Skip to main content
NCBI home page
Mitochondrial DNA. Part B, Resources logoLink to Mitochondrial DNA. Part B, Resources
. 2021 Aug 13;6(9):2640–2642. doi: 10.1080/23802359.2021.1963339

The complete mitochondrial genome of the Variable Platyfish Xiphophorus variatus

Anna Nicole Eastis 1,✉, Kayla Marie Fast 1, Michael Warren Sandel 1
PMCID: PMC8366644  PMID: 34409164

Abstract

We present the complete mitochondrial genome sequence of the Variable Platyfish, Xiphophorus variatus (Meek 1904) (Cyprinodontiformes: Poeciliidae). The genome consists of 16,624 bp which encodes 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and 1 control region. Genome-wide nucleotide composition is 27.79% adenine, 31.11% cytosine, 15.63% guanine, and 25.48% thymine. The X. variatus mitochondrial genome shares similar GC content and identical gene order and gene strand location with other members of Poeciliidae. The sequence presented herein will be of utility for future phylogenetic and biomedical research and for designing primers for species detection from environmental DNA samples.

Keywords: Oxford Nanopore, Xiphophorus variatus, mitochondrial genome, invasive species

The genus Xiphophorus contains 26 species of live-bearing platyfish and swordtails and is a member of the order Cyprinodontiformes. Xiphophorus species serve as important vertebrate models for biomedical research, sexual selection, and sex determinism (Kallman 1973; Schartl 1995; Kingston et al. 2003; Meyer et al. 2006). The Variable Platyfish, Xiphophorus variatus (Meek 1904), is native to watersheds draining to the Gulf of Mexico, from southern Tamaulipas into northern Veracruz states (Page and Burr 1991; Culumber and Rosenthal 2013). The species has been introduced to nonnative watersheds in tropical and subtropical regions of every continent except Antarctica, which is thought to be due to its popularity in the aquarium trade (Cohen et al. 2014). The introduction of Xiphophorus species is associated with concurrent declines in the abundance and diversity of native species, which is a cause for concern among conservation organizations aiming to control the spread of invasive species (Máiz-Tomé et al. 2018; Nico 2019). We present a complete mitochondrial genome to aid in noninvasive detection of X. variatus in environmental DNA samples and to provide a resource to teams investigating phylogenetics and functional genomics of mitochondrial DNA (mtDNA).

Fin clip samples of Xiphophorus variatus strain ‘Zarco’ were obtained from Texas State University Xiphophorus Genetic Stock Center and preserved in 100% ethanol. Specimens were collected from the Arroyo Zarco locality west of Encino, Tamaulipas, Mexico (Walter et al. 2006). Genomic DNA was extracted from a portion of the caudal fin using the Qiagen DNeasy Blood and Tissue kit and was deposited into the Laboratory of AQuatic Evolution (LAQE) at the University of West Alabama (No. 1755Xvariatus, Anna Eastis, eastisa@uwa.edu). DNA quality and quantity were assessed with agarose gel electrophoresis and a NanoDrop spectrophotometer, respectively.

We sequenced the whole mitochondrial genome using a Flongle flow cell utilized for Oxford Nanopore Technologies (ONT, Oxford, UK) MinION, which is a third-generation sequencing technology (Maestri et al. 2019). The reads were assembled to a reference (mtDNA of Xiphophorus maculatus – GenBank NC_011379.1) using Geneious software, v11.1.3 (https://www.geneious.com; Kearse et al. 2012). The alignments were checked by eye in Bioedit v7.2.5 (Hall 1999). The genome was annotated using MitoAnnotator through the MitoFish portal (Iwasaki et al. 2013). The mitochondrial genome of X. variatus (GenBank accession number MW 934558) has a length of 16,624 bp. The frequencies of adenine, cytosine, guanine, and thymine are 27.79%, 31.11%, 15.63%, 25.48%, respectively, and showed a GC content of 46.73%. Eighteen additional Poeciliidae mitogenomes were used in alignment using the MAFFT online server (Katoh et al. 2019). Maximum-likelihood phylogenetic analysis was conducted in RAxML-HPC 8.2.12 (Stamatakis 2014) and viewed in Dendroscope v3.7.3 (Huson and Scornavacca 2020). The resulting phylogeny, Figure 1, shows the monophyly of Xiphophorus, Poecilia, Gambusia, and Poeciliopsis. This is consistent with the results of previous phylogenetic studies of the family Poeciliidae (Pollux et al. 2014; Jeon et al. 2016). Within Xiphophorus, most relationships are strongly supported and consistent with previous studies. The position of X. maculatus, however, is inconsistent with the mtDNA analysis of Kang et al.(2013) which resolved X. maculatus within a clade containing X. variatus and all other northern platyfish species. The analysis presented here provides moderate support for a sister relationship between X. maculatus, the Southern Platyfish, and Xiphophorus hellerii, the Green Swordtail. We expect that increased taxonomic sampling will aid in resolving this node and other relationships within the genus.

Figure 1.

