Abstract
Recent genome sequencing of Trichoderma species has opened the way for their diversity in the assessment and comparative analysis of microsatellites. Here, we compared microsatellites of three taxonomically different Trichoderma species such as T. asperellum, T. citrinoviride, and T. longibrachiatum. Our results highlight abundance and diversity of microsatellite patterns in all the test genomes. The highest relative abundance (283.6) with a relative density (3424.7) of SSRs was identified in all three sequence sets of T. citrinoviride. Among all three sequence sets, selection of these isolates were based on maximum frequency of SSRs which was of trinucleotide repeats (79.8%), whereas the dinucleotide repeat represented <8%. With the help of bioinformatics tools, species-specific diagnostic primers were developed and validated by silica PCR. Out of 31 primer sets, only 18 pairs of primer indicated successful amplification among all the species tested. A total of 34 alleles were detected and 7 loci have polymorphism information content (PIC) values greater than 0.40. In cross-species examination, of 31 markers, amplification of 5 of them was in the corresponding microsatellite regions of 18 different isolates of Trichoderma and showed monomorphic banding pattern. Microsatellite locus ThSSR3 was highly specific for Trichoderma, as amplification was not detected in closely related other 29 taxa. Primer set, ThSSR3F/ThSSR3R, amplified a specific amplicon of 600 bp from all Trichoderma species. According to intensive literature survey, the motif-based comparison is first reported here and was performed in recently sequenced three different species of Trichoderma.
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References
Al-Sadi AM, Al-Oweisi FA, Edwards SG, Al-Nadabi H, Al-Fahdi AM (2015) Genetic analysis reveals the diversity and genetic relationship among Trichoderma isolate from potting media, cultivated soil and uncultivated soil. BMC Microbiol 15:147–158. https://doi.org/10.1186/s12866-015-0483-8
Bissett J, Szakacs G, Nolan CA, Druzhinina I, Gradinger C, Kubicek CP (2003) New species of Trichoderma from Asia. Can J Bot 81:570–586. https://doi.org/10.1139/b03-051
Błaszczyk L, Popiel D, Chełkowski J, Koczyk G, Samuels GJ, Sobieralski K, Siwulski M (2011) Species diversity of Trichoderma in Poland. J Appl Genet 52(2):233–243. https://doi.org/10.1007/s13353-011-0039-z
Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1686077&tool=pmcentrez&rendertype=abstract
Buhariwalla HK, Srilakshmi P, Kannan S, Kanchi RS, Chandra S, Satyaprasad K, Waliyar F, Thakur RP, Crouch JH (2005) AFLP analysis of Trichoderma spp. from India compared with sequence and morphological-based diagnostics. J Phytopathol 153:389–400. https://doi.org/10.1111/j.1439-0434.2005.00989.x
Carpenter MA, Stewart A, Ridgway HJ (2005) Identification of novel Trichoderma hamatum genes expressed during mycoparasitism using subtractive hybridization. FEMS Microbiol Lett 251:105–112. https://doi.org/10.1016/j.femsle.2005.07.035
Chakraborty BN, Chakraborty U, Sunar K, Dey PL (2011) RAPD profile and rDNA sequence analysis of Talaromyces flavus and Trichoderma species. Indian J Biotechnol 10:487–495
Chaverri P, Branco-Rocha F, Jaklitsch WM, Gazis RO, Degenkolb T, Samuels GJ (2015) Systematics of the Trichoderma harzianum species complex and the reidentification of commercial biocontrol strains. Mycologia 107:558–590. https://doi.org/10.3852/14-147
Coenye T, Vandamme P (2005) Characterization of mononucleotide repeats in sequenced prokaryotic genomes. DNA Res 12:221–233. https://doi.org/10.1093/dnares/dsi009
Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, Grimwood J, Schmutz J, Taga M, White GJ, Zhou S, Schwartz DC, Freitag M, Ma LJ, Danchin EG, Henrissat B, Coutinho PM, Nelson DR, Straney D, Napoli CA, Barker BM, Gribskov M, Rep M, Kroken S, Molnár I, Rensing C, Kennell JC, Zamora J, Farman ML, Selker EU, Salamov A, Shapiro H, Pangilinan J, Lindquist E, Lamers C, Grigoriev IV, Geiser DM, Covert SF, Temporini E, Vanetten HD (2009) The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genet 5(8):e1000618. https://doi.org/10.1371/journal.pgen.1000618
Contreras-Cornejo HA, Ortiz-Castro R, López-Bucio J, Mukherjee PK (2013) In: Mukherjee PK, Horwitz BA, Singh US, Mala M, Schmoll M (eds) Trichoderma: biology and applications. CABI, Wallingford. https://doi.org/10.1079/9781780642475.0000
Cordier C, Edel-Hermann V, Martin-Laurent F, Blal B, Steinberg C, Alabouvette C (2007) SCAR-based real-time PCR to identify a biocontrol strain (T1) of Trichoderma atroviride and study its population dynamics in soils. J Microbiol Meth 68:60–68. https://doi.org/10.1016/j.mimet.2006.06.006
Dhusia K, Kesarwani P, Yadav PK (2016) Epitope prediction for MSP119 protein in Plasmodium yoelii using computational approaches. Netw Model Anal Heal Inf Bioinf 5:19. https://doi.org/10.1007/s13721-016-0127-4
Dodd SL, Hill RA, Stewart A (2004) Monitoring the survival and spread of the biocontrol fungus Trichoderma atroviride (C65) on kiwifruit using a molecular marker. Australas Plant Pathol 33:189–196. https://doi.org/10.1071/AP03070
Dutech C, Enjalbert J, Fournier E, Delmotte F, Barre’s B, Carlier J, Tharreau D, Giraud T (2007) Challenges of microsatellite isolation in fungi. Fungal Genet Biol 44:933–949. https://doi.org/10.1016/j.fgb.2007.05.003
Galarza L, Akagi Y, Takao K, Kim CS, Maekawa N, Itai A, Peralta E, Santos E, Kodama M (2015) Characterization of Trichoderma species isolated in Ecuador and their antagonistic activities against phytopathogenic fungi from Ecuador and Japan. J Gen Plant Path 81:201–210. https://doi.org/10.1007/s10327-015-0587-x
Garnica DP, Pinzon AM, Quesada-Ocampo LM, Bernal AJ, Barreto E, Grunwald, NJ, Restrepo S (2006) Survey and analysis of microsatellites from transcript sequences in Phytophthora species: frequency, distribution, and potential as markers for the genus. BMC Genomics 7:245(1–11). https://doi.org/10.1186/1471-2164-7-245
Gong X, Fu Y, Jiang D, Li G, Yi X, Peng Y (2007) L-arginine is essential for conidiation in the filamentous fungus Coniothyrium minitans. Fungal Genet Biol 44:1368–1379. https://doi.org/10.1016/j.fgb.2007.07.007
Gonthier P, Sillo F, Lagostina E, Roccotelli A, Cacciola OS, Stenlid J, Garbelotto M (2015) Selection processes in simple sequence repeats suggest a correlation with their genomic location: insights from a fungal model system. BMC Genomics 16:1107(1–12). https://doi.org/10.1186/s12864-015-2274-x
Grover A, Sharma PC (2011) Is spatial occurrence of microsatellites in the genome a determinant of their function and dynamics contributing to genome evolution? Curr Sci 100:859–869
Gupta S, Tripathi KP, Roy S, Sharma A (2010) Analysis of unigene derived microsatellite markers in family Solanaceae. Bioinformation 5:113–121. https://doi.org/10.6026/97320630005113
Hermosa MR, Grondona I, Díaz-Mínguez JM, Iturriaga EA, Monte E (2001) Development of a strain-specific SCAR marker for the detection of Trichoderma atroviride 11, a biological control agent against soil borne fungal plant pathogens. Curr Genet 38:343–350. https://doi.org/10.1007/s002940000173
Jain A, Chaudhary S, Sharma PC (2014) Mining of microsatellites using next-generation sequencing of sea buckthorn (Hippophae rhamnoides L.) transcriptome. Physiol Mol Biol Plants 20:115–123. https://doi.org/10.1007/s12298-013-0210-6
