Molecular divergence and species delimitation of the cultivated oyster mushrooms: Integration of IGS1 and ITS

The Scientific World Journal

Volumn 2014, Issue , 2014, Pages

  Avin, Farhat Ahmadi ^a,b   Bhassu, Subha ^a,b   Tan, Yee Shin ^a,b   Shahbazi, Pedram ^b   Vikineswary, Sabaratnam ^a,b  

^a UNIVERSITY OF MALAYA   (Malaysia)

^b UNIVERSITY OF MALAYA   (Malaysia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING SITE; CLASSIFICATION; GENETICS; METABOLISM; MOLECULAR EVOLUTION; PHYLOGENY; PHYSIOLOGY; PLEUROTUS; SPECIES DIFFERENCE;

BINDING SITES; EVOLUTION, MOLECULAR; PHYLOGENY; PLEUROTUS; SPECIES SPECIFICITY;

EID: 84893878393     PISSN: None     EISSN: 1537744X     Source Type: Journal    
DOI: 10.1155/2014/793414     Document Type: Article

References (53)

1. Wang Y., Zeng F., Hon C. C., Zhang Y., Leung F. C. C., The mitochondrial genome of the Basidiomycete fungus Pleurotus ostreatus (oyster mushroom). FEMS Microbiology Letters 2008 280 1 34 41 2-s2.0-38849095278 10.1111/j.1574-6968. 2007.01048.x (Pubitemid 351207295)
2. Adebayo E. A., Oloke J. K., Yadav A., Barooah M., Bora T. C., Improving yield performance of Pleurotus pulmonarius through hyphal anastomosis fusion of dikaryons. World Journal of Microbiology and Biotechnology 2013 29 1029 1037
3. Adejumo T. O., Awosanya O. B., Proximate and mineral composition of four edible mushroom species from South Western Nigeria. African Journal of Biotechnology 2005 4 10 1084 1088 2-s2.0-27144507119 (Pubitemid 41500679)
4. Zervakis G., Balis C., A pluralistic approach in the study of Pleurotus species with emphasis on compatibility and physiology of the European morphotaxa. Mycological Research 1996 100 6 717 731 2-s2.0-0000531838 (Pubitemid 126527531)
5. Ravash R., Shiran B., Alavi A. A., Bayat F., Rajaee S., Zervakis G. I., Genetic variability and molecular phylogeny of Pleurotus eryngii species-complex isolates from Iran, and notes on the systematics of Asiatic populations. Mycological Progress 2010 9 2 181 194 2-s2.0-77952422130 10.1007/s11557-009- 0624-2
6. Choi D. B., Ding J. L., Cha W. S., Homology search of genus Pleurotus using an internal transcribed spacer region. Korean Journal of Chemical Engineering 2007 24 3 408 412 2-s2.0-36949034564 10.1007/s11814-007-0070-2
7. Chang Y. S., Lee S. S., Utilisation of macrofungi species in Malaysia. Fungal Diversity 2004 15 15 22 2-s2.0-2342437336 (Pubitemid 38554728)
8. Urbanelli S., Della Rosa V., Punelli F., Porretta D., Reverberi M., Fabbri A. A., Fanelli C., DNA-fingerprinting (AFLP and RFLP) for genotypic identification in species of the Pleurotus eryngii complex. Applied Microbiology and Biotechnology 2007 74 3 592 600 2-s2.0-33847101762 10.1007/s00253-006-0684- z (Pubitemid 46294996)
9. Ma K. H., Lee G. A., Lee S. Y., Gwag J. G., Kim T. S., Kong W. S., Seo K. I., Lee G. S., Park Y. J., Development and characterization of new microsatellite markers for the oyster mushroom (Pleurotus ostreatus). Journal of Microbiology and Biotechnology 2009 19 9 851 857 2-s2.0-70849106754 10.4014/jmb.0811.604
10. Yan P. S., Jiang J. H., Preliminary research of the RAPD molecular marker-assisted breeding of the edible basidiomycete Stropharia rugoso-annulata. World Journal of Microbiology and Biotechnology 2005 21 4 559 563 2-s2.0-22944481185 10.1007/s11274-004-3271-4 (Pubitemid 41044509)
11. Gonzalez P., Labarère J., Phylogenetic relationships of Pleurotus species according to the sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6 and V9 domains. Microbiology 2000 146 1 209 221 2-s2.0-0041491214 (Pubitemid 30066322)
12. Nguyen H. D. T., Seifert K. A., Description and DNA barcoding of three new species of Leohumicola from South Africa and the United States. Persoonia: Molecular Phylogeny and Evolution of Fungi 2008 21 57 69 2-s2.0-58049212065 10.3767/003158508X361334
13. Seifert K. A., Samson R. A., DeWaard J. R., Houbraken J., Lévesque C. A., Moncalvo J. M., Louis-Seize G., Hebert P. D. N., Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proceedings of the National Academy of Sciences of the United States of America 2007 104 10 3901 3906 2-s2.0-34247236615 10.1073/pnas.0611691104 (Pubitemid 47181551)
