classified as a single group. However, further experiment to discriminate its genetic relationship between the white group and brown group did not verify its validity. The inferred tree exhibited a phylogenetic relationship between Korea white fruitbody forming strains of ASI 4210, 4166, 4178 and Japan white fruitbody forming strains of ASI 4209, 4167 confirmed to be genetically closely related.

팽이버섯(Flammulina velutipes) 25품종의 유전체 재분석 데이터를 표준유전체(KACC42781)와 비교하여 genomewide single nucleotide polymorphism (SNP)를 선발하였다. 균주에 따른 mapping율의 차이는 균주간 변이를 반영하였으며, genome-wide SNP분포는 homozygous SNP, heterozygous SNP로 구분되었으며 모두 균주에 따른 변이가 크게 나타났다. 수집균주들 사이의 유연관계를 살펴보기 위해, 계통수를 그려본 결과, Group I은 F. velutipes var. 계통인 ASI 4062, 4148, 4195이 묶여지고, Group II는 ASI 4188 F. elastica, ASI 4190 F. fennae, ASI 4194 F. rossica의 다른 종이 별도의 그룹을 형성하였다. 그 외 F. velutipes 19개 계통은 같은 그룹으로 나타났으며 그 유전적 자리를 잘 반영하였다. 한편 백색 group과 갈색 group을 유연관계로 분석하고자 시도하였으나 색깔에 따른 group은 이루어지지 않았다. 한국 백색 품종인 ASI 4210, 4166, 4178과 일본 백색 품종인 ASI 4209, 4167을 분석한 결과 phylogenetic tree상에서 한국 백색 품종과 일본 백색 품종간의 유전적 상동성이 매우 높음을 확인할 수 있었다.

Keywords

References

  1. Oh SI, Lee MS. Functional activities of ethanol extracts from Flammulina velutipes. Kor J Food Nutr 2010;23:15-22.
  2. Tonomura H. Flammulina velutipes. In: Chang ST, Hayes WA, editors. Biology and cultivation of edible mushrooms. New York: Academic Press; 1978. p. 409-21.
  3. Chang ST, Miles PG. Edible mushrooms and their cultivation. Boca Ration: CRC Press; 1989.
  4. Kitamoto Y, Nakamata M, Masuda P. Production of a novel white Flammulina velutipes by breeding. In: Chang ST, Buswell JA, Miles PG, editors. Genetics and breeding of edible mushrooms. Philadelphia: Gordon and Breach; 1993. p. 65-86.
  5. Kong WS, Jang KY, Lee CY, Koo J, Shin PG, Jhune CS, Oh YL, Yoo YB, Suh JS. Breeding progress and characterization of a Korean white variety 'Baek-A' in Flammulina velutipes. J Mushroom Sci Prod 2013;11:159-63. https://doi.org/10.14480/JM.2013.11.3.159
  6. Mitchell JI, Roberts PJ, Moss ST. Sequence or structure: a short review on the application of nucleic acid sequence information to fungal taxonomy. Mycologist 1995;9:67-75. https://doi.org/10.1016/S0269-915X(09)80212-7
  7. Park YJ, Baek JH, Lee S, Kim C, Rhee H, Kim H, Seo JS, Park HR, Yoon DE, Nam JY, et al. Whole genome global gene expression analyses of the model mushroom Flammulina velutipes reveal a high capacity for lignocellulose degradation. PLoS One 2014;9:e93560. https://doi.org/10.1371/journal.pone.0093560
  8. Cox MP, Peterson DA, Biggs PJ. SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 2010;11:485. https://doi.org/10.1186/1471-2105-11-485
  9. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013;30:2725-9. https://doi.org/10.1093/molbev/mst197
  10. Ness RW, Siol M, Barrett SC. De novo sequence assembly and charcacterization of the floral transcriptome in croossand self-fertilizing plants. BMC Genomics 2011;12:298. https://doi.org/10.1186/1471-2164-12-298
  11. Garg R, Patel RK, Tyagi AK, Jain M. De novo assembly of chickpea transcriptomeusing short reads for gene discovery and marker identification. DNA Res 2011;18:53-63. https://doi.org/10.1093/dnares/dsq028
  12. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioninformatics 2009;25:1754-60. https://doi.org/10.1093/bioinformatics/btp324
  13. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009;25:2078-9. https://doi.org/10.1093/bioinformatics/btp352
  14. Kim JE, Oh SK, Lee JH, Lee BM, Jo SH. Genome-wide SNP calling using next generation sequencing data in tomato. Mol Cells 2014;37:36-42. https://doi.org/10.14348/molcells.2014.2241
  15. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28:2731-9. https://doi.org/10.1093/molbev/msr121
  16. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007;24:1596-9. https://doi.org/10.1093/molbev/msm092
  17. Jimenez-Gomez JM, Maloof JN. Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. BMC Plant Biol 2009;9:85. https://doi.org/10.1186/1471-2229-9-85
  18. Jung JK, Park SW, Liu Wy, Kang BC. Discovery of single mucleotide polymorphism in Capicum and SNP markers for cultivar identification. Euphytica 2010;175:91-107. https://doi.org/10.1007/s10681-010-0191-2
  19. Park YJ, Kim JK, Kong WS, Song ES, Lee CS, Kim H, Hahn JH, Kang HW, Lee BM. Electrophoretic karyotyping and construction of a bacterial artificial chromosome library of the winter mushroom Flammulina velutipes. Microbiol Res 2010;165:321-8. https://doi.org/10.1016/j.micres.2009.06.003
  20. Hughes KW, McGhee LL, Methven AS, Johnson JE, Petersen RH. Patterns of geographic speciation in the genus Flammulina based on sequences of the ribosomal ITS1-5.8S-ITS2 area. Mycologia 1999;91:978-86. https://doi.org/10.2307/3761628