1Iodothyronine deiodinase (DI) family

As explained in the introduction, Idothreonine deiodinase family is a commonly present protein family in mammals. This family is composed of three different proteins but only DI and DI1 are present in both Danio rerio and Ophiodon elongatus.

DI

After running the tblastn, seven hits on six different scaffolds were identified but only four of the scaffolds had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, results obtained from the complete analysis allowed us to reduce the possible scaffolds to one (JACSYO010000262.1), which had the best T-coffee alignment

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 917287 and 918078, comprising 1 exon in the reverse strand (-). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 985) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian produced a better prediction, as the sequence obtained contains 1 exon in the reverse strand (-) and includes a Met at the beginning of the protein (which did not happen with the Exonerate prediction). SECIS Search3 identified a SECIS element for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the reverse strand, specifically between positions 916820 and 916748 of the JACSYO010000262.1 scaffold.

In conclusion, we can say that the gene DI is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish DI.

DI1

After running the tblastn, six hits on four different scaffolds were identified and all of them had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, results obtained from the complete analysis allowed us to reduce the possible scaffolds to one (JACSYO010002145.1), which had the best T-coffee alignment.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 2097519 and 2098905, comprising 3 exons in the forward strand (+). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 998) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian produced a better prediction, as the sequence obtained contains 4 exons in the forward strand (+) and includes a Met at the beginning of the protein (which did not happen with the Exonerate prediction). SECIS Search3 identified two SECIS elements for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the reverse strand, specifically between positions 2099993-2100065 and 2099729-2099795 of the JACSYO010002145.1 scaffold. Despite the fact that both of the SECIS elements could be correct, the representation will only show one of them.

In conclusion, we can say that the gene DI1 is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish DI1.

The results observed in this phylogenetic tree are coherent with the ones we extracted from our data. The proteins of the Ophiodon elongatus are closely related to their homologues in Danio rerio and afterwards they link the whole DI family.

2Glutathione peroxidase (GPx) family

GPx

After running the tblastn, twenty hits on nine different scaffolds were identified and all of them had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, results obtained from the complete analysis allowed us to reduce the possible scaffolds to two (JACSYO010000406.1 and JACSYO010000471.1), which both had good T-coffee alignments.

As we can observe with Exonerate, the gene of the scaffold JACSYO010000406.1 is located in the Ophiodon elongatus genome between positions 810181 and 811527, comprising 2 exons in the forward strand (+). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 998) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains a Sec in the same position as the reference protein.

The gene of the scaffold JACSYO010000471.1 is located in the Ophiodon elongatus genome between positions 2900773 and 2902385, comprising 2 exons in the reverse strand (-). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 999) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains a Sec in the same position as the reference protein.

Because the two scaffolds of Ophiodon elongatus contain the GPx protein, we think that it might have duplicated.

The analysis conducted in Seblastian also predicted a sequence that contains 2 exons for each protein of each of the scaffolds, in the reverse and forward strand (as we had found with exonerate). SECIS Search3 identified a SECIS element for this sequence in each of the scaffolds. For the scaffold JACSYO010000406.1 the SECI element is found in the 3’-UTR segment of the forward strand, between positions 811696 and 811766. For the scaffold JACSYO010000471.1 the SECIS element is found in the 3’-UTR segment of the reverse strand, between positions 2900534 and 2900608.

In conclusion, we can say that the gene GPx is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. In addition, we can say that this selenoprotein has been duplicated in the Ophiodon elongatus genome.

GPx2

After running the tblastn, twenty-one hits on eleven different scaffolds were identified and nine scaffolds had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, results obtained from the complete analysis allowed us to reduce the possible scaffolds to one (JACSYO010002173.1), which had the best T-coffee alignment.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 858742 and 813855, comprising 2 exons in the forward strand (+). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had very high similarity (with a score of 1000) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the region containing the selenocystein aligns with the protein of Danio rerio perfectly.

The analysis conducted in Seblastian also predicted a sequence that contains 4 exons in the forward strand (+) and includes a Met at the beginning of the protein (which also happened with the Exonerate prediction). SECIS Search3 identified a SECIS element for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the forward strand, specifically between positions 859962 and 860029 of the JACSYO010002173.1 scaffold.

