Year 2019, Volume 32, Issue 1, Pages 31 - 34 2019-04-01

Genome-wide identification and annotation of microsatellite markers in white truffle (Tuber magnatum)
Beyaz trüf mantarında (Tuber magnatum) mikrosatelit markörlerinin tüm genom düzeyinde tanımlanması ve anotasyonu

Ayşe Özgür UNCU [1] , Ali Tevfik UNCU [2]

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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.


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.


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Primary Language en
Subjects Science
Journal Section Makaleler
Authors

Author: Ayşe Özgür UNCU (Primary Author)
Institution: Necmettin Erbakan Üniversitesi
Country: Turkey


Author: Ali Tevfik UNCU
Institution: Necmettin Erbakan Üniversitesi
Country: Turkey


Bibtex @research article { mediterranean487250, journal = {Mediterranean Agricultural Sciences}, issn = {}, eissn = {2528-9675}, address = {Akdeniz University}, year = {2019}, volume = {32}, pages = {31 - 34}, doi = {10.29136/mediterranean.487250}, title = {Genome-wide identification and annotation of microsatellite markers in white truffle (Tuber magnatum)}, key = {cite}, author = {UNCU, Ayşe Özgür and UNCU, Ali Tevfik} }
APA UNCU, A , UNCU, A . (2019). Genome-wide identification and annotation of microsatellite markers in white truffle (Tuber magnatum). Mediterranean Agricultural Sciences, 32 (1), 31-34. DOI: 10.29136/mediterranean.487250
MLA UNCU, A , UNCU, A . "Genome-wide identification and annotation of microsatellite markers in white truffle (Tuber magnatum)". Mediterranean Agricultural Sciences 32 (2019): 31-34 <http://dergipark.org.tr/mediterranean/issue/41736/487250>
Chicago UNCU, A , UNCU, A . "Genome-wide identification and annotation of microsatellite markers in white truffle (Tuber magnatum)". Mediterranean Agricultural Sciences 32 (2019): 31-34
RIS TY - JOUR T1 - Genome-wide identification and annotation of microsatellite markers in white truffle (Tuber magnatum) AU - Ayşe Özgür UNCU , Ali Tevfik UNCU Y1 - 2019 PY - 2019 N1 - doi: 10.29136/mediterranean.487250 DO - 10.29136/mediterranean.487250 T2 - Mediterranean Agricultural Sciences JF - Journal JO - JOR SP - 31 EP - 34 VL - 32 IS - 1 SN - -2528-9675 M3 - doi: 10.29136/mediterranean.487250 UR - https://doi.org/10.29136/mediterranean.487250 Y2 - 2019 ER -
EndNote %0 Mediterranean Agricultural Sciences Genome-wide identification and annotation of microsatellite markers in white truffle (Tuber magnatum) %A Ayşe Özgür UNCU , Ali Tevfik UNCU %T Genome-wide identification and annotation of microsatellite markers in white truffle (Tuber magnatum) %D 2019 %J Mediterranean Agricultural Sciences %P -2528-9675 %V 32 %N 1 %R doi: 10.29136/mediterranean.487250 %U 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