Please wait a minute...
Journal of Integrative Agriculture  2018, Vol. 17 Issue (11): 2458-2466    DOI: 10.1016/S2095-3119(18)61967-7
Horticulture Advanced Online Publication | Current Issue | Archive | Adv Search |
Intergenic spacer 1 (IGS1) polymorphism map: A marker for the initial classification of cultivated Lentinula edodes strains in China
SONG Xiao-xia*, ZHAO Yan*, SONG Chun-yan, LI Chuan-hua, CHEN Ming-jie, HUANG Jian-chun, TAN Qi
Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, P.R.China
Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      
Abstract  
China is currently the world’s leading producer of Lentinula edodes and owns many cultivated strains of this species.  This study was performed in order to investigate intergenic spacer 1 (IGS1) polymorphism and classification among 49 popular cultivated strains.  The great majority of the 49 strains possessed two different IGS1 sequences, with distinct lengths and homologies.  Based on the length and homology of the IGS1 sequences of the 49 strains, the strains were classified into two groups: A and B.  Group A was subdivided into six subgroups.  Forty-seven strains were homozygous or heterozygous among these six subgroups in group A, Cr01 was heterozygous between A and B, and Guangxiang 9 was homozygous in group B.  An IGS1 polymorphism map of each cultivated L. edodes strain is reported for the first time and could be used as a marker for the initial classification and management of cultivated L. edodes strains in China. 
 
Keywords:  Lentinula edodes        strain        intergenic spacer        polymorphism        genotype  
Received: 10 November 2017   Accepted:
Fund: This work was supported by the earmarked fund for China Agriculture Research System (CARS-20), the Youth Talent Development Plan of Shanghai Municipal Agricultural System, China (20160113) and the Agriculture Research System of Shanghai, China (201809).
Corresponding Authors:  Correspondence CHEN Ming-jie, Tel: +86-21-62200747, Fax: +86-21-62201337, E-mail: mjfungi@126.com    
About author:  SONG Xiao-xia, E-mail: sxx8866@163.com; ZHAO Yan, E-mail: jiandan289@126.com; * These authors contributed equally to this study.

Cite this article: 

SONG Xiao-xia, ZHAO Yan, SONG Chun-yan, LI Chuan-hua, CHEN Ming-jie, HUANG Jian-chun, TAN Qi. 2018. Intergenic spacer 1 (IGS1) polymorphism map: A marker for the initial classification of cultivated Lentinula edodes strains in China. Journal of Integrative Agriculture, 17(11): 2458-2466.

Babasaki K, Neda H, Murata H. 2007. megB1, a novel macroevolutionary genomic marker of the Fungal phylum Basidiomycota. Bioscience, Biotechnology, and Biochemistry, 71, 1927–1939.
Bhardwa S, Sutar R, Bachhawat A K, Singhi S, Chakrabarti A. 2007. PCR-based identification and strain typing of Pichia anomala using the ribosomal intergenic spacer region IGS1. Journal of Medical Microbiology, 56, 185–189.
Bunyard B A, Chaichuchote S, Nicholson M S, Royse D J. 1996a. Ribosomal DNA analysis for resolution of genotypic classes of Pleurotus. Mycological Research, 100, 143–150.
Bunyard B A, Nicholson M S, Royse D J. 1996b. Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genetics and Biology, 20, 243–253.
Chang S T, Miles P G. 1987. Historical record of the early cultivation of Lentinus in China. Mushroom Journal of the Tropics, 7, 31–37.
Chang S T, Miles P G. 2004. Mushrooms: Cultivation, Nutritional Value, Medicinal Effect and Environmental Impact. CRC Press, Boca Raton.
Chen J, Moinard M, Xu J P, Wang S X, Foulongne-Oriol M, Zhao R L, Hyde K D, Callac P. 2016. Genetic analyses of the internal transcribed spacer sequences suggest introgression and duplication in the medicinal mushroom Agaricus subrufescens. PLoS ONE, 11, e0156250.
Fu L Z, Zhang H Y, Wu X Q, Li H B, Wei H L, Wu Q Q, Wang L A. 2010. Evaluation of genetic diversity in Lentinula edodes strains using RAPD, ISSR, and SRAP markers. World Journal of Microbiology & Biotechonology, 26, 709–716.
Ganley A R D, Kobayashi T. 2007. Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data. Genome Research, 17, 184–191.