In conclusion, we can say that the gene GPx2 is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element.

GPx3

After running the tblastn, eighteen hits on nine different scaffolds were identified and all of them had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, results obtained from the complete analysis allowed us to reduce the possible scaffolds to one (JACSYO010000535.1), which had the best T-coffee alignment.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 68906 and 70533, comprising 4 exons in the forward strand (+). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 985) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the Selenocysteine of protein sequence of Danio rerio aligns with the one from Ophiodon elongatus.

The analysis conducted in Seblastian was not able to predict any sequence, but the SECIS Search3 identified two SECIS elements for this sequence. We selected only one of the SECIS predicted, because it had a grade A (the other one had a grade B), and it is near the exonic sequence of the gene. It is found in the 3’-UTR segment of the forward strand, specifically between positions 70629 and 70706 of the JACSYO010000535.1 scaffold.

In conclusion, we can say that the gene GPx3 is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element.

GPx4

After running the tblastn, eighteen hits on eleven different scaffolds were identified but only eight of the scaffolds had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, results obtained from the complete analysis allowed us to reduce the possible scaffolds to one (JACSYO010001924.1), which had the best T-coffee alignment.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 1623795 and 1625702, comprising 3 exons in the reverse strand (-). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had very high similarity (with a score of 1000) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian produced a quite different prediction, as the sequence obtained contains 2 exons in the reverse strand (-), instead of 3. SECIS Search3 identified a SECIS element for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the reverse strand, specifically between positions 1622955 and 1623034 of the JACSYO010001924.1 scaffold.

In conclusion, we can say that the gene GPx4 is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element.

GPx7

After running the tblastn, seventeen hits on twelve different scaffolds were identified but only six of the scaffolds had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, results obtained from the complete analysis allowed us to reduce the possible scaffolds to one (JACSYO010002134.1), which had the best T-coffee alignment.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 801284 and 802063, comprising 2 exons in the reverse strand (-). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 994) so we can conclude that a coding sequence for this protein is found in the studied organism. The analysed protein does not contain any Selenocysteine, but it has two cysteines, indicating that it probably is a cystein-homologous protein.

The analysis with Seblastian was not able to predict any protein alignment. SECIS Search3 identified 12 SECIS element for this sequence. As all of them had a grade B and had similar Infernal score values, we were not able to select the one(s) that fits best the Ophiodon elongatus genome. An example of one of the SECIS found is the one represented in the image, which is found in the 3’-UTR segment of the reverse strand, between positions 778084 and 778151 of the JACSYO010002134.1 scaffold.

In conclusion, we can say that the gene GPx7 is a cysteine-homolgue protein found in Ophiodon elongatus, due to the presence of a Cys residue and even though a SECIS element was identified through SECIS Search3 (this indicates that the protein could have been a selenoprotein on the past but lost the Sec residue).

GPx8

After running the tblastn, twenty-one hits on fourteen different scaffolds were identified but only seven of the scaffolds had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, results obtained from the complete analysis allowed us to reduce the possible scaffolds to two (JACSYO010000919.1 and JACSYO010002134.1), which had the best T-coffee alignments.

As we can observe with Exonerate, the gene, for the scaffold JACSYO010000919.1 is located in the Ophiodon elongatus genome between positions 388811 and 390588, comprising 3 exons in the reverse strand (-). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had very high similarity (with a score of 1000) so we can conclude that a coding sequence for this protein is found in the studied organism.

For the scaffold JACSYO010002134.1, the gene is located in the Ophiodon elongatus genome between positions 801287 and 805048, comprising 3 exons in the reverse strand (-). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 996) so we can conclude that a coding sequence for this protein is found in the studied organism.

The analysed protein does not contain Sec, but it has a common Cys in both sequences aligned, making GPx8 a possible Cys-containing homologue protein.

The analysis conducted in Seblastian for the first scaffold (JACSYO010000919.1) was not able to make any prodictions. No SECIS element was predicted for this scaffold either. For the scaffold JACSYO010002134.1, Seblastian was not able to make any predictions, but SECIS Search3 identified twelve different SECIS, all of them in the reverse strand, with similar positions and infernal score, so we were not able to elucidate which one(s) are present in the genome of Ophiodon elongatus.

