Browsing by Author "Froufe, Elsa"
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- Dataset of the complete mitogenome of the deep-sea sailfin roughshark, Oxynotus paradoxus Frade, 1929Publication . Matos, Ana; Gomes-dos-Santos, André; Graça Aranha, Sofia; Dias, Ester; Veríssimo, Ana; Teodosio, Maria; Figueiredo, Ivone; Castro, L. Filipe C．; Froufe, ElsaChondrichthyans comprise a diverse group of vertebrate species with extraordinary ecological relevance. Yet, multiple members of this evolutionary lineage are associated with sig-nificant extinction risk. The sailfin roughshark Oxynotus para-doxus is a deep-water benthic shark currently listed as vul-nerable due to population declines in parts of its range. Here we provide the first complete mitochondrial genome of O. paradoxus, comprising also the first record for the genus and family Oxynotidae. These data can facilitate future monitor-ing of the genetic diversity in this and related species. Ge-nomic DNA was extracted from O. paradoxus collected in the eastern North Atlantic off western Portugal (37.59 degrees N, 9.51 degrees W) and sent for Illumina Paired-End (2 x 150 bp) library con-struction and whole genome sequencing on a Novaseq60 0 0 platform. Trimmomatic (version 0.38) was used to remove adapters and MitoZ (version 3.4) to assemble and anno-tate the mitogenome. This mitogenome with 17 100 bp has a total of 38 genes, 13 of which are protein-coding genes, 23 transfer RNA genes, and 2 ribosomal RNA genes. Eight transfer RNAs and 1 protein-coding gene (NADH de-hydrogenase subunit 6, NAD6) are in the complementary strand. In the provided phylogenetic inference, with all avail-able and verified Squalomorphii mitogenomes, the four or-ders are well separated, and as expected, O. paradoxus is placed in the Squaliformes order. This data reinforces the need for more genomic resources for the Oxynotidae family.(c) 2023 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/ )
- Genetic diversity and population genetic analysis of Donax vittatus (Mollusca: Bivalvia) and phylogeny of the genus with mitochondrial and nuclear markersPublication . Fernandez-Perez, Jenyfer; Froufe, Elsa; Nanton, Ana; Gaspar, Miguel; Mendez, JosefinaIn this study, the genetic diversity of Donax vittatus across the Iberian Peninsula was investigated using four mitochondrial (COI, Cytb, 16S F and M types) and three nuclear (H8, 18S and 285) genes. These same molecular markers were also sequenced in D. semistriatus and D variegatus to address the phylogenetic relationships of the species of the genus Donax common along the European coasts. Our results showed high haplotype diversity in combination with a low nucleotide diversity and a star-shaped network with a predominant haplotype, indicating a recent population expansion for the examined sampling sites of D. vittatus. Furthermore, analyses of population differentiation performed with COI mitochondrial marker, including global Far estimation and pairwise Far values, indicated the non-existence of significant genetic structure in D. vittatus of Northwest Iberian populations. Because these localities show a high genetic similarity, we suggest that D. vittatus could be a potentially alternative exploitable resource, as complement to the D. trunculus fisheries, whose natural stocks have decreased dramatically in some areas. Furthermore, we present for the first time, evidence of DUI in the clams D. vittatus and D. semistriatus. (C) 2017 Elsevier Ltd. All rights reservd.
- Phylogeographical history of the white seabream Diplodus sargus (Sparidae): Implications for insularityPublication . Gonzalez-Wangueemert, Mercedes; Froufe, Elsa; Perez-Ruzafa, Angel; Alexandrino, PauloPartial sequences of the mitochondrial control region and its comparison with previously published cytochrome b (cyt-b) and microsatellite data were used to investigate the influence of island isolation and connectivity on white seabream genetic structure. To achieve this, a total of 188 individuals from four island localities (Castellamare and Mallorca, Mediterranean Sea; Azores and Canary Islands, Atlantic Ocean) and five coastal localities (Banyuls, Murcia and Tunisia, Mediterranean Sea; Galicia and Faro, Atlantic Ocean) were analysed. Results showed high haplotype diversity and low to moderate nucleotide diversity in all populations (except for the Canary Islands). This pattern of genetic diversity is attributed to a recent population expansion which is corroborated by other results such as cyt-b network and demographic analyses. Low differentiation among Mediterranean/Atlantic and coastal/island groups was shown by the AMOVA and FST values, although a weak phylogeographic break was detected using cyt-b data. However, we found a clear and significant island/ distance effect with regard to the Azores islands. Significant genetic differentiation has been detected between the Azores islands and all other populations. The large geographical distance between the European continental slope and the Azores islands is a barrier to gene flow within this region and historic events such as glaciation could also explain this genetic differentiation.
- The complete mitochondrial genome of the endemic Iberian pygmy skate Neoraja iberica Stehmann, Séret, Costa, & Baro 2008 (Elasmobranchii, Rajidae)Publication . Gomes-dos-Santos, André; Machado, André M.; Graça Aranha, Sofia; Dias, Ester; Veríssimo, Ana; Castro, L. Filipe C.; Froufe, ElsaSkates, Chondrichthyes fishes from order Rajiformes, are the most species-rich group of all Batoidea. However, their phylogenetic relationships and systematics is still a highly discussed and controversial subject. The use of complete mitogenome has shown to be a promising tool to fill this gap of knowledge. Here, the complete mitogenome of the Iberian pygmy skate Neoraja iberica (Stehmann, Séret, Costa & Baro 2008) was sequenced and assembled. The mitogenome is 16,723 bp long and its gene content (i.e. 13 protein-coding genes, 22 transfer RNA, and 2 ribosomal RNA genes) and arrangement are the expected for Batoidea. Phylogenetic reconstructions, including 89 Rajiformes and two outgroup Rhinopristiformes, recovered family Rajidae as monophyletic, and further divided in the monophyletic tribe Rajini, sister to tribes Amblyrajini and Rostrorajini. The newly sequenced N. iberica mitogenome is the first representative of the tribe Rostrorajini.