Genomics & Informatics

Korea Genome Organization (한국유전체학회)
권호 표지
DOI QR코드

DOI QR Code

Characterization of six new complete mitochondrial genomes of Chiasmodontidae (Scombriformes, Percomorpha) and considerations about the phylogenetic relationships of the family

  • Received : 2022.06.24
  • Accepted : 2023.01.14
  • Published : 2023.03.31
Download PDF
⟨ Previous Next ⟩

Abstract

The fishes of the Chiasmodontidae family, known as swallower fishes, are species adapted to live in deep seas. Several studies have shown the proximity of this family to Tetragonuridae and Amarsipidae. However, the phylogenetic position of this clade related to other Pelagiaria groups remains uncertain even when phylogenomic studies are employed. Since the low number of published mitogenomes, our study aimed to assemble six new mitochondrial genomes of Chiasmodontidae from database libraries to expand the discussion regarding the phylogeny of this group within Scombriformes. As expected, the composition and organization of mitogenomes were stable among the analyzed species, although we detected repetitive sequences in the D-loop of species of the genus Kali not seen in Chiasmodon, Dysalotus, and Pseudoscopelus. Our phylogeny incorporating 51 mitogenomes from several families of Scombriformes, including nine chiasmodontids, recovered interfamilial relationships well established in previous studies, including a clade containing Chiasmodontidae, Amarsipidae, and Tetragonuridae. However, phylogenetic relationships between larger clades remain unclear, with disagreements between different phylogenomic studies. We argue that such inconsistencies are not only due to biases and limitations in the data but mainly to complex biological events in the adaptive irradiation of Scombriformes after the Cretaceous-Paleogene extinction event.

Keywords

Acknowledgement

This study was financed in part by scholarship grants from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil - CAPES (www.capes.gov.br/) (awarded to IHRO).