14. Estrada A. E. R., Jimenez-Gasco M. D. M., Royse D. J., Pleurotus eryngii species complex: sequence analysis and phylogeny based on partial EF1 α and RPB2 genes. Fungal Biology 2010 114 5-6 421 428 2-s2.0-77953491568 10.1016/j.funbio.2010.03.003
15. White T. J., Bruns T., Lee S., Taylor J., PCR Protocols: A Guide to Methods and Applications 1990 New York, NY, USA Academic Press
16. Begerow D., Nilsson H., Unterseher M., Maier W., Current state and perspectives of fungal DNA barcoding and rapid identification procedures. Applied Microbiology and Biotechnology 2010 87 1 99 108 2-s2.0-77952765171 10.1007/s00253-010-2585-4
17. Seifert K. A., Progress towards DNA barcoding of fungi. Molecular Ecology Resources 2009 9 1 83 89 2-s2.0-65349088516 10.1111/j.1755-0998.2009.02635.x
18. Schoch C. L., Seifert K. A., Huhndorf S., Robert V., Spouge J. L., Levesque C. A., Chen W., Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences of the United States of America 2012 109 16 6241 6246 2-s2.0-84859972408 10.1073/pnas.1117018109
19. Schoch C. L., Seifert K. A., Caldeira K., Myhrvold N. P., Alvarez R. A., Pacala S. W., Winebrake J. J., Chameides W. L., Hamburg S. P., Mullins R. D., Limits of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences as species barcodes for Fungi. Proceedings of the National Academy of Sciences 2012 109 10741 10742
20. Avin F. A., Bhassu S., Shin T. Y., Sabaratnam V., Molecular classification and phylogenetic relationships of selected edible Basidiomycetes species. Molecular Biology Reports 2012 39 7355 7364 2-s2.0-84856773801 10.1007/s11033-012-1567-2
21. Schoch C. L., Seifert K. A., Reply to Kiss: internal transcribed spacer (ITS) remains the best candidate as a universal DNA barcode marker for Fungi despite imperfections. Proceedings of the National Academy of Sciences 2012 109 27, article E1812 10.1073/pnas.1207508109
22. Zhang J. X., Huang C. Y., Ng T. B., Wang H. X., Genetic polymorphism of ferula mushroom growing on Ferula sinkiangensis. Applied Microbiology and Biotechnology 2006 71 3 304 309 2-s2.0-33745507141 10.1007/s00253-005-0139-y (Pubitemid 43962134)
23. Babasaki K., Neda H., Murata H., megB1, a novel macroevolutionary genomic marker of the fungal phylum basidiomycota. Bioscience, Biotechnology and Biochemistry 2007 71 8 1927 1939 2-s2.0-36148991047 10.1271/bbb.70144 (Pubitemid 350113163)
24. Saito T., Tanaka N., Shinozawa T., Characterization of subrepeat regions within rDNA intergenic spacers of the edible basidiomycete Lentinula edodes. Bioscience, Biotechnology and Biochemistry 2002 66 10 2125 2133 2-s2.0-1842848046 (Pubitemid 39251214)
25. Dupuis J. R., Roe A. D., Sperling F. A. H., Multi-locus species delimitation in closely related animals and fungi: one marker is not enough. Molecular Ecology 2012 21 4422 4436 10.1111/j.1365-294X.2012.05642.x
26. Avin F. A., Bhassu S., Sabaratnam V., A simple and low-cost technique of DNA extraction from edible mushrooms examined by molecular phylogenetics. Research on Crops 2013 14 897 901
27. Hoffmann B., Eckert S. E., Krappmann S., Braus G. H., Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune. Genetics 2001 157 1 149 161 2-s2.0-0035148956 (Pubitemid 32066304)
28. Zoller S., Lutzoni F., Scheidegger C., Genetic variation within and among populations of the threatened lichen Lobaria pulmonaria in Switzerland and implications for its conservation. Molecular Ecology 1999 8 12 2049 2059 2-s2.0-0033382509 10.1046/j.1365-294X.1999.00820.x (Pubitemid 30079114)
29. Gardes M., Bruns T. D., ITS primers with enhanced specificity for basidiomycetes-application to the identification of Mycorrhizae and rusts. Molecular Ecology 1993 2 2 113 118 2-s2.0-0027580147
30. Tamura K., Dudley J., Nei M., Kumar S., MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 2007 24 8 1596 1599 2-s2.0-34547781750 10.1093/molbev/msm092 (Pubitemid 47236692)
31. Librado P., Rozas J., DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009 25 11 1451 1452 2-s2.0-65649117685 10.1093/bioinformatics/btp187
32. Rozen S., Skaletsky H., Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology 2000 132 365 386 2-s2.0-0033990048
33. Ye J., Coulouris G., Zaretskaya I., Cutcutache I., Rozen S., Madden T., Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 2012 13 article 134 10.1186/1471-2105-13-134