Jaklitsch WM, Voglmayr H (2015) Biodiversity of Trichoderma (Hypocreaceae) in Southern Europe and Macaronesia. Stud Mycol 80:1–87. https://doi.org/10.1016/j.simyco.2014.11.001
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
Kaur G, Chandna R, Pandey R, Abrol YP, Iqbal M, Ahmad A (2011) Sulfur starvation and restoration affect nitrate uptake and assimilation in rapeseed. Protoplasma 248:299–311. https://doi.org/10.1007/s00709-010-0171-3
Kim T, Booth JG, Gauch HG (2008) Simple sequence repeats in Neurospora crassa: distribution, polymorphism, and evolutionary inference. BMC Genomics 9:31. https://doi.org/10.1186/1471-2164-9-31
Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA, Mukherjee PK, Mukherjee M, Kredics L, Alcaraz LD, Aerts A, Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F, Deshpande N, von Döhren H, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gómez-Rodríguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernández-Oñate M, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lübeck M, Lübeck PS, Margeot A, Metz B, Misra M, Nevalainen H, Omann M, Packer N, Perrone G, Uresti-Rivera EE, Salamov A, Schmoll M, Seiboth B, Shapiro H, Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A, Wilkinson HH, Zhang M, Coutinho PM, Kenerley CM, Monte E, Baker SE, Grigoriev IV (2011) Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol 12:R40. https://doi.org/10.1186/gb-2011-12-4-r40
Kullnig-Gradinger CM, Szakacs G, Kubicek CP (2002) Phylogeny and evolution of the genus Trichoderma: a multigene approach. Mycol Res 106:757–767. https://doi.org/10.1017/S0953756202006172
Kumar S, Rai S, Maurya DK, Kashyap PL, Srivastava AK, Anandaraj M (2013) Cross-species transferability of microsatellite markers from Fusarium oxysporum for the assessment of genetic diversity in Fusarium udum. Phytoparasitica 41:615–622. https://doi.org/10.1007/s12600-013-0324-y
Liu Z, Yang X, Sun D, Song J, Chen G, Juba O, Yang Q (2010) Expressed sequence tags-based identification of genes in a biocontrol strain Trichoderma asperellum. Mol Biol Rep 37:3673–3681. https://doi.org/10.1007/s11033-010-0019-0
Mahfooz S, Maurya DK, Srivastava AK, Kumar S, Arora DK (2012) A comparative in silico analysis on frequency and distribution of microsatellites in coding regions of three formaespeciales of Fusarium oxysporum and development of EST-SSR markers for polymorphism studies. FEMS Microbiol Lett 328:54–60. https://doi.org/10.1111/j.1574-6968.2011.02483.x
Mahfooz S, Srivastava A, Srivastava AK, Arora DK (2015) A comparative analysis of distribution and conservation of microsatellites in the transcripts of sequenced Fusarium species and development of genic-SSR markers for polymorphism analysis. FEMS Microbiol Lett 362(17):fnv131. https://doi.org/10.1093/femsle/fnv131
Martinez D, Berka RM, Henrissat B et al (2008) Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocreajecorina). Nat Biotechnol 26:553–560. https://doi.org/10.1038/nbt1403
Martins WS, Lucas DCS, Neves KFDS, Bertioli DJ (2009) WebSat--a web software for microsatellite marker development. Bioinformation 3:282–283. https://doi.org/10.6026/97320630003282
Marzluf GA (1997) Genetic regulation of nitrogen metabolism in the fungi. Microbiol Mol Biol Rev 61:17–32. http://www.ncbi.nlm.nih.gov/pubmed/9106362
Metzgar D, Bytof J, Wills C (2000) Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res 10:72–80. https://doi.org/10.1101/gr.10.1.72
Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200. https://doi.org/10.1038/ng822
