The complete mitochondrial genome of the endemic Iberian pygmy skate Neoraja iberica Stehmann, Séret, Costa, & Baro 2008 (Elasmobranchii, Rajidae)

Abstract

Skates, 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.

Full text

MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the endemic Iberian pygmy skate
Neoraja iberica Stehmann, S
eret, Costa, & Baro 2008 (Elasmobranchii, Rajidae)
Andr
e Gomes-dos-Santos
a,b
, Andr
e M. Machado
a
, Sofia Grac¸a Aranha
c
, Ester Dias
a
, Ana Ver

ıssimo
d
,
L. Filipe C. Castro
a,b
and Elsa Froufe
a
a
CIIMAR/CIMAR –Interdisciplinary Centre of Marine and Environmental Research, Universityof Porto, Matosinhos, Portugal;
b
Department of
Biology, Faculty of Sciences, University of Porto, Porto, Portugal;
c
CCMAR –Centre of Marine Sciences, Universidade do Algarve, Faro,
Portugal;
d
CIBIO –Research Centre in Biodiversity and Genetic Resources, Vair~
ao, Portugal
ABSTRACT
Skates, 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 know-
ledge. Here, the complete mitogenome of the Iberian pygmy skate Neoraja iberica (Stehmann, S
eret,
Costa & Baro 2008) was sequenced and assembled. The mitogenome is 16,723bp 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.
ARTICLE HISTORY
Received 5 January 2021
Accepted 27 January 2021
KEYWORDS
Chondrichthyes;
Elasmobranchii; Iberian
Peninsula; mitogenome;
phylogenetics
Within the Batoidea (skates, stingrays, sawfishes, electric rays,
and guitarfishes), the order Rajiformes (skates) is one of the
most species rich (250 species so far described) despite its
seemingly morphological stasis (Ebert and Compagno 2008).
Skates also tend to have very localized distributions, reflected
in a high degree of endemism with several new species
being described recently (Igl
esias et al. 2010; Stehmann et al.
2008; Stevenson et al. 2004). Nevertheless, phylogenetic rela-
tionship inferences and systematics of the Batoidea remain
controversial mostly due to low taxon sampling, unresolved/
poorly supported topologies using either morphological and
molecular data, and also incongruent morphological and
molecular topologies (Aschliman, 2011; Aschliman et al. 2012;
Douady et al. 2003; Gait
an-Espitia et al. 2016; Last, White,
et al. 2016; McEachran and Aschliman 2004; Rodr

ıguez-
Cabello et al. 2013; Serra-Pereira et al. 2011). Although the
application of molecular approaches have been fundamental
to understand the phylogenetic relationships and assert the
systematics within Rajiformes, these are still under discussion
with several interpretations available (Last, Weigmann, et al.
2016; Last, White, et al. 2016). Consequently, from here for-
ward, we follow the nomenclature proposed by the most
recent taxonomic/systematic review of Rajiformes (Last,
Weigmann, et al. 2016).
Skates (Order Rajiformes) are among the most threatened
groups of vertebrates and are particularly prone to overex-
ploitation (Davidson et al. 2016; Dulvy et al. 2014). Thus, the
inability to efficiently infer phylogenetic relationships and
assert the systematics of the group is clearly a concern for
fishing management and conservation planning. Most species
have low fecundity, late sexual maturity, and long generation
times that hinder efficient population restocking and since
skates’meat and gill rakers are valuable commercial resour-
ces, over-fishing has devastating effects in many populations
(Serra-Pereira et al. 2011; Wannell et al. 2020). This is further
aggravated by frequently bottom trawling bycatch of these
organisms (Wannell et al. 2020). Complete mitogenomes
have been successfully used for comparative studies and
phylogenetic inferences in cartilaginous fishes (e.g. Alam
et al. 2014; Gait
an-Espitia et al. 2016; Gomes-dos-Santos et al.
2020; Inoue et al. 2010). This is especially relevant in cartil-
aginous fish due to their slow mtDNA mutation rates that
can hinder the efficient resolution of traditional partial mito-
chondrial markers (Gait
an-Espitia et al. 2016; Martin 1995).
The Iberian pygmy skate Neoraja iberica (Stehmann et al.
2008) was recently characterized as an endemic species from
the south coast of Portugal and Spain (Serra-Pereira et al.
2011; Stehmann et al. 2008). The very few studies published
to date on this species relied on morphological analyses,
CONTACT L. Filipe C. Castro filipe.castro@ciimar.up.pt CIIMAR/CIMAR –Interdisciplinary Centre of Marine and Environmental Research, University of Porto,
Terminal de Cruzeiros de Leix~
oes. Av. General Norton De Matos s/n 4450208 Matosinhos, Portugal; Department of Biology, Faculty of Sciences, University of
Porto, Rua do Campo Alegre 1021/1055, Porto, Portugal; Elsa Froufe elsafroufe@gmail.com CIIMAR/CIMAR –Interdisciplinary Centre of Marine and
Environmental Research, University of Porto, Terminal de Cruzeiros de Leix~
oes. Av. General Norton De Matos s/n 4450208 Matosinhos, Portugal
ß2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use,
distribution, and reproduction in any medium, provided the original work is properly cited.
MITOCHONDRIAL DNA PART B
2021, VOL. 6, NO. 3, 848–850
https://doi.org/10.1080/23802359.2021.1884030