Hibbett D S, Fukumasa-Nakai Y, Tsuneda A, Donoghue M J. 1995. Phylogenetic diversity in shiitake inferred from nuclear ribosomal DNA sequences. Mycologia, 87, 618–638.
Hibbett D S, Hansen K, Donoghue M J. 1998. Phylogeny and biogeography of Lentinula inferred from an expanded rDNA dataset. Mycological Research, 102, 1041–1049.
Hoff K J. 2009. The effect of sequencing errors on metagenomic gene prediction. BMC Genomics, 10, 520.
International Mycological Association. 2017. Mycobank database fungal databases, nomenclature and species banks. [2017-11-06]. http://www.mycobank.org/
Jo S H, Koo D H, Kim J F, Hur C G, Lee S, Yang T J, Kwon S Y, Choi D. 2009. Evolution of ribosomal DNA-derived satellite repeat in tomato genome. BMC Plant Biology, 9, 42.
Kwon H W, Choi M A, Kim D W, Oh Y L, Hyun M W, Kong W S, Kim S H. 2016. Ribosomal intergenic spacer 1 based characterization of button mushroom (Agaricus bisporus) strains. Mycobiology, 44, 314–318.
Kwon H W, Choi M A, Yun Y H, Oh Y L, Kong W S, Kim S H. 2015. Genetic and biochemical characterization of monokaryotic progeny strains of button mushroom (Agaricus bisporus). Mycobiology, 43, 81–86.
Li C, Gong W B, Zhang L, Yang Z Q, Nong W Y, Bian Y B, Kwan H S, Cheung M K, Xiao Y. 2017. Association mapping reveals genetic loci associated with important agronomic traits in Lentinula edodes, shiitake mushroom. Frontiers in Microbiology, 8, 237.
Liu J, Wang Z R, Li C, Bian Y B, Xiao Y. 2015. Evaluating genetic diversity and constructing core collections of Chinese Lentinula edodes cultivars using ISSR and SRAP markers. Journal of Basic Microbiology, 55, 749–760.
Liu J Y, Ying Z H, Liu F, Liu X R, Xie B G. 2012. Evalution of the use of SCAR markers for screening genetic diversity of Lentinula edodes strains. Current Microbiology, 64, 317–325.
Prokopowich C D, Gregory T R, Crease T J. 2003. The correlation between rDNA copy number and genome size in eukaryotes. Genome, 46, 48–50.
Saghai-Maroof M A, Soliman K M, Jorgensen R A, Allard R W. 1984. Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proceedings of the National Academy of Sciences of the United States of America, 81, 8014–8018.
Saito T, Tanaka N, Shinozawa T. 2002. Characterization of subrepeat regions within rDNA intergenic spacers of the edible Basidiomycete Lentinula edodes. Bioscience, Biotechnology, and Biochemistry, 66, 2125–2133.
Simon U K, Weiß M. 2008. Intragenomic variation of fungal ribosomal genes is higher than previously thought. Molecular Biology and Evolution, 25, 2251–2254.
Song X X, Li C H, Tan Q, Li Q Z, Ma D D, Chen M J. 2015. The summary of resources of some cultivated strains of Lentinula edodes in China. Journal of Fungal Research, 13, 146–154. (in Chinese)
Song X X, Wang Q, Zhao Y, Huang J C, Song C Y, Chen M J, Tan Q. 2018a. Cx activity and IGS1 sequence difference among monokaryotic and dikayotic mycelia of L808, Lentinula edodes. Acta Agriculturae Shanghai, 34, 54–58. (in Chinese)
Song X X, Zhao Y, Song C Y, Li C H, Song Y, Chen M J, Bao D P, Tan Q. 2018b. ITS1/5.8S/ITS2, a good marker for initial classification of shiitake culinary-medicinal Lentinula edodes (Agaricomycetes) strains in China. International Journal of Medicinal Mushrooms, 20, 227–242.
Sugita T, Kodama M, Saito M, Ito T, Kato Y, Tsuboi R, Nishikawa A. 2003. Sequence diversity of the intergenic spacer region of the rRNA gene of Malassezia globosa colonizing the skin of patients with atopic dermatits and healthy individuals. Journal of Clinical Microbiology, 41, 3022–3027.
Sugita T, Nakajima M, Ikeda R, Matsushima T, Shinoda T. 2002. Sequence analysis of the ribosomal DNA intergenic spacer 1 regions of Trichosporon species. Journal of Clinical Microbiology, 40, 1826–1830.
