Journal of Mushroom (한국버섯학회지)

The Korean Society of Mushroom Science (한국버섯학회)
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Characterization of simple sequence repeats (SSRs) in Pleurotus pulmonarius cultivars

산느타리(Pleurotus pulmonarius) 품종의 초위성체(simple sequence repeats) 특성구명

  • Choi, Jong In (Gyeonggi-do Agricultural Research &Extension Services) ;
  • Na, Kyeong Sook (Department of mushroom science, Korea National college of Agriculture and fisheries) ;
  • Oh, Min-Ji (Mushroom Research Division, National Institute of Horticultural & Herbal Science, RDA) ;
  • Ryu, Jae-San (Department of mushroom science, Korea National college of Agriculture and fisheries)
  • 최종인 (경기도농업기술원 버섯연구소) ;
  • 나경숙 (한국농수산대학 버섯학과) ;
  • 오민지 (농촌진흥청 버섯과) ;
  • 류재산 (한국농수산대학 버섯학과)
  • Received : 2021.02.09
  • Accepted : 2021.11.05
  • Published : 2021.12.31
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Abstract

Simple sequence repeats (SSRs) were isolated from major Pleurotus pulmonarius cultivars in Korea, namely 'HS47' (monokaryon, gamete of 'Santari'), 'GB19' (monokaryon, gamete of 'Santari'), 'Hosan,' 'Yeoleumneutali1,' 'Sambok,' 'Gangsan,' 'Yaksan,' 'Jasan,' 'Hyangsan,' and 'Yeoleumneutali2,' and characterized via HiSeq genome sequencing and bioinformatic analysis. The genome sizes of the monokaryons 'HS47' and 'GB19' were estimated to be 37.3 and 37.2 Mb, respectively, and those of the other dikaryotic cultivars ranged from 47.1 to 61.1 Mb. A total of 711 (smallest) and 1,106 (1.5 times the smallest) SSRs were found in the 'HS47' and 'Gangsan' genomes, respectively. Hexanucleotide and octanucleotide motifs accounted for the top two fractions of all SSRs. CGA/TCG, A/T, and CTC/GAG were the most frequently detected nucleotides in the SSRs. Most of the SSRs were 21~30 nucleotides long (hypervariable for application), accounting for 70% of all lengths of SSRs.

국내의 주요 산느타리 품종인 호산47(일핵, 산타리 배우자), GB19(일핵, 산타리 배우자), 호산, 여름느타리1호, 삼복, 강산, 약산, 자산, 향산, 여름느타리2호의 유전체를 Hiseq을 이용하여 해독하였고 이 서열 정보에서 SSR을 분리하여 특성구명을 하였다. 일핵균사인 호산 47, GB19의 유전체의 크기는 각각 37.3와 37.2 Mbp이고, 이핵균사인 나머지 산느타리 품종의 유전체 크기는 47.1~61.1 Mbp인 것으로 밝혀졌다. 품종별 총 SSR의 수는 HS47이 711개로 가장 적고, 강산이(GS)이 1.5배 많은 1,106개로 최다를 기록하였다. SSR의 repeat motif 중에서 hexanucleotide와 octanucleotide가 가장 많은 빈도로 관찰되었고, 가장 많이 관찰되는 반복서열은 CGA/TCG, A/T, CTC/GAG이었다. SSR의 길이는 모든 품종에서 변이가 많아 유용성이 높은 20~30 nt가 가장 높은 비중인 70%를 차지하였다.

Keywords

Acknowledgement

본 연구는 본 연구는 농림축산식품부 Golden Seed project 사업(원예종자사업단, 과제번호: 213007-05-5-SBI30)에 의해 이루어진 것으로 연구비 지원에 감사드립니다.