with only a few partial COI mitochondrial sequences being
available. Furthermore, no mitogenomes for Neoraja genus
are currently available. Therefore, producing a complete
mitogenome is a timely and valuable resource.
Liver and muscle tissue samples from a N. iberica speci-
men were collected and stored in 96% ethanol. The speci-
men was captured in June 2020 off the south coast of
Portugal (between Lat: 36.777.215, Long: 8.817.514 and Lat:
36.779.223, Long: 8.612.814), onboard of a commercial
crustacean bottom trawler and at depths of approximately
500 m. Morphological identification was performed onboard.
The specimen is stored at the Interdisciplinary Center of
Marine and Environmental Research (specimen code
Neoib001). Liver tissue was used for genomic DNA extraction
and whole-genome sequencing of 150 bp paired-end (PE)
reads were obtained using Hiseq X Ten machine at
Novogene Europe.
Complete mitogenome assembly and annotation were
obtained using MitoZ version 2.3. (Meng et al. 2019).
Annotation was further validated by comparison with mitoge-
nomes from other members of the Family Rajidae available
on NCBI, including representatives of the two rajid tribes:
Amblyrajini and Rajini. For the phylogenetic analysis, all
available mitogenomes from species from Family Rajidae and
from two species from Order Rhinopristiformes (Accession
numbers NC_023951.1 and NC_022821.1) were retrieved from
GenBank (03/12/2020). The 13 protein-coding genes (PCGs)
were individually aligned using MAFFT version 7.453 (Katoh
and Standley 2013) and afterward concatenated using
FASconCAT-G (https://github.com/PatrickKueck/FASconCAT-G)
(final length: 11,435 bp). The best partition-scheme, best fit-
ted evolutionary models and maximum-ikelihood (ML) phyl-
ogeny were obtained using IQ-TREE version 1.6.12
(Kalyaanamoorthy et al. 2017; Nguyen et al. 2015). The newly
sequenced complete mitogenome of N. iberica is available in
GenBank under the accession number MW377218. The length
of the mitogenome is 16,723 bp and the gene composition
and arrangement is, as expected for Batoidea, the typical for
vertebrate mtDNA: 13 PCGs, 22 transfer RNA, 2 ribosomal
RNA genes, with 14 tRNA, 2 rRNA all PCG (except NAD6)
being present in the heavy strand (Satoh et al. 2016).
The resulting phylogenetic tree (Figure 1) recovered
Family Rajidae as monophyletic, further divided in the mono-
phyletic tribe Rajini, sister to tribes Amblyrajini and
Rostrorajini. The newly sequenced N. iberica represents the
first mitogenome sequenced Rostrorajini taxa. The present
Figure 1. Maximum likelihood phylogenetic tree based on concatenated sequences of 13 protein-coding genes from 89 Rajiformes and two outgroup
Rhinopristiformes mitogenomes. GenBank accession numbers are presented before species names. The above the branches indicate both bootstrap support values
above 95%.
MITOCHONDRIAL DNA PART B 849