In conclusion, we can say that the gene GPx8 is a cysteine-containing homologue found in Ophiodon elongatus, due to the presence of a Cys residue, despite the fact that a SECIS element was identified through SECIS Search3 (this indicates that the protein could have been a selenoprotein on the past but lost the Sec residue).

Regarding the phylogenetic tree of the GPx protein family, we can see that GPx2, GPx3 and GPx4 proteins predicted from Ophiodon elongatus’ genome pair specifically with their homologues in Danio rerio, confirming that these proteins are Selenoproteins present in Ophiodon elongatus.

However, GPx has similar alignments with proteins predicted from two different scaffolds of Ophiodon elongatus, which affirms our hypothesis that this protein might be duplicated in the Ophiodon elongatus’ genome.

Considering the GPx8 protein, in which we could not decide between two scaffolds of Ophiodon elongatus, we can see that the scaffold which pairs better with Danio rerio’s GPx8 protein is JACSYO010002134.1, which is the only of the two scaffolds analysed for which SECIS3 Search found possible SECIS sequences. This confirms that GPx8 protein of Danio rerio has an homologous protein in Ophiodon elongatus, whose sequence is found in the scaffold JACSYO010002134.1.

When observing protein GPx7, even though the protein predicted from Ophiodon elongatus pairs better with a GPx8 protein also predicted from the analysed organism genome, we found that this GPx8 predicted protein is probably not a good prediction.

In addition, proteins GPx, GPx2 and GPx3 are related, as seen in the phylogenetic tree, confirming relationship between them. GPx7 and GPx8 are related, and they are also related with GPx4, indicating that they evolved from GPx4.

In conclusion, the phylogenetic tree obtained confirms that our predicted selenoproteins and cysteine-containing proteins are homologous of the human ones, and they evolved in the same way.

3Methathione sulfoxide reductase A (MsrA) family

MsrA

After running the tblastn, twelve hits on five different scaffolds were identified. Since the hits from only two of the scaffolds (JACSYO010002166.1 and JACSYO010001682.1) had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied, the other three scaffolds were not further studied. We completed the analysis with both of the scaffolds, and both showed a good T-coffee alignment.

For the scaffold JACSYO010002166.1, as we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 2194476 and 2265221, comprising 6 exons in the forward strand (+). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 993).

For the scaffold JACSYO010001682.1, as we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 1851193 and 1867206, comprising 4 exons in the forward strand (+). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 999)

We can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Cys in the same position as the reference protein.

The analysis by Seblastian didn’t find any results for none of the two scaffolds. SECIS Search3 only identified a SECIS element for the scaffold JACSYO010001682.1 of this sequence between positions 1812445 and 1812512. Because this SECIS element found in the scaffold are previous than the exons of the scaffold, we can not conclude that this SECIS element corresponds to the protein analysed and if the protein is indeed a cystein-containing protein in Ophiodon elongatus

When doing the phylogeny, more proximity is observed between the scaffold JACSYO010002166.1 of Ophiodon elongatus MsrA protein and the MsrA protein of Danio rerio, meaning that the protein found in the JACSYO010002166.1 scaffold is probably the cystein-containing homologous protein of Ophiodon elongatus.

4Fep15 family

Fep15

After running the tblastn, four hits on two different scaffolds were identified and both had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, results obtained from the complete analysis allowed us to reduce the possible scaffolds to one (JACSYO010002146.1), which had the best T-coffee alignment.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 1123108 and 1125051, comprising 4 exons in the reverse strand (-). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 978) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains a Sec in the same position as the reference protein.

The analysis conducted in Seblastian also predicted a sequence that contains 4 exons in the reverse strand (-) and includes a Met at the beginning of the protein (which did not happen with the Exonerate prediction). SECIS Search3 identified a SECIS element for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the reverse strand, specifically between positions 1122987 and 1123079 of the JACSYO010002146.1 scaffold.

In conclusion, we can say that the gene Fep15 is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish Fep15.

