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Rapid Communication

Describing novel mitochondrial genomes of Antarctic amphipods

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Pages 810-818 | Received 17 Oct 2021, Accepted 02 May 2022, Published online: 10 May 2022

References

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. 366Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17):810–3402.
  • Andres HG, Lörz AN, Brandt A. 2002. A common but undescribed huge species of Eusirus Krøyer, 1845 (Crustacea, Amphipoda, Eusiridae) from Antarctica. Mitteilungen Aus Dem Hamburgischen Zoologischen Museum Und Institut. 99:109–126.
  • Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data [Online]. [cited 2019 July 28] http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
  • Baird HP, Miller KJ, Stark JS. 2011. Evidence of hidden biodiversity, ongoing speciation and diverse patterns of genetic structure in giant Antarctic amphipods. Mol Ecol. 20(16):3439–3454.
  • Ballard JWO, Whitlock MC. 2004. The incomplete natural history of mitochondria. Mol Ecol. 13(4):729–744.
  • Barr CM, Neiman M, Taylor DR. 2005. Inheritance and recombination of mitochondrial genomes in plants, fungi and animals. New Phytol. 168(1):39–50.
  • Bauzà-Ribot MM, Juan C, Nardi F, Oromí P, Pons J, Jaume D. 2012. Mitogenomic phylogenetic analysis supports continental-scale vicariance in subterranean thalassoid crustaceans. Curr Biol. 22(21):2069–2074.
  • Beermann J, Westbury MV, Hofreiter M, Hilgers L, Deister F, Neumann H, Raupach MJ. 2018. Cryptic species in a well-known habitat: applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida). Sci Rep. 8(1):1–26.
  • Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 69(2):313–319.
  • Bernt M, Merkle D, Ramsch K, Fritzsch G, Perseke M, Bernhard D, Schlegel M, Stadler PF, Middendorf M. 2007. CREx: inferring genomic rearrangements based on common intervals. Bioinformatics. 23(21):2957–2958.
  • Boore JL. 1999. Animal mitochondrial genomes. Nucleic Acids Res. 27(8):1767–1780.
  • Boore JL, Lavrov DV, Brown WM. 1998. Gene translocation links insects and crustaceans. Nature. 392(6677):667–668.
  • Bousfield EL. 1978. A revised classification and phylogeny of amphipod crustaceans. Ottawa: Royal Society of Canada.
  • Cameron SL. 2014. How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research. Syst Entomol. 39(3):400–411.
  • Caterino MS, Cho S, Sperling FA. 2000. The current state of insect molecular systematics: a thriving Tower of Babel. Annu Rev Entomol. 45(1):1–54.
  • Chevreux B, Wetter T, Suhai S. 1999. Genome sequence assembly using trace signals and additional sequence information. Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB 1999), Vol. 99, p. 45–56.
  • Chevreux E. 1905. Diagnoses d’amphipodes nouveaux provenant de l’expédition antarctique du Français. I. Lysianassidae. Bull Soc Zool Fr. 30:159–165.
  • Cormier A, Wattier R, Teixeira M, Rigaud T, Cordaux R. 2018. The complete mitochondrial genome of Gammarus roeselii (Crustacea, Amphipoda): insights into mitogenome plasticity and evolution. Hydrobiologia. 825(1):197–210.
  • Dowton M, Austin AD. 1999. Evolutionary dynamics of a mitochondrial rearrangement “hot spot” in the Hymenoptera. Mol Biol Evol. 16(2):298–309.
  • D’Udekem D’Acoz C, Schon I, Robert H. 2018. The genus Charcotia Chevreux, 1906 in the Southern Ocean, with the description of a new species (Crustacea, Amphipoda, Lysianassoidea). Belg J Zool. 148(1):31–82.