study highlights the importance of increasing the sampling
and mitogenome sequencing of Rostrorajini, as well as other
skates, to clarify the phylogenetic relationships within the
most species-rich group of Chondrichthyes.
Disclosure statement
No potential conflict of interest was reported by the author(s).
Funding
This work was funded by the Project The Sea and the Shore,
Architecture and Marine Biology: The Impact of Sea Life on the Built
Environment (PTDC/ART-DAQ/29537/2017) from FCT/MCTES through
national funds (PIDDAC) and co-financing from the European Regional
Development Fund (FEDER) POCI-01-0145-FEDER-029537, in the aim of
the new partnership agreement PT2020 through COMPETE 2020 –
Competitiveness and Internationalization Operational Program (POCI)
and by Foundation for Science and Technology (FCT) UIDB/04423/2020,
UIDP/04423/2020 which also supported A.G.S. (SFRH/BD/137935/2018),
S.G.A (SFRH/BD/147493/2019) and A.V. (DL57/2016). Additional funding
was provided by FEDER Funds through the Operational Competitiveness
Factors Program COMPETE and by national funds through FCT within the
scope of Project PTDC/ASP-PES/28053/2017.
ORCID
Andr
e Gomes-dos-Santos http://orcid.org/0000-0001-9973-4861
Ana Ver

ıssimo http://orcid.org/0000-0003-3396-9822
Elsa Froufe http://orcid.org/0000-0003-0262-0791
Data availability statement
The genome sequence data that support the findings of this study are
openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/)
under the accession number MW377218. The associated BioProject, SRA,
and Bio-Sample numbers are PRJNA694536, SRS8105111, and
SAMN17526303, respectively.
References
Alam MT, Petit RA, Read TD, Dove ADM. 2014. The complete mitochon-
drial genome sequence of the world’s largest fish, the whale shark
(Rhincodon typus), and its comparison with those of related shark
species. Gene. 539(1):44–49.
Aschliman NC. 2011. Batoid tree of life: recovering the patterns and tim-
ing of the evolution of skates, rays and allies (Chondrichthyes:
Batoidea). PhD Thesis, Florida State University Electronic Theses,
Treatises and Dissertations. 2011. Available: http://diginole.lib.fsu.edu/
cgi/viewcontent.cgi?article=4215&context=etd.
Aschliman NC, Claeson KM, McEachran J. 2012. Phylogeny of batoidea.
In: Carrier JC, Musick JA, Heithaus MR, editors. Biology of sharks and
their relatives. Boca Raton (FL): CRC Press; p. 57–95.
Davidson LNK, Krawchuk MA, Dulvy NK. 2016. Why have global shark
and ray landings declined: improved management or overfishing? Fish
Fish. 17(2):438–458.
Douady CJ, Dosay M, Shivji MS, Stanhope MJ. 2003. Molecular phylogen-
etic evidence refuting the hypothesis of Batoidea (rays and skates) as
derived sharks. Mol Phylogenet Evol. 26(2):215–221.
Dulvy NK, Fowler SL, Musick JA, Cavanagh RD, Kyne PM, Harrison LR,
Carlson JK, Davidson LN, Fordham SV, Francis MP, et al. 2014.
Extinction risk and conservation of the world’s sharks and rays. eLife.
3: e00590.
Ebert DA, Compagno LJV. 2008. Biodiversity and systematics of skates
(Chondrichthyes: Rajiformes: Rajoidei). Biology of skates. Netherlands:
Springer; p. 5–18.
Gait
an-Espitia JD, Solano-Iguaran JJ, Tejada-Martinez D, Quintero-Galvis
JF. 2016. Mitogenomics of electric rays: evolutionary considerations
within Torpediniformes (Batoidea; Chondrichthyes). Zool J Linn Soc.
178(2):257–266.
Gomes-dos-Santos A, Arrondo NV, Machado AM, Ver