5Selenoprotein (Sel)family

Sel15

After running the tblastn, four hits on three different scaffolds were identified but only one scaffold had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. Therfore, the study was only performed on the scaffold JACSYO010001861.1.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 2709194 and 2713255, comprising 4 exons in the reverse strand (-). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 1000) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian produced a better prediction, as the sequence obtained contains 5 exons in the reverse strand (-) and includes a Met at the beginning of the protein (which did not happen with the Exonerate prediction). SECIS Search3 identified a SECIS element for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the reverse strand, specifically between positions 2708249 and 2708322 of the JACSYO010001861.1 scaffold.

In conclusion, we can say that the gene Sel15 is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish Sel15.

SelH

After running the tblastn, three hits on two different scaffolds were identified but only one scaffold had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. Therfore, the study was only performed on the scaffold JACSYO010000469.1.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 3211813 and 3213920, comprising 3 exons in the reverse strand (-). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 922) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian produced a similar prediction, because despite the sequence obtained contains 2 exons in the reverse strand (-), it does not include a Met at the beginning of the protein (the same as in the Exonerate prediction). SECIS Search3 identified a SECIS element for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the reverse strand, specifically between positions 3210334 and 3210249 of the JACSYO010000469.1 scaffold.

In conclusion, we can say that the gene SelH is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelH.

SelI

After running the tblastn, thirteen hits on four different scaffolds were identified but only three of the scaffolds had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, results obtained from the complete analysis allowed us to reduce the possible scaffolds to one (JACSYO010001293.1), which had the best T-coffee alignment

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 222962 and 235187, comprising 10 exons in the forward strand (+). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 922) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian produced a better prediction, as the sequence obtained contains 10 exons in the forward strand (+) and includes a Met at the beginning of the protein (which did not happen with the Exonerate prediction). SECIS Search3 identified a SECIS element for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the reverse strand, specifically between positions 236306 and 236379 of the JACSYO010001293.1 scaffold.

In conclusion, we can say that the gene SelI is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelI.

SelJ

After running the tblastn, fifteen hits on two different scaffolds were identified and both of the scaffolds had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, results obtained from the complete analysis allowed us to reduce the possible scaffolds to one (JACSYO010000511.1), as it had a better T-Coffee alignment around de Sec position.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 798545 and 800865, comprising 9 exons in the reverse strand (-). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 999) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian produced a similar prediction, as the sequence obtained contains 9 exons in the reverse strand (-) and does not include a Met at the beginning of the protein (the same as in the Exonerate prediction). SECIS Search3 identified a SECIS element for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the reverse strand, specifically between positions 798405 and 798478 of the JACSYO010000511.1 scaffold.

In conclusion, we can say that the gene SelJ is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelJ.

SelK

After running the tblastn, two hits on two different scaffolds were identified but only one of the scaffolds (JACSYO010000981.1) had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 267080 and 268351, comprising 4 exons in the forward strand (+). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 983) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian could not predict any selenoprotein but SECIS Search3 identified two SECIS elements for this sequence. However, one of them was found on the reverse strand (-), so it is rejected because it is not found on the same strand as the predicted gene. The other one has a good infernal and covels score and is found in the 3’-UTR segment of the forward strand (+), specifically between positions 268623 and 268712 of the JACSYO010000981.1 scaffold.

In conclusion, we can say that the gene SelK is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelK.

SelL

After running the tblastn, eight hits on two different scaffolds were identified and both of the scaffolds had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, results obtained from the complete analysis allowed us to reduce the possible scaffolds to one (JACSYO010001682.1), as it was the only one which presented a Sec residue in the same position as the reference protein.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 2876969 and 2879747, comprising 4 exons in the reverse strand (-). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 997) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian produced a similar prediction, because despite the sequence obtained contains 8 exons in the reverse strand (-), it does not include a Met at the beginning of the protein (the same as in the Exonerate prediction). SECIS Search3 identified a SECIS element for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the reverse strand, specifically between positions 2876719 and 2876796 of the JACSYO010001682.1 scaffold.

In conclusion, we can say that the gene SelL is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelL.