References

  1. Fricke R, Eschmeyer WN, Fong JD. Genera/species by family/subfamily in Eschmeyer's Catalog of Fishes. San Francisco: California Academy of Sciences, 2022. Accessed 2022 Jun 24. Available from: https://researcharchive.calacademy.org/research/ichthyology/catalog/SpeciesByFamily.asp.
  2. Marshall NB. Developments in Deep-Sea Biology. Poole: Blandford Press, 1979.
  3. Melo MR. Revision of the genus Chiasmodon (Acanthomorpha: Chiasmodontidae), with the description of two new species. Copeia 2009;2009:583-608. https://doi.org/10.1643/CI-08-048
  4. Miya M, Friedman M, Satoh TP, Takeshima H, Sado T, Iwasaki W, et al. Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families. PLoS One 2013;8:e73535.
  5. Betancur RR, Wiley EO, Arratia G, Acero A, Bailly N, Miya M, et al. Phylogenetic classification of bony fishes. BMC Evol Biol 2017;17:162.
  6. Campbell MA, Sado T, Shinzato C, Koyanagi R, Okamoto M, Miya M. Multilocus phylogenetic analysis of the first molecular data from the rare and monotypic Amarsipidae places the family within the Pelagia and highlights limitations of existing data sets in resolving pelagian interrelationships. Mol Phylogenet Evol 2018;124:172-180. https://doi.org/10.1016/j.ympev.2018.03.008
  7. Arcila D, Hughes LC, Melendez-Vazquez B, Baldwin CC, White WT, Carpenter KE, et al. Testing the utility of alternative metrics of branch support to address the ancient evolutionary radiation of tunas, stromateoids, and allies (Teleostei: Pelagiaria). Syst Biol 2021;70:1123-1144. https://doi.org/10.1093/sysbio/syab018
  8. Harrington RC, Friedman M, Miya M, Near TJ, Campbell MA. Phylogenomic resolution of the monotypic and enigmatic Amarsipus, the bagless glassfish (Teleostei, Amarsipidae). Zool Scr 2021;50:411-422. https://doi.org/10.1111/zsc.12477
  9. Nelson JS, Grande TC, Wilson MV. Fishes of the World. 5th ed. Hoboken: John Wiley & Sons, 2016.
  10. Orrell TM, Collette BB, Johnson GD. Molecular data support separate scombroid and xiphioid clades. Bull Mar Sci 2006;79:505-519.
  11. Near TJ, Dornburg A, Eytan RI, Keck BP, Smith WL, Kuhn KL, et al. Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes. Proc Natl Acad Sci U S A 2013;110:12738-12743. https://doi.org/10.1073/pnas.1304661110
  12. Friedman M, Feilich KL, Beckett HT, Alfaro ME, Faircloth BC, Cerny D, et al. A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean. Proc Biol Sci 2019;286:20191502.
  13. Mobili F, Miyaki CY, Pellegrino KC, et al. Ultraconserved elements sequencing as a low-cost source of complete mitochondrial genomes and microsatellite markers in non-model amniotes. PLoS One 2015;10:e0138446.
  14. Picardi E, Pesole G. Mitochondrial genomes gleaned from human whole-exome sequencing. Nat Methods 2012;9:523-524. https://doi.org/10.1038/nmeth.2029
  15. Jalili V, Afgan E, Gu Q, Clements D, Blankenberg D, Goecks J, et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Res 2020;48:W395-W402. https://doi.org/10.1093/nar/gkaa434
  16. Dierckxsens N, Mardulyn P, Smits G. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res 2017;45:e18.
  17. Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, et al. MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol Biol Evol 2013;30:2531-2540. https://doi.org/10.1093/molbev/mst141
  18. Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011;12:402.
  19. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 1999;27:573-580. https://doi.org/10.1093/nar/27.2.573
  20. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32:1792-1797. https://doi.org/10.1093/nar/gkh340
  21. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018;35:1547-1549. https://doi.org/10.1093/molbev/msy096
  22. Vaidya G, Lohman DJ, Meier R. SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics 2011;27:171-180. https://doi.org/10.1111/j.1096-0031.2010.00329.x
  23. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020;37:1530-1534. https://doi.org/10.1093/molbev/msaa015
  24. Kalyaanamoorthy S, Minh BQ, Wong TK, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017;14:587-589. https://doi.org/10.1038/nmeth.4285
  25. Miya M, Kawaguchi A, Nishida M. Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences. Mol Biol Evol 2001;18:1993-2009. https://doi.org/10.1093/oxfordjournals.molbev.a003741
  26. Pasa R, Menegidio FB, Rodrigues-Oliveira IH, da Silva IB, de Campos ML, Rocha-Reis DA, et al. Ten complete mitochondrial genomes of Gymnocharacini (Stethaprioninae, Characiformes). insights into evolutionary relationships and a repetitive element in the controlregion (D-loop). Front Ecol Evol 2021;9:650783.
  27. Tamashiro RA, White ND, Braun MJ, Faircloth BC, Braun EL, Kimball RT. What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data? Mol Phylogenet Evol 2019;130:132-142. https://doi.org/10.1016/j.ympev.2018.10.008
  28. Brandley MC, Schmitz A, Reeder TW. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst Biol 2005;54:373-390. https://doi.org/10.1080/10635150590946808
  29. Crespi BJ, Fulton MJ. Molecular systematics of Salmonidae: combined nuclear data yields a robust phylogeny. Mol Phylogenet Evol 2004;31:658-679. https://doi.org/10.1016/j.ympev.2003.08.012
  30. De Re FC, Robe LJ, Wallau GL, Loreto EL. Inferring the phylogenetic position of the Drosophila flavopilosa group: incongruence within and between mitochondrial and nuclear multilocus datasets. J Zool Syst Evol Res 2017;55:208-221. https://doi.org/10.1111/jzs.12170
  31. Zadra N, Rizzoli A, Rota-Stabelli O. Chronological incongruences between mitochondrial and nuclear phylogenies of Aedes mosquitoes. Life (Basel) 2021;11:181.
  32. Hawkins MT, Leonard JA, Helgen KM, McDonough MM, Rockwood LL, Maldonado JE. Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens. BMC Evol Biol 2016;16:80.
  33. Hallstrom BM, Janke A. Mammalian evolution may not be strictly bifurcating. Mol Biol Evol 2010;27:2804-2816. https://doi.org/10.1093/molbev/msq166
  34. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 2006;23:254-267. https://doi.org/10.1093/molbev/msj030