Figure 1.

Open in a new tab

The evolutionary history of Poeciliidae mitogenomes was inferred by using the maximum-likelihood method in the RAxML-HPC BlackBox through the CIPRES portal using 16,944 bp. The resulting file was viewed in Dendroscope. Numbers on branch lengths are bootstrap support values in %. The study species, Xiphophorus variatus, is boldened.

Acknowledgment

We would like to thank Texas State University Xiphophorus Genetic Stock Center for providing the specimen used for this study.

Funding Statement

The present work was financially supported by the National Center for Research Resources and the National Institute of General Medical Sciences of the NIH.

Disclosure statement

No potential conflict of interest was reported by the author(s).

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 no. MW934558. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA742674, SRX11313963, and SAMN19969452, respectively.

References

  1. Cohen AE, Dugan LE, Hendrickson DA, Martin FD, Huynh J, Labay BJ, Casarez MJ.. 2014. Population of Variable Platyfish (Xiphophorus variatus) established in Waller Creek, Travis County, Texas. The Southwest Natur. 59(3):413–419. [Google Scholar]
  2. Culumber ZW, Rosenthal GG.. 2013. Mating preferences do not maintain the tailspot polymorphism in the platyfish, Xiphophorus variatus. Behav Ecol. 24(6):1286–1291. [Google Scholar]
  3. Hall TA.1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Boston (MA): Science Open. [Google Scholar]
  4. Huson DH, Scornavacca C.. 2020. User manual for dendroscope V3.7.5, p. 33. [Google Scholar]
  5. Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, Mabuchi K, Takeshima H, Miya M, et al. 2013. MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol Biol Evol. 30(11):2531–2540. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Jeon YS, Johnson SB, Won Y-J, Vrijenhoek RC.. 2016. Complete mitochondrial genome of the headwater livebearer, Poeciliopsis monacha: the mother of clones. Mitochondrial DNA B Resour. 1(1):793–794. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Kallman KD.1973. The sex-determining mechanism of the Platyfish, Xiphophorus maculatus. In Schröder, JH, editor. Genetics and mutagenesis of fish. Berlin (Germany): Springer Berlin Heidelberg; pp. 19–28. [Google Scholar]
  8. Kang JH, Schartl M, Walter RB, Meyer A.. 2013. Comprehensive phylogenetic analysis of all species of swordtails and platies (Pisces: Genus Xiphophorus) uncovers a hybrid origin of a swordtail fish, Xiphophorus monticolus, and demonstrates that the sexually selected sword originated in the ancestral lineage of the genus, but was lost again secondarily. BMC Evol Biol. 13(1):25. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Katoh K, Rozewicki J, Yamada KD.. 2019. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 20(4):1160–1166. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28(12):1647–1649. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kingston JJ, Rosenthal GG, Ryan MJ.. 2003. The role of sexual selection in maintaining a colour polymorphism in the pygmy swordtail, Xiphophorus pygmaeus. Animal Behaviour. 65(4):735–743. [Google Scholar]
  12. Maestri S, et al. 2019. A rapid and accurate MinION-based workflow for tracking species biodiversity in the field. Genes. 10:468. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Máiz-Tomé L, Sayer C, Darwall W.. 2018. The status and distribution of freshwater biodiversity in Madagascar and the Indian Ocean islands hotspot. Cambridge (UK): Gland. [Google Scholar]
  14. Meyer A, Salzburger W, Schartl M.. 2006. Hybrid origin of a swordtail species (Teleostei: Xiphophorus clemenciae) driven by sexual selection: hybrid speciation via sexual selection. Mol Ecol. 15(3):721–730. [DOI] [PubMed] [Google Scholar]
  15. Nico L.2019. Xiphophorus variatus (Meek, 1904), U.S. Geological Survey, Nonindigenous Aquatic Species Database. Gainesville (FL): USGS; [Accessed 2021 April 26]. https://nas.er.usgs.gov/queries/factsheet.aspx?SpeciesID=874
  16. Page LM, Burr BM.. 1991. A field guide to freshwater fishes of North America north of Mexico. Boston (MA): Houghton Mifflin. [Google Scholar]
  17. Pollux BJA, Meredith RW, Springer MS, Garland T, Reznick DN.. 2014. The evolution of the placenta drives a shift in sexual selection in livebearing fish. Nature. 513(7517):233–236. [DOI] [PubMed] [Google Scholar]
  18. Schartl M.1995. Platyfish and swordtails: a genetic system for the analysis of molecular mechanisms in tumor formation. Trends Genet. 11(5):185–189. [DOI] [PubMed] [Google Scholar]
  19. Stamatakis A.2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30(9):1312–1313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Walter RB, Hazlewood L, Kazianis S.. 2006. The Xiphophorus genetic stock center manual. 131. San Marcos: Texas State University. [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

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 no. MW934558. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA742674, SRX11313963, and SAMN19969452, respectively.

Articles from Mitochondrial DNA. Part B, Resources are provided here courtesy of Taylor & Francis

RESOURCES