SelM

After running the tblastn, five hits on four different scaffolds were identified and two of the scaffolds had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, results obtained from the complete analysis allowed us to reduce the possible scaffolds to one (JACSYO010000247.1), which had the best T-coffee alignment.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 719097 and 721152, comprising 5 exons in the forward strand (+). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 999) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian produced a better prediction, as the sequence obtained contains 5 exons in the forward strand (+) and includes a Met at the beginning of the protein (which did not happen with the Exonerate prediction). SECIS Search3 identified a SECIS element for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the forward strand (+), specifically between positions 721635 and 721716 of the JACSYO010000247.1 scaffold.

In conclusion, we can say that the gene SelM is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelM.

SelN

After running the tblastn, eleven hits on three different scaffolds were identified and only one of the scaffolds (JACSYO010002166.1) had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 2926593 and 2931928, comprising 9 exons in the forward strand (+). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 994) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian produced a better prediction, as the sequence obtained contains 12 exons in the forward strand (+) and includes a Met at the beginning of the protein (which did not happen with the Exonerate prediction). SECIS Search3 identified a SECIS element for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the forward strand (+), specifically between positions 2932459 and 2932532 of the JACSYO010002166.1 scaffold.

In conclusion, we can say that the gene SelN is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelN.

SelO

After running the tblastn, twenty-one hits on three different scaffolds were identified and all the scaffolds had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, results obtained from the complete analysis allowed us to reduce the possible scaffolds to one (JACSYO010000740.1), which had the best T-coffee alignment.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 133486 and 138062, comprising 9 exons in the forward strand (+). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 997) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian produced a better prediction, as the sequence obtained contains 9 exons in the forward strand (+) and includes a Met at the beginning of the protein (the same as in the Exonerate prediction). SECIS Search3 identified a SECIS element for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the forward strand (+), specifically between positions 138546 and 138624 of the JACSYO010000740.1 scaffold.

In conclusion, we can say that the gene SelO is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelO.

SelP

After running the tblastn, eight hits on four different scaffolds were identified and two of the scaffolds had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, results obtained from the complete analysis allowed us to reduce the possible scaffolds to one (JACSYO010000335.1), which had the best T-coffee alignment.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 348133 and 348881, comprising 2 exons in the forward strand (+). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 969) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian produced a better prediction, as the sequence obtained contains 4 exons in the forward strand (+) and includes a Met at the beginning of the protein (which did not happen with the Exonerate prediction). SECIS Search3 identified two SECIS elements for this sequence but we selected the one with better infernal and covels score which is found in the 3’-UTR segment of the forward strand (+), specifically between positions 350194 and 350194 of the JACSYO010000335.1 scaffold.

In conclusion, we can say that the gene SelP is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelP.

SelR

After running the tblastn, ten hits on three different scaffolds were identified and two of the scaffolds had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. Results obtained from the complete analysis could not allow us to reduce the possible scaffolds to one due to the fact that the T-Coffee results were good for both indicating that there could be a duplication. Therefore, we will analyse both scaffolds.

As we can observe with Exonerate, the gene is located in the JACSYO010001932.1 of the Ophiodon elongatus genome between positions 1586927 and 1588059, comprising 3 exons in the forward strand (+). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 1000) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian produced a similar prediction, as the sequence obtained contains 3 exons in the forward strand (+) and includes a Met at the beginning of the protein (the same as in the Exonerate prediction). SECIS Search3 identified a SECIS elements for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the forward strand (+), specifically between positions 1589047 and 1589121 of the JACSYO010001932.1 scaffold.

On the other scaffold (JACSYO010002129.1), the gene is located between positions 3429717 and 3433976, comprising 3 exons in the reverse strand (-). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 1000) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian produced a similar prediction, because despite the sequence obtained contains 4 exons in the reverse strand (-), it includes a Met at the beginning of the protein (the same as in the Exonerate prediction). SECIS Search3 identified two SECIS elements for this sequence but one of them was discarded because it is predicted before the end of our gene. Therfore, we selected the one which is found in the 3’-UTR segment of the reverse strand, specifically between positions 3429498 and 3429571 of the JACSYO010002129.1 scaffold.

In conclusion, we can say that the gene SelR is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelR and SelR1.

SelR1

After running the tblastn, ten hits on three different scaffolds were identified and two of the scaffolds had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. Results obtained from the complete analysis could not allowed us to reduce the possible scaffolds to one due to the fact that the T-Coffee results were good for both indicating that there could be a duplication. Therefore, we will analyse both scaffolds.

