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http://dx.doi.org/10.4489/KJM.2015.43.4.231

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

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)
Publication Information
The Korean Journal of Mycology / v.43, no.4, 2015 , pp. 231-238 More about this Journal
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.
Keywords
Flammulina velutipes; SNP; Single nucleotide polymorphisms; Phylogenetic analysis;
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Times Cited By KSCI : 3  (Citation Analysis)
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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.   DOI
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.   DOI
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.   DOI
8 Cox MP, Peterson DA, Biggs PJ. SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 2010;11:485.   DOI
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.   DOI
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.   DOI
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.   DOI
12 Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioninformatics 2009;25:1754-60.   DOI
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.   DOI
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.   DOI
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.   DOI
16 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.   DOI
17 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.   DOI
18 Jimenez-Gomez JM, Maloof JN. Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. BMC Plant Biol 2009;9:85.   DOI
19 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.   DOI
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.   DOI