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Beyaz trüf mantarında (Tuber magnatum) mikrosatelit markörlerinin tüm genom düzeyinde tanımlanması ve anotasyonu

Year 2019, Volume: 32 Issue: 1, 31 - 34, 01.04.2019
https://doi.org/10.29136/mediterranean.487250

Abstract

Ektomikoriza
mantarı
Tuber magnatum Pico, en yüksek ekonomik değere sahip trüf
mantarı türüdür. Trüf mantarlarının talep gören aroma özellikleri ve yüksek
fiyatlar ile pazarlanmaları bu mantar türlerini önemli bir araştırma konusu
haline getirmekte, trüf mantarı aroma bileşenleri, bu mantarların üreme
mekanizmaları, trüf mantarı genomlarının karakterizasyonu, ve genetik
çeşitlilik ve popülasyon yapılarının belirlenmesi konularında çalışmalar
gerçekleştirilmektedir. Trüf mantarları önceden doğal ormanlık arazilerden
toplanır iken, 1970’lerde fidan inokülasyon protokollerinin geliştirilmesi ile
trüf mantarı yetiştiriciliği sistematik bir tarımsal aktivite haline gelmiştir.
Ancak en değerli trüf mantarı olan
T. magnatum ile fidan inokülasyonu,
mikorizanın DNA-temelli protokoller olmaksızın yalnızca morfolojik yöntemler
ile tanımlanmasındaki sorunlardan ötürü yakın zamanda uygulamaya
geçirilebilmiştir. Bu çalışma kapsamında
T. magnatum genomuna özel
mikrosatelit markörleri geliştirilmiş ve fonksiyonel anotasyonları
gerçekleştirilmiştir. Çalışma dahilinde biyoinformatik analiz yöntemleri
kullanılarak
T. magnatum genom sekansında mikrosatelit dizileri belirlenmiş,
diziler PCR markörlerine çevrilmiş, markörler genom sekansında haritalanarak
alel büyüklükleri hesaplanmıştır. Çalışma sonucunda
T.magnatum türüne
özel
  11 189 yeni mikrosatelit
markörü geliştirilmiştir. Anotasyon analizleri gerçekleştirilerek
T.
magnatum
proteinleri ile eşleşen, bu sebeple fonksiyonel genomik
çalışmaları için özellikle elverişli 3377 adet markör tanımlanmıştır. Çalışma
sonucunda sunulan
T. magnatum’a özel DNA markörü koleksiyonu bu değerli
trüf mantarı türü için önemli bir genomik araç kaynağı oluşturmaktadır.




