The complete validated mitochondrial genome of the yellownose skate Zearaja chilensis (Guichenot 1848) (Rajiformes, Rajidae)

Abstract

The yellownose skate Zearaja chilensis is endemic to South America. The species is the target of a valuable commercial fishery in Chile, but is highly susceptible to over-exploitation. The complete mitochondrial genome was described from 694,593 sequences obtained using Ion Torrent Next Generation Sequencing. The total length of the mitogenome was 16,909 bp, comprising 2 rRNAs, 13 protein-coding genes, 22 tRNAs and 2 non-coding regions. Comparison between the proposed mitogenome and one previously described from "raw fish fillets from a skate speciality restaurant in Seoul, Korea" resulted in 97.4% similarity, rather than approaching 100% similarity as might be expected. The 2.6% dissimilarity may indicate the presence of two separate stocks or two different species of, ostensibly, Z. chilensis in South America and highlights the need for caution when using genetic resources without a taxonomic reference or a voucher specimen.

Skate-ing on thin ice: molecular ecology of longnose skates in the Southeast Pacific Ocean

“…27) and provides an alternative to mtDNA sequencing for accurate species identification of, for example, unidentified 'skate wings'. The separate species status has also been confirmed by phylogenomic reconstruction using whole mitochondrial genomes for both species (Vargas-Caro et al, 2016a, b). Our results provide evidence for three management units (San Antonio-Valdivia, Chiloé…”

“…The structure of the mitogenome is similar to those of other skates, with 16,909 base-pairs (bp) in length and comprising 13 protein-coding regions, 22 tRNA genes, 2 rRNA genes and 2 non-coding areas (origin of replication and control region). However, Vargas-Caro et al, (2016a) compared the mitochondrial genome Z. chilensis by with one from Chilean waters and found 97.4% similarity (instead of close to 100% as might be expected). As the tissue sample used by was taken from a raw fillet in a Korean restaurant (without examination of the specimen), the 2.6% of difference may indicate the presence of two separate stocks of Z. chilensis in South America, or two different species.…”

“…Estalles et al, 2011;Kyne & Sympfendorfer, 2007;Lamilla et al, 2009. Last & Gledhill, 2007;Menni & Lucifora, 2007;Kyne & Simpfendorfer, 2010;Lamilla et al, 2010;Vargas-Caro, 2010;Mabragaña et al, 2011b;Perier et al, 2011;Queirolo et al, 2011;Arkhipkin et al, 2012;Bustamante et al, 2012;Concha et al, 2012;Deli Antoni et al, 2012;Lamilla et al, 2012a, b;Naylor et al, 2012;Bovcon et al, 2013;Lamilla et al, 2013;Bustamante et al, 2014a, b;Espindola et al, 2014Sáez et al, 2014;Vargas-Caro et al, 2016a. Menni et al, 2010;Naylor et al, 2012.…”

“…As the tissue sample used by was taken from a raw fillet in a Korean restaurant (without examination of the specimen), the 2.6% of difference may indicate the presence of two separate stocks of Z. chilensis in South America, or two different species. The uncertainties highlight the need for caution when using genetic resources without a taxonomic reference or voucher specimen (Vargas-Caro et al, 2016a).…”

“…To develop species-specific microsatellite genetic markers for each species, raw genomic DNA data from two voucher specimens (Vargas-Caro et al, 2016a, b) were retrieved from the Genomic Database Repository, eFish (Zearaja chilensis BioVoucher: 2014-ZCH-1004Dipturus trachyderma BioVoucher: 2015-DTR-004). Sequences between 150 and 400 bp were explored for microsatellite motifs using the software QDD v.3.1 (Meglécz et al, 2014).…”