As we can observe with Exonerate, the gene is located in the JACSYO010001932.1 of the Ophiodon elongatus genome between positions 1586927 and 1588059, comprising 3 exons in the forward strand (+). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 1000) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein. In fact, this prediction is exactly the same as the one on SelR, which we will discuss later on in the discussion of the phylogenetic tree.

The analysis conducted in Seblastian produced a similar prediction, as the sequence obtained contains 3 exons in the forward strand (+) and includes a Met at the beginning of the protein (the same as in the Exonerate prediction). SECIS Search3 identified a SECIS element for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the forward strand (+), specifically between positions 1589047 and 1589121 of the JACSYO010001932.1 scaffold.

On the other scaffold (JACSYO010002129.1), the gene is located between positions 3432772 and 3433976, comprising 3 exons in the reverse strand (-). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 1000) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein. In fact, the prediction of the protein is exactly the same as the one on SelR, it only shows a difference in the position of the third exon. This will discuss later on in the discussion of the phylogenetic tree.

However, Seblastian does not predict any selenoprotein nor SECIS element inside the sequence studied.

In conclusion, we cannot affirm that the gene SelR1 is a selenoprotein found in Ophiodon elongatus, because even though it presents a Sec residue on the same position as the reference protein, no SECIS element was found. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelR and SelR1.

SelR2

After running the tblastn, thirteen hits on seven different scaffolds were identified and two of the scaffolds had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, results obtained from the complete analysis allowed us to reduce the possible scaffolds to one (JACSYO010000605.1), which had the best T-coffee alignment.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 1743106 and 1744400, comprising 4 exons in the forward strand (+). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 999) so we can conclude that a coding sequence for this protein is found in the studied organism.

The analysis conducted in Seblastian could not produce a prediction but SECIS Search3 identified a SECIS element for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the forward strand (+), specifically between positions 1705384 and 1705384 of the JACSYO010000605.1 scaffold.

In conclusion, we can say that the gene SelR2 is on the Ophiodon elongatus genome but is not a selenoprotein (because it has not a Sec residue nor SECIS elements). In fact, it is a cysteine-containing homolog found in Ophiodon elongatus, due to the presence of a Cys residue, even though a SECIS element was identified through SECIS Search3 (this indicates that the protein could have been a selenoprotein on the past but lost the Sec residue). Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelR2.

SelR3

After running the tblastn, fifteen hits on six different scaffolds were identified and three of the scaffolds had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, results obtained from the complete analysis allowed us to reduce the possible scaffolds to one (JACSYO010001636.1), which had the best T-coffee alignment.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 1500866 and 1509463, comprising 6 exons in the forward strand (+). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 980) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

Seblastian does not predict any selenoprotein nor SECIS element inside the sequence studied, which is expected as this protein doesn’t have a Sec residue which indicates it is a Cys-containing homolog.

In conclusion, we can say that the gene SelR3 is on the Ophiodon elongatus genome but is not a selenoprotein (because it has not a Sec residue nor SECIS elements). In fact, it is a Cys-containing homolog found in Ophiodon elongatus, due to the presence of a Cys residue and the absence of SECIS elements and Seblastian prediction. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelR3.

SelS

After running the tblastn, five hits on three different scaffolds were identified but only one scaffold (JACSYO010001703.1) had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 922421 and 926886, comprising 5 exons in the forward strand (+). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 946) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian could not produce a prediction, but SECIS Search3 identified two SECIS elements for this sequence from where we selected the one with better infernal and covels score which is found in the 3’-UTR segment of the forward strand (+), specifically between positions 927177 and 927253 of the JACSYO010001703.1 scaffold.

In conclusion, we can say that the gene SelS is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelS.

SelT

After running the tblastn, nine hits on three different scaffolds were identified and two of the scaffolds had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, results obtained from the complete analysis allowed us to reduce the possible scaffolds to one (JACSYO010001924.1), which had the best T-coffee alignment.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 3746598 and 3750901, comprising 5 exons in the reverse strand (-). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 970) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian produced a similar prediction, as the sequence obtained contains 5 exons in the reverse strand (-) and includes a Met at the beginning of the protein (the same as in the Exonerate prediction). SECIS Search3 identified a SECIS element for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the revserse strand (-), specifically between positions 3746256 and 3746329 of the JACSYO010001924.1 scaffold.