References

  • Amicucci A, Rossi I, Potenza L, Zambonelli A, Agostini D, Palma F, Stocchi V (1996) Identification of ectomycorrhizae from Tuber species by RFLP analysis of the ITS region. Biotechnology Letters 18: 821-826.
  • Bertini L, Rossi I, Zambonelli A, Amicucci A, Sacchi A, Cecchini M, Gregori G, Stocchi V (2006) Molecular identification of Tuber magnatum ectomycorrhizae in the field. Microbiology Research 161: 59-64.
  • Bolchi A, Ruotolo R, Marchini G, Vurro E, Sanita di Toppi L, Kohler A, Tisserant E, Martin F, Ottonello S (2011) Genome-wide inventory of metal homeostasis-related gene products including a functional phytochelatin synthase in the hypogeous mycorrhizal fungus Tuber melanosporum. Fungal Genetics and Biology 48: 573-584.
  • Dutech C, Enjalbert J, Fournier E, Delmotte F, Barres B, Carlier J, Tharreau D, Giraud T (2007) Challenges of microsatellite isolation in fungi. Fungal Genetics and Biology 44: 933-949.
  • Linde CC, Selmes H (2012) Genetic diversity and mating type distribution of Tuber melanosporum and their significance to truffle cultivation in artificially planted truffieres in Australia. Applied and Environmental Microbiology 78: 6534-6539.
  • Martin F, Kohler A, Murat C, Balestrini R, Coutinho PM, Jaillon O et al. (2010) Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature Letters 464: 1033-1038.
  • Mello A, Murat C, Vizzini A, Gavazza V, Bonfante P (2005) Tuber magnatum Pico, a species of limited geographical distribution: its genetic diversity inside and outside a truffle ground. Environmental Microbiology 7: 55-65.
  • Mello A, Lumini E, Napoli C, Bianciotto V, Bonfante P (2015) Arbuscular mycorrhizal fungal diversity in the Tuber melanosporum brule. Fungal Biology 119: 518-527.
  • Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nature Genetics 30: 194-200.
  • Murat C, Vizzini A, Bonfante P, Mello A (2005) Morphological and molecular typing of the below-ground fungal community in a natural Tuber magnatum truffle-ground. FEMS Microbiology Letters 245: 307-313.
  • Murat C, Riccioni C, Belfiori B, Cichocki N, Labbe J, Morin E, Tisserant E, Paolocci F, Rubini A, Martin F (2011) Distribution and localization of microsatellites in Perigord black truffle genome and identification of new molecular markers. Fungal Genetics and Biology 48: 592-601.
  • Murat C (2015) Forty years of inoculating seedlings with truffle fungi: past and future perspectives. Mycorrhiza 25: 77-81.
  • NCBI (2018a) National Center for Biotechnology Information Database. https://www.ncbi.nlm.nih.gov/genome/?term=txid42249[orgn] Accessed 1 October 2018.
  • NCBI (2018b) National Center for Biotechnology Information Database. https://www.ncbi.nlm.nih.gov/ipg/?term=Tuber%20magnatum Accessed 9 October 2018.
  • Paolocci F, Rubini A, Granetti B, Arcioni S (1999) Rapid molecular approach for a reliable identification of Tuber spp. ectomycorrhizae. FEMS Microbiology Ecology 28: 23-30.
  • Payen T, Murat C, Gigant A, Morin E, De Mita S, Martin F (2015) A survey of genome-wide single nucleotide polymorphisms through genome resequencing in the Perigord black truffle (Tuber melanosporum Vittad.). Molecular Ecology Resources 15: 1243-1255.
  • Rizzello R, Zampieri E, Vizzini A, Autino A, Cresti M, Bonfante P, Mello A (2012) Authentication of prized white and black truffles in processed products using quantitative real-time PCR. Food Research International 48: 792-797.
  • Rubini A, Topini F, Riccioni C, Paolocci F, Arcioni S (2004) Isolation and characterization of polymorphic microsatellite loci in white truffle (Tuber magnatum). Molecular Ecology Notes 4: 116-118.
  • Rubini A, Paolocci F, Riccioni C, Vendramin GG, Arcioni S (2005) Genetic and phylogeographic structures of the symbiotic fungus Tuber magnatum. Applied and Environmental Microbiology 71: 6584-6589.
  • Rubini A, Belfiori B, Riccioni C, Tisserant E, Arcioni S, Martin F, Paolocci F (2010a) Isolation and characterization of MAT genes in the symbiotic ascomycete Tuber melanosporum. New Phytologist 189: 710-722.
  • Rubini A, Belfiori B, Riccioni C, Arcioni S, Martin F, Paolocci F (2010b) Tuber melanosporum: mating type distribution in a natural plantation and dynamics of strains of different mating types on the roots of nursery-inoculated host plants. New Phytologist 189: 723-735.
  • Schuler GD (1997) Sequence mapping by electronic PCR. Genome Research 7: 541-550. Splivallo R, Novero M, Bertea C, Bossi S, Bonfante P (2007a) Truffle volatiles inhibit growth and induce an oxidative burst in Arabidopsis thaliana. New Phytologist 175: 417-424.
  • Splivallo R, Bossi S, Maffei M, Bonfante P (2007b) Discrimination of truffle fruiting body versus mycelial aromas by stir bar sorptive extraction. Phytochemistry 68: 2584-2598.
  • Splivallo R, Ottonello S, Mello A, Karlovsky P (2011) Truffle volatiles: from chemical ecology to aroma biosynthesis. New Phytologist 189: 688-699.
  • Splivallo R, Valdez N, Kirchoff N, Castiella Ona M, Schmidt JP, Feussner I, Karlovsky P (2012) Intraspecific genotypic variability determines concentrations of key truffle volatiles. New Phytologist 194: 823-835.
  • Uncu AO, Gultekin V, Allmer J, Frary A, Doganlar S (2015) Genomic simple sequence repeat markers reveal patterns of genetic relatedness and diversity in sesame. The Plant Genome, 8, doi: 10.3835/plantgenome2014.11.0087.
  • Wang X, Wang L (2016) GMATA: An integrated software package for genome-scale SSR mining, marker development and viewing. Frontiers in Plant Science 7: 1350.
  • Zampieri E, Rizzello R, Bonfante P, Mello A (2012) The detection of mating type genes of Tuber melanosporum in productive and non productive soils. Applied Soil Ecology 57: 9-15.