34. Xu K., Kanno M., Yu H., Li Q., Kijima A., Complete mitochondrial DNA sequence and phylogenetic analysis of Zhikong scallop Chlamys farreri (Bivalvia: Pectinidae). Molecular Biology Reports 2011 38 5 3067 3074 2-s2.0-80052446704 10.1007/s11033-010-9974-8
35. Excoffier L., Laval G., Schneider S., Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 2005 1 47 50
36. Bandelt H. J., Forster P., Röhl A., Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 1999 16 1 37 48 2-s2.0-0032900678 (Pubitemid 29024937)
37. Forbi J. C., Vaughan G., Purdy M. A., Campo D. S., Xia G. L., Ganova-Raeva L. M., Ramachandran S., Thai H., Khudyakov Y. E., Epidemic history and evolutionary dynamics of Hepatitis B virus infection in two remote communities in rural Nigeria. PLoS ONE 2010 5 7 2-s2.0-77955346625 10.1371/journal.pone.0011615 e11615
38. Quinteiro J., Rodríguez-Castro J., Rey-Méndez M., Population genetic structure of the stalked barnacle Pollicipes pollicipes (Gmelin, 1789) in the northeastern Atlantic: influence of coastal currents and mesoscale hydrographic structures. Marine Biology 2007 153 1 47 60 2-s2.0-35348822099 10.1007/s00227-007-0783-0 (Pubitemid 47583380)
39. Lechner B. E., Petersen R., Rajchenberg M., Albertó E., Presence of Pleurotus ostreatus in Patagonia, Argentina. Revista Iberoamericana de Micologia 2002 19 2 111 114 2-s2.0-0036069035 (Pubitemid 34773800)
40. Siddiquee S., Tan S. G., Yusuf U. K., Fatihah N. H. N., Hasan M. M., Characterization of Malaysian Trichoderma isolates using random amplified microsatellites (RAMS). Molecular Biology Reports 2012 39 1 715 722 2-s2.0-84855188840 10.1007/s11033-011-0790-6
41. Ro H. S., Kim S. S., Ryu J. S., Jeon C. O., Lee T. S., Lee H. S., Comparative studies on the diversity of the edible mushroom Pleurotus eryngii: ITS sequence analysis, RAPD fingerprinting, and physiological characteristics. Mycological Research 2007 111 6 710 715 2-s2.0-34447537766 10.1016/j.mycres. 2007.03.016 (Pubitemid 47077625)
42. Choi D., Park S. S., Ding J. L., Cha W. S., Effects of Fomitopsis pinicola extracts on antioxidant and antitumor activities. Biotechnology and Bioprocess Engineering 2007 12 5 516 524 2-s2.0-36049047313 10.1007/BF02931349 (Pubitemid 350090379)
43. Zervakis G. I., Venturella G., Papadopoulou K., Genetic polymorphism and taxonomic infrastructure of the Pleurotus eryngii species-complex as determined by RAPD analysis, isozyme profiles and ecomorphological characters. Microbiology 2001 147 11 3183 3194 2-s2.0-0035166523 (Pubitemid 33077008)
44. Fries E. M., Epicrisis systematis mycologici, seu synopsis hymenomycetum 1838 Typographia Academica
45. Singer R., New and interesting species of Basidiomycetes. Mycologia 1945 37 4 425 439 10.2307/3754629
46. Pegler D. N., Yi-Jian Y. A., The distinction between Lentinus sajor-caju and Pleurotus ostreatus and their taxonomy. Acta Metallurgica Sinica 1995 17 1 3
47. Li X. L., Yao Y. J., Revision of the taxonomic position of the Phoenix Mushroom. Mycotaxon 2005 91 61 73 2-s2.0-18044369722
48. Shnyreva A. A., Sivolapova A. B., Shnyreva A. V., The commercially cultivated edible oyster mushrooms Pleurotus sajor-caju and P. pulmonarius are two separate species, similar in morphology but reproductively isolated. Russian Journal of Genetics 2012 48 1080 1088
49. Zervakis G., Sourdis J., Balis C., Genetic variability and systematics of eleven Pleurotus species based on isozyme analysis. Mycological Research 1994 98 3 329 341 2-s2.0-0028105367 (Pubitemid 2070599)
50. Iracabal B., Zervakis G., Labarere J., Molecular systematics of the genus Pleurotus: analysis of restriction polymorphisms in ribosomal DNA. Microbiology 1995 141 6 1479 1490 2-s2.0-0029016922
51. Meyer C. P., Paulay G., DNA barcoding: error rates based on comprehensive sampling. PLoS Biology 2005 3 12, article e422 10.1371/journal.pbio.0030422 2-s2.0-34548104344 (Pubitemid 41796331)
52. Gilmore S. R., GrÄfenhan T., Louis-Seize G., Seifert K. A., Multiple copies of cytochrome oxidase 1 in species of the fungal genus Fusarium. Molecular Ecology Resources 2009 9 1 90 98 2-s2.0-65349108697 10.1111/j.1755-0998.2009.02636.x
53. Vialle A., Feau N., Allaire M., Didukh M., Martin F., Moncalvo J. M., Hamelin R. C., Evaluation of mitochondrial genes as DNA barcode for Basidiomycota. Molecular Ecology Resources 2009 9 1 99 113 2-s2.0-65349191257 10.1111/j.1755-0998.2009.02637.x