Niwattanakul S, Singthongchai J, Naenudorn E, Wanapu S (2013) Using of Jaccard coefficient for keywords similarity. Int Multi Conf Eng Comput Sci:380–384
Padoni J (2000) A introduction to the exploration of multivariate biological data. Backhuys https://books.google.co.in/books/about/Introduction_to_the_exploration_of_multi.html?id=UydFAQAAIAAJ&redir_esc=y
Rahim F (2008) In silico comparison of simple sequence repeats in high nucleotides-rich genomes of microorganism. Pak J Biol Sci 11:2372–2381. https://doi.org/10.3923/pjbs.2008.2372.2381
Rai S, Kashyap PL, Kumar S, Srivastava AK, Ramteke PW (2016) Comparative analysis of microsatellites in five different antagonistic Trichoderma species for diversity assessment. World J Microbiol Biotechnol 32:8. https://doi.org/10.1007/s11274-015-1964-5
Rohlf FJ (2000) NTSYS-pc. Numerical taxonomy and multivariate analysis system. Version 2.1, Exeter Software: Applied Biostatistics Inc, Setauket, New York. ISBN:0-925031-30-5
Scherm B, Schmoll M, Balmas V, Kubicek CP, Migheli Q (2009) Identification of potential marker genes for Trichoderma harzianum strains with high antagonistic potential against Rhizoctonia solani by a rapid subtraction hybridization approach. Curr Genet 55:81–91. https://doi.org/10.1007/s00294-008-0226-6
Seidl V, Song L, Lindquist E, Gruber S, Koptchinskiy A, Zeilinger S, Schmoll M, Martínez P, Sun J, Grigoriev I, Herrera-Estrella A, Baker SE, Kubicek CP (2009) Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey. BMC Genomics 10:567(1–13). https://doi.org/10.1186/1471-2164-10-567
Shahid M, Srivastava M, Kumar V, Singh A, Pandey S (2014) Microbial and biochemical technology genetic determination of potential Trichoderma species using ISSR (Microsatellite) marker in Uttar Pradesh, India. J Microb Biochem Technol 63:174–178. https://doi.org/10.4172/1948-5948.1000139
Singh R, Kumar S, Kashyap PL, Srivastava AK, Mishra S, Sharma AK (2014) Identification and characterization of microsatellite from Alternaria brassicicola to assess cross-species transferability and utility as a diagnostic marker. Mol Biotechnol 56:1049–1059. https://doi.org/10.1007/s12033-014-9784-7
Skoneczny D, Oskiera M, Szczech M, Bartoszewski G (2015) Genetic diversity of Trichoderma atroviride strains collected in Poland and identification of loci useful in the detection of within-species diversity. Folia Microbiol (Praha) 60:297–307. https://doi.org/10.1007/s12223-015-0385-z
Solanki MK, Singh N, Singh RK, Singh P, Srivastava AK, Kumar S, Kashyap PL, Arora DK (2011) Plant defense activation and management of tomato root rot by a chitin-fortified Trichoderma/Hypocrea formulation. Phytoparasitica 39:471–481. https://doi.org/10.1007/s12600-011-0188-y
Woo SL, Scala F, Ruocco M, Lorito M (2006) The molecular biology of the interactions between Trichoderma spp., phytopathogenic fungi, and plants. Phytopathology 96:181–185. https://doi.org/10.1094/PHYTO-96-0181
Xie B, Li D, Shi W, Qin Q, Wang X, Rong J, Sun C, Huang F, Zhang X, Dong X, Chen X, Zhou B, Zhang Y, Song X (2015) Deep RNA sequencing reveals a high frequency of alternative splicing events in the fungus Trichoderma longibrachiatum. BMC Genomics 16:54(1–15). https://doi.org/10.1186/s12864-015-1251-8
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Rai, S., Ramteke, P.W., Sagar, A., Dhusia, K., Kesari, S.K. (2019). Diversity Assessment of Antagonistic Trichoderma Species by Comparative Analysis of Microsatellites. In: Sayyed, R., Reddy, M., Antonius, S. (eds) Plant Growth Promoting Rhizobacteria (PGPR): Prospects for Sustainable Agriculture. Springer, Singapore. https://doi.org/10.1007/978-981-13-6790-8_20
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