Genome-wide identification and annotation of microsatellite markers in white truffle (Tuber magnatum)

Year 2019, Volume: 32 Issue: 1, 31 - 34, 01.04.2019
https://doi.org/10.29136/mediterranean.487250

Abstract

The white truffle Tuber magnatum Pico is an ectomycorrhizal fungus, which produces the most economically valuable edible ascomata, referred to as truffles. Highly appreciated sensory properties and exceptional market prices make truffle fungi an important focus of research. Accordingly, there is increasing interest to characterize truffle aroma volatiles, fully understand their reproduction and, characterize their genomes, analyze their population structure and molecular genetic diversity. While production of truffle species was confined before to natural woodlands, development of host seedling inoculation protocols in 1970s established truffle production as a managed agricultural activity. On the other hand, T. magnatum inoculated seedling production was achieved only recently, since morphological criteria were insufficient for the precise identification of T. magnatum mycorrhizas without DNA-based identification protocols. The present research describes the development and functional annotation of novel microsatellite markers in T. magnatum genome. A bioinformatics workflow was applied in order to mine for microsatellite sequences in T. magnatum genome assembly, convert the loci to PCR markers, map marker amplification on genomic sequences and calculate allele sizes. As a result, 11 189 microsatellite markers specific to T. magnatum were developed. Annotation analysis was performed for marker sequences, resulting in 3377 marker loci matching with T. magnatum proteins. Thus, these markers have high potential to tag genes of interest in functional genomic analyses. As a result of the present work, a large database of T. magnatum specific DNA markers was introduced as a useful genomic resource for the valuable ectomycorrhizal fungus species.




