2.5. Identification of genes involved in sucrose metabolism in Fragaria vesca.
In order to identify each Fragaria vesca paralogues, the Hidden Markov model (HMM) profiles from Pfam (https://pfam.xfam.org/) or InterPro (http://www.ebi.ac.uk/interpro/) databases were used as a query against predicted protein sequences of Fragaria vesca from genome database for Rosaceae (GDR, https://www.rosaceae.org/). The profiles used as query was as follows: SPS (family IPR012819, Superfamily IPR023214, domains IPR000368/IPR001296/IPR006380, PF00862/PF00534/PF05116), SS (family IPR012820, domains IPR000368/ IPR001296, PF00862/PF00534) and invertases(family IPR001362; domains PF00251/PF08244) (CWINV, Superfamily IPR013148/IPR013189, Domains IPR013320/IPR023296, UniProtKB Q9ZP42; VINV, Family IPR001362, Superfamily IPR23296, Domains IPR013148, UniProtKB Q08IC1). Thus, for SPS 4 homologues were found clustering together (FvSPS1, FvH4_2g28820. FvH4_4g13520, FvSPS2). For SS, 4 homologues which clustering together (FvSS1, FvH4_1g07260, FvSS2, FvH4_4g18710) were analyzed and the other 2 homologues (FvH4_1g27400, FvH4_5g18160) belonging to another cluster were not analyzed. For CWINV, 3 homologues which clustering together (FvCWINV1, FvH4_6g33780, FvCWINV2) were analyzed. In the case of FvH4_6g19270 was not analyzed because it was not in the same cluster but also the expression level in fruit was very low. For VINV the only 2 homologues found in a cluster were analyzed (FvVINV1, FvVINV2).
In order to perform functional phylogenetic trees, the paralogues obtained were used to find near orthologues in monocots and dicots in which the specific enzymatic activities have been described.