Identification and in silico comparison of transposable elements of Solanum tuberosum subsp. andigena from two localities of Peru

ABSTRACTThe potato is one of the main crops in Peru, being one of the pillars in the country’s economy. It also has a cultural importance, being a basic element of Peruvian gastronomy and an emblematic crop of the Peruvian highlands, where small farmers over time have been able to conserve and cultivate 6048 native varieties. In Peru, around 300,000 hectares of potatoes are planted annually, and in 2019 Peru remained the main potato producer in Latin America, registering an annual production of 5.3 million tons. Therefore, it is necessary to study and characterize the genome of this very important tuber for the country. Although there are many potato genomic studies in the world and in Peru; these have been based on the search for genes of importance, genetic diversity, etc. and little has been deeply studied about the transposable elements (ETs) that are part of its genome. It is known that in many eukaryotes, transposable elements are powerful drivers of genome evolution, and they occupy a considerable part in plant genomes, so with these studies, more could be understood about how these ETs have intervened in the evolution of the potato in Peru; thus, how these mechanisms would help in the future to the survival of the species in scenarios of climate change, among others. This study proposes the identification and comparison of the transposable elements of the only 2 complete genomes of potatoes grown in Peru, found in the NCBI database, one from the department of Puno and the other from Cusco. There are various approaches to search for ETs in genomes, but for a complete and reliable annotation, it has been shown that the best strategy is the adoption of combined approaches, in this study, we will use 2 approaches, one based on homology, with the program RepeatMasker, and the other de novo, with the RepeatModeler2 program.