References

  • Amicucci A, Rossi I, Potenza L, Zambonelli A, Agostini D, Palma F, Stocchi V (1996) Identification of ectomycorrhizae from Tuber species by RFLP analysis of the ITS region. Biotechnology Letters 18: 821-826.
  • Bertini L, Rossi I, Zambonelli A, Amicucci A, Sacchi A, Cecchini M, Gregori G, Stocchi V (2006) Molecular identification of Tuber magnatum ectomycorrhizae in the field. Microbiology Research 161: 59-64.
  • Bolchi A, Ruotolo R, Marchini G, Vurro E, Sanita di Toppi L, Kohler A, Tisserant E, Martin F, Ottonello S (2011) Genome-wide inventory of metal homeostasis-related gene products including a functional phytochelatin synthase in the hypogeous mycorrhizal fungus Tuber melanosporum. Fungal Genetics and Biology 48: 573-584.
  • Dutech C, Enjalbert J, Fournier E, Delmotte F, Barres B, Carlier J, Tharreau D, Giraud T (2007) Challenges of microsatellite isolation in fungi. Fungal Genetics and Biology 44: 933-949.
  • Linde CC, Selmes H (2012) Genetic diversity and mating type distribution of Tuber melanosporum and their significance to truffle cultivation in artificially planted truffieres in Australia. Applied and Environmental Microbiology 78: 6534-6539.
  • Martin F, Kohler A, Murat C, Balestrini R, Coutinho PM, Jaillon O et al. (2010) Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature Letters 464: 1033-1038.
  • Mello A, Murat C, Vizzini A, Gavazza V, Bonfante P (2005) Tuber magnatum Pico, a species of limited geographical distribution: its genetic diversity inside and outside a truffle ground. Environmental Microbiology 7: 55-65.
  • Mello A, Lumini E, Napoli C, Bianciotto V, Bonfante P (2015) Arbuscular mycorrhizal fungal diversity in the Tuber melanosporum brule. Fungal Biology 119: 518-527.
  • Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nature Genetics 30: 194-200.
  • Murat C, Vizzini A, Bonfante P, Mello A (2005) Morphological and molecular typing of the below-ground fungal community in a natural Tuber magnatum truffle-ground. FEMS Microbiology Letters 245: 307-313.
  • Murat C, Riccioni C, Belfiori B, Cichocki N, Labbe J, Morin E, Tisserant E, Paolocci F, Rubini A, Martin F (2011) Distribution and localization of microsatellites in Perigord black truffle genome and identification of new molecular markers. Fungal Genetics and Biology 48: 592-601.
  • Murat C (2015) Forty years of inoculating seedlings with truffle fungi: past and future perspectives. Mycorrhiza 25: 77-81.
  • NCBI (2018a) National Center for Biotechnology Information Database. https://www.ncbi.nlm.nih.gov/genome/?term=txid42249[orgn] Accessed 1 October 2018.
  • NCBI (2018b) National Center for Biotechnology Information Database. https://www.ncbi.nlm.nih.gov/ipg/?term=Tuber%20magnatum Accessed 9 October 2018.
  • Paolocci F, Rubini A, Granetti B, Arcioni S (1999) Rapid molecular approach for a reliable identification of Tuber spp. ectomycorrhizae. FEMS Microbiology Ecology 28: 23-30.
  • Payen T, Murat C, Gigant A, Morin E, De Mita S, Martin F (2015) A survey of genome-wide single nucleotide polymorphisms through genome resequencing in the Perigord black truffle (Tuber melanosporum Vittad.). Molecular Ecology Resources 15: 1243-1255.
  • Rizzello R, Zampieri E, Vizzini A, Autino A, Cresti M, Bonfante P, Mello A (2012) Authentication of prized white and black truffles in processed products using quantitative real-time PCR. Food Research International 48: 792-797.
  • Rubini A, Topini F, Riccioni C, Paolocci F, Arcioni S (2004) Isolation and characterization of polymorphic microsatellite loci in white truffle (Tuber magnatum). Molecular Ecology Notes 4: 116-118.
  • Rubini A, Paolocci F, Riccioni C, Vendramin GG, Arcioni S (2005) Genetic and phylogeographic structures of the symbiotic fungus Tuber magnatum. Applied and Environmental Microbiology 71: 6584-6589.
  • Rubini A, Belfiori B, Riccioni C, Tisserant E, Arcioni S, Martin F, Paolocci F (2010a) Isolation and characterization of MAT genes in the symbiotic ascomycete Tuber melanosporum. New Phytologist 189: 710-722.
  • Rubini A, Belfiori B, Riccioni C, Arcioni S, Martin F, Paolocci F (2010b) Tuber melanosporum: mating type distribution in a natural plantation and dynamics of strains of different mating types on the roots of nursery-inoculated host plants. New Phytologist 189: 723-735.
  • Schuler GD (1997) Sequence mapping by electronic PCR. Genome Research 7: 541-550. Splivallo R, Novero M, Bertea C, Bossi S, Bonfante P (2007a) Truffle volatiles inhibit growth and induce an oxidative burst in Arabidopsis thaliana. New Phytologist 175: 417-424.
  • Splivallo R, Bossi S, Maffei M, Bonfante P (2007b) Discrimination of truffle fruiting body versus mycelial aromas by stir bar sorptive extraction. Phytochemistry 68: 2584-2598.
  • Splivallo R, Ottonello S, Mello A, Karlovsky P (2011) Truffle volatiles: from chemical ecology to aroma biosynthesis. New Phytologist 189: 688-699.
  • Splivallo R, Valdez N, Kirchoff N, Castiella Ona M, Schmidt JP, Feussner I, Karlovsky P (2012) Intraspecific genotypic variability determines concentrations of key truffle volatiles. New Phytologist 194: 823-835.
  • Uncu AO, Gultekin V, Allmer J, Frary A, Doganlar S (2015) Genomic simple sequence repeat markers reveal patterns of genetic relatedness and diversity in sesame. The Plant Genome, 8, doi: 10.3835/plantgenome2014.11.0087.
  • Wang X, Wang L (2016) GMATA: An integrated software package for genome-scale SSR mining, marker development and viewing. Frontiers in Plant Science 7: 1350.
  • Zampieri E, Rizzello R, Bonfante P, Mello A (2012) The detection of mating type genes of Tuber melanosporum in productive and non productive soils. Applied Soil Ecology 57: 9-15.
There are 28 citations in total.

