DNA Barcoding and Phylogeny of Ambystoma mexicanum Cultivated as a Model Organism in Regenerative Medicine Research at Mersin University Aquaculture Units of the Faculty of Fisheries

Abstract

Ambystoma mexicanum belongs to the family Ambystomatidae. It is one of the 30 species of the genus Ambystoma, which lives in a wide geography from southern Mexico to southern Alaska. It is accepted as a model organism in evolutionary biology, developmental biology, and regenerative medicine research. It can regenerate the brain, heart, and kidney organs as well as limb regeneration. Accurate identification of the model organism is important for the reproducibility and comparability of experiments. We aimed to confirm the species identification of axolotls using integrated taxonomic methods that were grown at Mersin University Aquaculture Units of the Faculty of Fisheries. Cytochrome oxidase subunit 1 (COI) and cytochrome b (Cytb) gene fragments of mtDNA sequences were used as molecular markers for phylogenetic analyses and species delimitation methods and compared with the sequences that were submitted to NCBI GenBank as species of Ambystoma. In the analyses that were conducted with different data sets, the individuals in question were grouped as a candidate species with the A. mexicanum species whose sequences were given in previous studies. All sequences obtained in this study and A. mexicanum sequences obtained from NCBI GenBank were grouped as haplotypes and their genetic distances were found to be 0 and it was determined that the individuals which were the subject of this study definitely belong to the A. mexicanum species. The results revealed that some species within the genus Ambystoma, especially A. barbouri and A. texanum, may be species complexes. On the other hand, A. mexicanum was grouped together with A. andersoni as candidate species in all analyses performed with the combined datasets of COI, Cytb, and COI+Cytb. These results revealed that the taxa in question are paraphyletic and should be assigned to the A. mexicanum species.

Keywords

• Regenerative Medicine
• Axolotl
• phylogeny
• species delimitation
• Cytochromes b
• Cytochrome Oxidase Subunit I.

Mersin Üniversitesi Su Ürünleri Fakültesi Uygulama Birimleri’nde Rejeneratif Tıp Araştırmalarında Model Organizma Olarak Yetiştirilen Ambystoma mexicanum’un DNA Barkodlaması ve Filogenisi

Abstract

Ambystoma mexicanum Ambystomatidae familyasında yer alır. Güney Meksika’dan Güney Alaska’ya kadar geniş bir coğrafyada yaşayan Ambystoma cinsinin 30 türünden biridir. Limb rejenerasyonunun yanında beyin, kalp, böbrek organlarını rejenere edebilmeleri nedeniyle, evrimsel biyoloji, gelişim biyolojisi ve rejeneratif tıp araştırmalarında model organizma olarak kabul edilir. Model organizmaların kullanıldığı araştırmalarda canlının tür teşhisinin doğru yapılması deneylerin tekrarlanabilirliği ve karşılaştırılabilirliği açısından önemlidir. Bu çalışmada; Mersin Üniversitesi Su Ürünleri Fakültesi Uygulama Birimleri’nde yetiştirilen aksolotlların tür teşhisini bütünleşik taksonomik yöntemler kullanarak kesinleştirmek amacıyla mtDNA sitokrom oksidaz alt ünite 1 (COI) ve sitokrom b (Cytb) gen fragmentleri moleküler belirteç olarak kullanılmış ve NCBI GenBank’ta daha önce dizisi verilmiş olan Ambsytoma türleri ile filogenetik analizler ve tür sınırlarını belirleme yöntemleri ile karşılaştırılmıştır. Farklı veri setlerinin kullanıldığı analizlerin tamamında söz konusu bireyler daha önceki çalışmalarda elde edilen A. mexicanum türü ile aday tür olarak gruplanmıştır. Bu çalışmada elde edilen tüm diziler ile NCBI GenBank’tan elde edilen A. mexicanum dizileri haplotip olarak gruplanmış olup genetik uzaklıkları 0 bulunmuş ve bu çalışmanın konusu olan bireylerin kesin olarak A. mexicanum türüne ait olduğu belirlenmiştir. Sonuçlar Ambystoma cinsi içerisinde bazı türlerin özellikle A. barbouri ve A. texanum ‘un tür kompleksi olabileceğini ortaya koymuştur. Diğer yandan A. mexicanum, COI, Cytb ve COI+Cytb birleştirilmiş veri setleri ile yapılan tüm analizlerde A. andersoni ile aday tür olarak gruplanmıştır. Bu sonuçlar söz konusu taksonların parafiletik olduğunu ve A. mexicanum türüne atanması gerektiğini ortaya koymuştur.

Keywords

• Rejeneratif Tıp
• Aksolotl
• Filogeni
• Tür sınırlarını belirleme
• Sitokrom b
• Sitokrom oksidaz alt ünite 1.

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