Abstract

MotivationThe family Asteraceae represents one of the largest evolutive radiation of flowering plants, including more than 1500 genera and 23000 species, and comprising economically important as well as ornamental crops (Jansen, 1987; Bremer, 2008). Among members of this dicotyledon family two edible species, Carthamus tinctorius L. and Cynara cardunculus var. scolymus L., also have a phytopharmaceutical interest. The former, known as safflower, is the only member of this genus widely cultivated for industrial oil, as a livestock feed or for use in traditional medicine (Han et al., 2009). The second species, the globe artichoke, apart of its importance as a food, is popular for its dietary and therapeutic potentials, especially for hepato-biliary dysfunctions and digestive complaints (Gebhardt, 1998; López-Molina, 2005). The discovery of microRNAs (miRNAs) in different genomes provided a new paradigm in evolution studies, due to their ancient origin and the important role played in development regulation, since the egress of multicellular organisms. This system is highly conserved in plant and animal cells. Plant miRNAs derive from long primary transcripts giving rise to mature 21-24nt RNAs products, fundamental in RNA-based gene regulation (Bartell, 2004). In plants, miRNAs control messengers degradation or restrain translation, affecting somatic development and the response to biotic and abiotic stresses (Jones-Rhoades, 2006). A feature of miRNAs is their imperfect but extensive complementarity to corresponding mRNA targets, thus making their computational prediction possible. This approach is useful when data mining is performed on the basis of miRNA:mRNA targets conservation, among different species, and was herein applied to the study of Carthamus and Cynara spp.MethodsA comparative approach was used to identify both evolutionary and functionally conserved miRNAs as well as their targets, by detection of common expressed sequence tags (ESTs) in Carthamus and Cynara spp. A bioinformatic pipeline was developed at this regard to analyze publicly available ESTs dataset and identify miRNA candidates in these two related species. Complete EST datasets from Carthamus and Cynara (36323 and 42011 sequences, respectively) were screened looking for putative miRNA targets by means of RNAhybrid (Rehmsmeier, et al., 2004) software and using the mirBase mature miRNA sequences from Arabidopsis as a reference set. Afterward the NCBI Blast algorithm (Altschul et al., 1990) embedded in a Perl script was used to identify the homologous region in Carthamus and Cynara EST datasets. The RNAhybrid results and the homologous region calculated, have been downloaded into a relational database (DBMS MySql) ad hoc developed. We generate the "mapping" of the miRNA target on the "EST homologous region" by means SQL queries. Finally, the signal-to-noise ratio and specificity were assessed using two approaches: in the first one, for each Arabidopsis mature miRNA, the

Autore Pugliese

• Finetti Sialer Mariella Matilde , Catalano Domenico

Tutti gli autori

• Catalano D. ; Finetti-Sialer M.M

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Anno di pubblicazione

2010

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ISBN

978-88-6194-079-6

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