After having analyzed and discussed all our results, we have been able to come to some conclusions.
Firstly, it can be concluded that these selenoproteins have been identified in Miichthys miiuy's genome: Sel15, SELENOE, GPx1a, GPx1b, GPx2, GPx4a, GPx4b, GPx5/6, DIO1, DIO3a, DIO3b, SEPHS2, SELENOH, SELENOI, SELENOJ, SELENOK, SELENOM, SELENON, SELENOO1, SELENOP(1), MSRB1a, MSRB1b, MSRB2, SELENOS, SELENOT1, SELENOT2, SELENOU1a, SELENOW1, SELENOW2, TXNRD2 and TXNRD3. There are also three selenoproteins that it is not completely sure that are present in Miichthys miiuy's genome for different reasons that have been previously discussed, which are: GPx3b, DIO2 and SELENOP(2).
Regarding Cys-containing homologous proteins, it has been concluded that Miichthys miiuy has: GPx7, GPx8, MSRA(1), MSRA(2), SEPHS(1), MSRB3, SELENOU2 and SELENOU3.
Proteins that participate in selenoprotein biosynthesis have also been studied. It has been concluded that Miichthys miiuy contains these selenoprotein machinery genes: eEFsec, SBP2(1), SECp43(1) and SECp43(2). However, SBP2(2), SecS(1) and SecS(2) have not been found in Miichthys miiuy's genome, and it is not clear whether this organism contains PSTK protein.
Human proteins that are related to selenium metabolism have also been predicted in Miichthys miiuy's genome. These proteins are: ELAVL1, CELF1, EIF4A3, XPO1, G6PD, LRP8, RPL30, SCLY, SELENBP1, SARS2 and TTPA.
As it has been suggested in the discussion, some selenoproteins from SelenoDB are not well annotated. For this reason, another database could be used in order to align Miichthys miiuy's genome with these queries in future studies.
One limitation of our study is that selenoproteins have only been predicted using Exonerate program and Seblastian, but only in the cases that we have found more than one result in the Exonerate file is when Genewise has been performed. We suggest that for future studies, Genewise should be included in the automatic program.
Another limitation of our study is that only Zebrafish and Human have been used to predict selenoproteins in Miichthys miiuy's genome. Even though these two species are really well studied and well annotated, we suggest that this same study could be predicted by aligning Miichthys miiuy's genome to the queries from another phylogenetically closer organism, such as Stickleback.
All in all, since many selenoproteins have been predicted in Miichthys miiuy's genome, this information may be useful for future studies about selenoproteomes in vertebrates.