Details

Primary Language English
Journal Section Makaleler
Authors

Ayşe Özgür Uncu

Ali Tevfik Uncu

Publication Date April 1, 2019
Submission Date November 24, 2018
Published in Issue Year 2019 Volume: 32 Issue: 1

Cite

APA Uncu, A. Ö., & Uncu, A. T. (2019). Genome-wide identification and annotation of microsatellite markers in white truffle (Tuber magnatum). Mediterranean Agricultural Sciences, 32(1), 31-34. https://doi.org/10.29136/mediterranean.487250
AMA Uncu AÖ, Uncu AT. Genome-wide identification and annotation of microsatellite markers in white truffle (Tuber magnatum). Mediterranean Agricultural Sciences. April 2019;32(1):31-34. doi:10.29136/mediterranean.487250
Chicago Uncu, Ayşe Özgür, and Ali Tevfik Uncu. “Genome-Wide Identification and Annotation of Microsatellite Markers in White Truffle (Tuber Magnatum)”. Mediterranean Agricultural Sciences 32, no. 1 (April 2019): 31-34. https://doi.org/10.29136/mediterranean.487250.
EndNote Uncu AÖ, Uncu AT (April 1, 2019) Genome-wide identification and annotation of microsatellite markers in white truffle (Tuber magnatum). Mediterranean Agricultural Sciences 32 1 31–34.
IEEE A. Ö. Uncu and A. T. Uncu, “Genome-wide identification and annotation of microsatellite markers in white truffle (Tuber magnatum)”, Mediterranean Agricultural Sciences, vol. 32, no. 1, pp. 31–34, 2019, doi: 10.29136/mediterranean.487250.
ISNAD Uncu, Ayşe Özgür - Uncu, Ali Tevfik. “Genome-Wide Identification and Annotation of Microsatellite Markers in White Truffle (Tuber Magnatum)”. Mediterranean Agricultural Sciences 32/1 (April 2019), 31-34. https://doi.org/10.29136/mediterranean.487250.
JAMA Uncu AÖ, Uncu AT. Genome-wide identification and annotation of microsatellite markers in white truffle (Tuber magnatum). Mediterranean Agricultural Sciences. 2019;32:31–34.
MLA Uncu, Ayşe Özgür and Ali Tevfik Uncu. “Genome-Wide Identification and Annotation of Microsatellite Markers in White Truffle (Tuber Magnatum)”. Mediterranean Agricultural Sciences, vol. 32, no. 1, 2019, pp. 31-34, doi:10.29136/mediterranean.487250.
Vancouver Uncu AÖ, Uncu AT. Genome-wide identification and annotation of microsatellite markers in white truffle (Tuber magnatum). Mediterranean Agricultural Sciences. 2019;32(1):31-4.

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