New insights into tomato microRNAs

Thaís Cunha de Sousa Cardoso, Tamires Caixeta Alves, Carolina Milagres Caneschi, Douglas dos Reis Gomes Santana, Christiane Noronha Fernandes-Brum, Gabriel Lasmar Dos Reis, Matheus Martins Daude, Thales Henrique Cherubino Ribeiro, Miguel Maurício Díaz Gómez, André Almeida Lima, Luiz Antônio Augusto Gomes, Marcos de Souza Gomes (+5 others)
2018 Scientific Reports  
Cultivated tomato, Solanum lycopersicum, is one of the most common fruits in the global food industry. Together with the wild tomato Solanum pennellii, it is widely used for developing better cultivars. MicroRNAs affect mRNA regulation, inhibiting its translation and/or promoting its degradation. Important proteins involved in these processes are ARGONAUTE and DICER. This study aimed to identify and characterize the genes involved in the miRNA processing pathway, miRNA molecules and target
more » ... in both species. We validated the presence of pathway genes and miRNA in different NGS libraries and 6 miRNA families using quantitative RT-PCR. We identified 71 putative proteins in S. lycopersicum and 108 in S. pennellii likely involved in small RNAs processing. Of these, 29 and 32 participate in miRNA processing pathways, respectively. We identified 343 mature miRNAs, 226 pre-miRNAs in 87 families, including 192 miRNAs, which were not previously identified, belonging to 38 new families in S. lycopersicum. In S. pennellii, we found 388 mature miRNAs and 234 pre-miRNAs contained in 85 families. All miRNAs found in S. pennellii were unpublished, being identified for the first time in our study. Furthermore, we identified 2471 and 3462 different miRNA target in S. lycopersicum and S. pennellii, respectively. The Solanaceae family is one of the largest families in the plant kingdom, including several plants of agronomic and medical importance. It is composed of approximately 100 genera and more than 3000 species that grow in all habitats, ranging from rainforests to deserts. Tomato is one of the most important fruit crops in the global food industry 1-5 . The genus Solanum is one of largest genera among the Angiosperms, containing approximately 1500 species 6 . Solanum lycopersicum, the cultivated tomato is one of the most consumed fruits worldwide 7,8 . In addition to its importance as food, the tomato has important agronomic characteristics, including fleshy fruits and multicellular and glandular trichomes, which model plants, like Arabidopsis thaliana, do not have. Thus, the common tomato has been used as a model for species that also have these characteristics 9-13 . Due to the specific characteristics and growing conditions, tomato varieties are constantly improved 14 . However, this crop is susceptible to insect attacks and more than 200 diseases caused by various types of pathogens, including viruses, bacteria, fungi and nematodes 15 . To aid in the control of these diseases, most producers opt for the use of chemical agents, which are often costly, at times ineffective, and have deleterious effects on the environment 16 . An alternative to these problems is to cross the cultivated tomato with wild species 12,17-20 . There are several known species of wild tomato, consisting of underexploited genetic resources, and of great importance for the improvement, research and development of culture 12, 18, [20] [21] [22] [23] [24] [25] [26] . Solanum pennellii is a wild tomato species that has been widely used for the construction and mapping of populations due to its tolerance to environmental stress 18, 20, 27, 28 . In this sense, a better understanding of the tomato molecular basis is required to achieve the efficiency and success in the selection of markers associated with characteristics of interest 4 . Current progress in sequencing the tomato genome has generated useful information to assist in the study of their genetic diversity 12,23 . The sequencing of the S. lycopersicum genome was completed in 2012 29 . Furthermore, the availability of a reference genome provided a framework for the genomic analysis of Solanaceae family, generating a source of important information for their molecular breeding 5, 13, 30 . In addition to S. lycopersicum, the S. pennellii genome was also sequenced, which provided a valuable resource for the understanding of several
doi:10.1038/s41598-018-34202-3 fatcat:a77lhuo7pncdtfshfagrhqfgry