ıssimo A, P
erez M,
Rom
an E, Castro LFC, Froufe E. 2020. The complete mitochondrial
genome of the deep-water cartilaginous fish Hydrolagus affinis (de
Brito Capello, 1868) (Holocephali: Chimaeridae). Mitochondrial DNA
Part B. 5(2):1810–1812.
Igl
esias SP, Toulhoat L, Sellos DY. 2010. Taxonomic confusion and market
mislabelling of threatened skates: important consequences for their
conservation status. Aquatic Conserv Mar Freshw Ecosyst. 20(3):
319–333.
Inoue JG, Miya M, Lam K, Tay BH, Danks JA, Bell J, Walker TI, Venkatesh
B. 2010. Evolutionary origin and phylogeny of the modern holocepha-
lans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective.
Mol Biol Evol. 27(11):2576–2586.
Kalyaanamoorthy S, Minh BQ, Wong TKF, Von Haeseler A, Jermiin LS.
2017. ModelFinder: fast model selection for accurate phylogenetic
estimates. Nat Methods. 14(6):587–589.
Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment soft-
ware version 7: improvements in performance and usability. Mol Biol
Evol. 30(4):772–780.
Last P, Weigmann S, Yang L. 2016. Changes to the nomenclature of the
skates (Chondrichthyes: Rajiformes), in: rays of the world:
Supplementary Information. Clayton (CA): CSIRO Special Publication;
p. 11–34.
Last P, White W, de Carvalho M, S
eret B, Stehmann M, Naylor G. editors.
2016. Rays of the world. Clayton (CA): CSIRO Publishing.
Martin AP. 1995. Mitochondrial DNA sequence evolution in sharks: rates,
patterns, and phylogenetic inferences. Mol Biol Evol. 12(6):1114–1123.
McEachran JD, Aschliman N. 2004. Phylogeny of batoidea. In: Carrier JC,
Musick JA, Heithaus MR, editors. Biology of sharks and their relatives.
Boca Raton (FL): CRC Press; p. 79–113.
Meng G, Li Y, Yang C, Liu S. 2019. MitoZ: a toolkit for animal mitochon-
drial genome assembly, annotation and visualization. Nucleic Acids
Res. 47(11):e63.
Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast
and effective stochastic algorithm for estimating maximum-likelihood
phylogenies. Mol Biol Evol. 32(1):268–274.
Park HK, Yoon M, Kim KY, Jung YH. Characterization and phylogenetic
analysis of the complete mitogenome of the Arctic skate Amblyraja
hyperborea (Rajiformes; Rajidae). Mitochondrial DNA Part B Resour.
5:1588–1589.
Rodr

ıguez-Cabello C, P
erez M, S
anchez F. 2013. New records of chon-
drichthyans species caught in the Cantabrian Sea (southern Bay of
Biscay). J Mar Biol Ass. 93(7):1929–1939.
Satoh TP, Miya M, Mabuchi K, Nishida M. 2016. Structure and variation of
the mitochondrial genome of fishes. BMC Genomics. 17:719.
Serra-Pereira B, Moura T, Griffiths AM, Serrano Gordo L, Figueiredo I.
2011. Molecular barcoding of skates (Chondrichthyes: Rajidae) from
the southern Northeast Atlantic. Zool. Scr. 40(1):76–84.
Stehmann MFW, S
eret B, Costa EM, Baro J. 2008. Neoraja iberica n. sp., a
new species of pygmy skate (Elasmobranchii, Rajidae) from the south-
ern upper slope of the Iberian Peninsula (Eastern North Atlantic).
Cybium. 32:51–71.
Stevenson DE, Orr JW, Hoff GR, McEachran JD. 2004. Bathyraja mariposa:
a new species of Skate (Rajidae: Arhynchobatinae) from the Aleutian
Islands. Copeia. 2004(2):305–314.
Wannell GJ, Griffiths AM, Spinou A, Batista R, Mendonc¸a MB, Wosiacki
WB, Fraser B, Wintner S, Papadopoulos AI, Krey G, et al. 2020. A new
minibarcode assay to facilitate species identification from processed,
degraded or historic ray (batoidea) samples. Conservat Genet Resour.
12(4):659–668.
850 A. GOMES-DOS-SANTOS ET AL.