References

  1. Bindler G, Plieske J, Bakaher N, Gunduz I, Ivanov N, Van der Hoeven R, Ganal M, Donini P. 2011. A high density genetic map of tobacco (Nicotiana tabacum L.) obtained from large scale microsatellite marker development. Theor Appl Genet 123: 219-230. https://doi.org/10.1007/s00122-011-1578-8
  2. Boekhout T. 1990. Flora agaricina neerlandica. CRC press, Boca Raton, Florida, USA. 20-40.
  3. Castillo-Lizardo M, Henneke G, Viguera E. 2014. Replication slippage of the thermophilic DNA polymerases B and D from the Euryarchaeota Pyrococcus abyssi. Front microbiol 5: 403. https://doi.org/10.3389/fmicb.2014.00403
  4. Choi JI, Lee YH, Jeon DH, Gwon HM, Chi JH, Shin PG. 2017. Mycelial and cultural characteristics of a new high-yield Pleurotus pulmonarius cultivar 'Santari' for bottle culture. J Mushroom 15: 190-194. https://doi.org/10.14480/JM.2017.15.4.190
  5. El-Rodeny W, Kimura M, Hirakawa H, Sabah A, Shirasawa K. 2014. Development of EST-SSR markers and construction of a linkage map in faba bean (Vicia faba). BreedSci 64: 252-263.
  6. Frey KG, Herrera-Galeano JE, Redden CL, Luu TV, Servetas SL, Mateczun AJ, Bishop-Lilly KA. 2014. Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood. BMC genomics 15: 1-14. https://doi.org/10.1186/1471-2164-15-1
  7. Guzman G. 2000. Genus Pleurotus (Jacq.: Fr.) P. Kumm. (Agaricomycetideae): diversity, taxonomic problems, and cultural and traditional medicinal uses. Int J med mushrooms 2: 95-l23. https://doi.org/10.1615/IntJMedMushr.v2.i2.10
  8. Han SK. Chang SK, Jong WJ, Kwag YN. 2016. Recorded mushrooms in Ulleungdo and Dokdo, Korea, Korea National Arboretum, Poncheon, Korea. pp. 165.
  9. Im CH, Park Y-H, Hammel KE, Park B, Kwon SW, Ryu HJ, Ryu J-S. 2016. Construction of a genetic linkage map and analysis of quantitative trait loci associated with the agronomically important traits of Pleurotus eryngii. Fungal Genet Biol 92: 50-64. https://doi.org/10.1016/j.fgb.2016.05.002
  10. Karaoglu H, Lee CMY, Meyer W. 2005. Survey of simple sequence repeats in completed fungal genomes. Mol Biol Evol 22: 639-649. https://doi.org/10.1093/molbev/msi057
  11. Khush GS, Brar DS, Hardy B. (Eds.). 2008. Rice Genetics Iv-Proceedings Of The Fourth International Rice Genetics Symposium (Vol. 4). World Scientific pp. 122.
  12. Kim KS, You CH, Kong WS, Kim YH, Cha DR, Ko MS. 1997. Breeding of Pleurotus sajor-caju cultivar with high yield and adaptable to high temperature. KSM newsletter 9: 22-22.
  13. Labbe J, Murat C, Morin E, Le Tacon F, Martin F. 2011. Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers. Curr Genet 57: 75-88. https://doi.org/10.1007/s00294-010-0328-9
  14. Lee HY, Moon S, Ro HS, Chung JW, Ryu H. 2020. Analysis of Genetic Diversity and Population Structure of Wild Strains and Cultivars Using Genomic SSR Markers in Lentinula edodes. Mycobiology 48: 115-121. https://doi.org/10.1080/12298093.2020.1727401
  15. Lee KJ, Kim KH, Cho BJ, Park YH. 2008. Cultural characteristics and consumer acceptance of Pleurotus pulmonarius. J Mushroom 6: 146-149.
  16. Lee NK, Lee JH, Mun YK, Park YH, Jeong TS, Kwon SB, Kim IJ. 2016. New cultivar of Pleurotus pulmonarius (Fr. Quelet), Jasan. Mushroom 20: 188-188.
  17. Li Y-C, Korol AB, Fahima T, Nevo E. 2004. Microsatellites within Genes: Structure, Function, and Evolution. Mol Biol Evol 21: 991-1007. https://doi.org/10.1093/molbev/msh073
  18. Miah G, Rafii M, Ismail M, Puteh A, Rahim H, Islam KN, Latif MA. 2013. A Review of Microsatellite Markers and Their Applications in Rice Breeding Programs to Improve Blast Disease Resistance. Int J Mol Sci 14: 22499-22528. https://doi.org/10.3390/ijms141122499
  19. Park B, Ha BS, Kim MK, Lee B, Choi JI, Ryu J-S. 2016. Characterization of simple sequence repeats in the Pleurotus ostreatus cultivars, 'Heuktari' and 'Miso'. J Mushroom 14: 174-178. https://doi.org/10.14480/JM.2016.14.4.174
  20. Park B, Ha BS, Lee SH, Kim MK, Choi JI, Ryu JS. 2019. Variable-number tandem repeat loci-discriminating Pleurotus ostreatus cultivars. Mycoscience 60: 132-135. https://doi.org/10.1016/j.myc.2018.09.004
  21. Park YH, Lee KJ, Jo BJ, Kim KH, Jeong EK, Park JS, Sung JM. 2008. Breeding of new Grifolaria frondosa, "Dae Whang" and Pleurotus pulmunarius, Hosan and their cultivational properties. Mushroom 6: 86-86.
  22. Peona V, Weissensteiner MH, Suh A. 2018. How complete are "complete" genome assemblies?-An avian perspective. Mol Ecol Resour 18: 1188-1195. https://doi.org/10.1111/1755-0998.12933
  23. Riley R, Salamov AA, Brown DW, Nagy LG, Floudas D. 2014. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proc Natl Acad Sci U.S.A 111: 9923-9928. https://doi.org/10.1073/pnas.1400592111
  24. Ryu J-S, Je HJ. 2012. Complete Genome Sequence of Pleurotus eryngii KNR2312 Using the Next Generation Sequencing (NGS). 80th meeting of the mycological society of America, The mycological society of America, New Haven, Connecticut, USA.
  25. Sharma VP, Kamal S, Upadhyay RC, Kumar S, Sanyal SK, Singh M. 2015. Taxonomy, phylogeny, cultivation and biological activities of a Lentinus species from Andaman & Nicobar islands (India). Emir J Food Agric 27: 570-576. https://doi.org/10.9755/ejfa.2015.04.135
  26. Shnyreva AA, Sivolapova AB, Shnyreva AV. 2012. The commercially cultivated edible oyster mushrooms Pleurotus sajor-caju and P. pulmonarius are two separate species, similar in morphology but reproductively isolated. Russ J Genet 48: 1080-1088. https://doi.org/10.1134/S1022795412110105
  27. Song Q, Jia G, Zhu Y, Grant, D, Nelson RT, Hwang EY, Cregan PB. 2010. Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1. 0) in soybean. Crop sci 50: 1950-1960. https://doi.org/10.2135/cropsci2009.10.0607
  28. Thiel T, Michalek W, Varshney R, Graner A. 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106: 411-422. https://doi.org/10.1007/s00122-002-1031-0
  29. Zimin AV, Puiu D, Hall R, Kingan S, Clavijo BJ, Salzberg SL. 2017. The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum. Gigascience, 6: gix097.
  30. Zmitrovich IV, Wasser SP. 2016. Is Widely Cultivated" Pleurotus sajor-caju", Especially in Asia, Indeed an Independent Species? Int J med mushrooms 18: 583-588. https://doi.org/10.1615/intjmedmushrooms.v18.i7.30