In conclusion, we can say that the gene SelT is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelT.

SelU

After running the tblastn, twelve hits on three different scaffolds were identified and all the scaffolds had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied. However, we could only obtain Exonerate results for two of them and results obtained from the complete analysis allowed us to reduce the possible scaffolds to one (JACSYO010001669.1), which had the best T-coffee alignment.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 53588 and 54961, comprising 4 exons in the forward strand (+). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 982) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian produced a better prediction, because the sequence obtained contains 5 exons in the forward strand (+) and includes a Met at the beginning of the protein (which did not happen with the Exonerate prediction). SECIS Search3 identified a SECIS element for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the forward strand (+), specifically between positions 55090 and 55160 of the JACSYO010001669.1 scaffold.

In conclusion, we can say that the gene SelU is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelU.

SelU2

After running the tblastn, eight hits on three different scaffolds were identified and only one of the scaffolds (JACSYO010002009.1) had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 707478 and 709150, comprising 6 exons in the reverse strand (-). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 994) so we can conclude that a coding sequence for this protein is found in the studied organism.

The analysis conducted in Seblastian could not produce a prediction but SECIS Search3 identified three SECIS elements for this sequence. All have good infernal and covels score, but two of them are is discarded because they were predicted before the end of our gene. The other one is found in the 3’-UTR segment of the revserse strand (-), specifically between positions 682679 and 682763 of the JACSYO010002009.1 scaffold.

In conclusion, we can say that the gene SelU2 is on the Ophiodon elongatus genome but is not a selenoprotein (because it has not a Sec residue nor SECIS elements). In fact, it is a Cys-containing homolog found in Ophiodon elongatus, due to the presence of a Cys residue, even though a SECIS element was identified through SECIS Search3 (this indicates that the protein could have been a selenoprotein on the past but lost the Sec residue). Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelU2.

SelU3

After running the tblastn, eight hits on four different scaffolds were identified and only one of the scaffolds (JACSYO010001618.1) had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 840617 and 845246, comprising 6 exons in the reverse strand (-). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 1000) so we can conclude that a coding sequence for this protein is found in the studied organism.

Seblastian does not predict any selenoprotein nor SECIS element inside the sequence studied, which is expected as this protein doesn’t have a Sec residue which indicates it is a Cys-containing homolog.

In conclusion, we can say that the gene SelU3 is on the Ophiodon elongatus genome but is not a selenoprotein (because it has not a Sec residue nor SECIS elements). In fact, it is a Cys-containing homolog found in Ophiodon elongatus, due to the presence of a Cys residue and the absence of SECIS elements and Seblastian prediction. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelU3.

SelW

After running the tblastn, two hits on one scaffold (JACSYO010000671.1) were identified and they had an e-value (smaller than 0.0001) and identity (bigger than 30%) good enough to be studied.

As we can observe with Exonerate, the gene is located in the Ophiodon elongatus genome between positions 1718117 and 1719393, comprising 4 exons in the reverse strand (-). The T-coffee alignment between the predicted protein in O.elongatus and the protein of reference (from D.rerio) had high similarity (with a score of 1000) so we can conclude that a coding sequence for this protein is found in the studied organism. Moreover, the analysed protein contains Sec in the same position as the reference protein.

The analysis conducted in Seblastian produced a similar prediction, as the sequence obtained contains 4 exons in the forward strand (+) and includes a Met at the beginning of the protein (the same as in the Exonerate prediction). SECIS Search3 identified a SECIS element for this sequence with good infernal and covels score which is found in the 3’-UTR segment of the reverse strand (-), specifically between positions 1717844 and 1717917 of the JACSYO010000671.1 scaffold.

In conclusion, we can say that the gene SelW is a selenoprotein found in Ophiodon elongatus, due to the presence of a Sec residu and a SECIS element. Moreover, from the information displayed in the phylogenetic tree we can also conclude that it is an homologous protein of the zebrafish SelW.

Sel family phylogenetic tree