Sugita T, Takeo K, Hama K, Virtudazo E, Takashima M, Nishikawa A, Kicsera J, Dorogi J, Komori S, Nakagaki K, Vollekova A, Slavikova E, Farkas V. 2005. DNA sequence diversity of intergenic spacer 1 region in the non-lipid-dependent species Malassezia pachydermatis isolated from animals. Medical Mycology, 43, 21–26.
Xiao Y, Cheng X J, Liu J, Li C, Nong W Y, Bian Y B, Cheung M K, Kwan H S. 2016. Population genomic analysis uncovers environmental stress-driven selection and adaptation of Lentinula edodes population in China. Scientific Reports, 6, 36789.
Xu X F, Li A, Cheng S M, Lin F X, Lin F C. 2006. Reappraisal of phylogenetic status and genetic diversity analysis of Asian population of Lentinula edodes. Progress in Natural Science: Materials International, 16, 274–280.
[1] WANG Deng-feng, YANG Xue-yun, WEI Yu-rong, LI Jian-jun, BOLATI Hongduzi, MENG Xiao-xiao, TUERXUN Gunuer, NUERDAN Nuerbaiheti, WU Jian-yong. Genome characterization of the Caprine arthritis-encephalitis virus in China: A retrospective genomic analysis of the earliest Chinese isolates[J]. >Journal of Integrative Agriculture, 2023, 22(3): 872-880.
[2] DU Qing-guo, YANG Juan, Shah SYED MUHAMMAD SADIQ, YANG Rong-xin, YU Jing-juan, LI Wen-xue. Comparative transcriptome analysis of different nitrogen responses in low-nitrogen sensitive and tolerant maize genotypes[J]. >Journal of Integrative Agriculture, 2021, 20(8): 2043-2055.
[3] LIU Na, CHENG Fang-yun, GUO Xin, ZHONG Yuan. Development and application of microsatellite markers within transcription factors in flare tree peony (Paeonia rockii) based on next-generation and single-molecule long-read RNA-seq[J]. >Journal of Integrative Agriculture, 2021, 20(7): 1832-1848.
[4] WANG Yu-long, FAN Lin-jin, JIANG Nan, GAO Li, LI Kai, GAO Yu-long, LIU Chang-jun, CUI Hong-yu, PAN Qing, ZHANG Yan-ping, WANG Xiao-mei, QI Xiao-le. An improved scheme for infectious bursal disease virus genotype classification based on both genome-segments A and B[J]. >Journal of Integrative Agriculture, 2021, 20(5): 1372-1381.
[5] LIU Kai, CHEN Zhan, SU Qin, YUE Lei, CHEN Wei-wen, ZHANG Wen-qing. Comparative analysis of the ecological fitness and transcriptome between two genotypes of the brown planthopper Nilaparvata lugens[J]. >Journal of Integrative Agriculture, 2020, 19(6): 1501-1511.
[6] KANG Liang, LIANG Qiong-yue, JIANG Qiang, YAO Yi-hua, DONG Meng-meng, HE Bing, GU Ming-hua. Screening of diverse cassava genotypes based on nitrogen uptake efficiency and yield[J]. >Journal of Integrative Agriculture, 2020, 19(4): 965-974.
[7] LIU Tai-guo, GE Run-jing, MA Yu-tong, LIU Bo, GAO Li, CHEN Wan-quan. Population genetic structure of Chinese Puccinia triticina races based on multi-locus sequences[J]. >Journal of Integrative Agriculture, 2018, 17(08): 1779-1789.
[8] MA Lei, ZHU Yuan-mao, YANG Ting, XUE Fei. Evaluation of an attenuated vaccine candidate based on the genotype C of bovine parainfluenza virus type 3 in albino guinea pigs[J]. >Journal of Integrative Agriculture, 2017, 16(09): 2047-2054.
[9] YANG Feng, WANG Qi, WANG Xu-rong, WANG Ling, LI Xin-pu, LUO Jin-yin, ZHANG Shi-dong, LI Hong-sheng. Genetic characterization of antimicrobial resistance in Staphylococcus aureus isolated from bovine mastitis cases in Northwest China[J]. >Journal of Integrative Agriculture, 2016, 15(12): 2842-2847.
No Suggested Reading articles found!