  • Englisch U. 2001. Analyse der Phylogenie der Amphipoda (Crustacea, Malacostraca) mit Hilfe von Sequenzen des Gens der RNA der kleinen ribosomalen Untereinheit [dissertation]. Bochum: Ruhr-Universität Bochum, Lehrstuhl für Spezielle Zoologie 1–312.
  • Gallardo VA. 1987. The sublittoral macrofaunal benthos of the Antarctic shelf. Environ Int. 13(1):71–81.
  • Grabowski M, Mamos T, Bącela-Spychalska K, Rewicz T, Wattier RA. 2017. Neogene paleogeography provides context for understanding the origin and spatial distribution of cryptic diversity in a widespread Balkan freshwater amphipod. PeerJ. 5:e3016.
  • Greco S, D'Agostino E, Manfrin C, Gaetano AS, Furlanis G, Capanni F, Santovito G, Edomi P, Giulianini PG, Gerdol M. 2021. RNA-sequencing indicates high hemocyanin expression as a key strategy for cold adaptation in the Antarctic amphipod Eusirus cf. giganteus Clade g3. Biocell 45(6):1611.
  • Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52(5):696–704.
  • Hahn C, Bachmann L, Chevreux B. 2013. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads–a baiting and iterative mapping approach. Nucleic Acids Res. 41(13):e129–e129.
  • Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser. 41:95–98.
  • Haran J, Timmermans MJ, Vogler AP. 2013. Mitogenome sequences stabilize the phylogenetics of weevils (Curculionoidea) and establish the monophyly of larval ectophagy. Mol Phylogenet Evol. 67(1):156–166.
  • Hassanin A. 2006. Phylogeny of Arthropoda inferred from mitochondrial sequences: strategies for limiting the misleading effects of multiple changes in pattern and rates of substitution. Mol Phylogenet Evol. 38(1):100–116.
  • Hassanin A, Leger Nelly, Deutsch J. 2005. Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of Metazoa, and consequences for phylogenetic inferences. Syst Biol. 54(2):277–298.
  • Hebert PD, Cywinska A, Ball SL, DeWaard JR. 2003. Biological identifications through DNA barcodes. Proc R Soc Lond B. 270(1512):313–321.
  • Horton T, Lowry J, De Broyer C, Bellan-Santini D, Coleman CO, Corbari L, Costello MJ, Daneliya M, Dauvin J-C, Fišer C, et al. 2021. World Amphipoda Database. [accessed 2021 Nov 23]. http://www.marinespecies.org/amphipoda.
  • Ito A, Aoki MN, Yokobori SI, Wada H. 2010. The complete mitochondrial genome of Caprella scaura (Crustacea, Amphipoda, Caprellidea), with emphasis on the unique gene order pattern and duplicated control region. Mitochondrial DNA. 21(5):183–190.
  • Jühling F, Pütz J, Bernt M, Donath A, Middendorf M, Florentz C, Stadler PF. 2012. Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements. Nucleic Acids Res. 40(7):2833–2845.
  • Katoh K, Rozewicki J, Yamada KD. 2019. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 20(4):1160–1166.
  • Keane TM, Creevey CJ, Pentony MM, Naughton TJ, Mclnerney JO. 2006. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol. 6(1):29.
  • Keis M, Remm J, Ho SYW, Davison J, Tammeleht E, Tumanov IL, Saveljev AP, Männil P, Kojola I, Abramov AV. 2013. Complete mitochondrial genomes and a novel spatial genetic method reveal cryptic phylogeographical structure and migration patterns among brown bears in north‐western Eurasia. J Biogeogr. 40(5):915–927.
  • Ki JS, Hop H, Kim SJ, Kim IC, Park HG, Lee JS. 2010. Complete mitochondrial genome sequence of the Arctic gammarid, Onisimus nanseni (Crustacea; Amphipoda): novel gene structures and unusual control region features. Comp Biochem Physiol Part D Genomics Proteomics. 5(2):105–115.
  • Kilpert F, Podsiadlowski L. 2006. The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features. BMC Genomics. 7(1):1–18.
  • Kilpert F, Podsiadlowski L. 2010. The mitochondrial genome of the Japanese skeleton shrimp Caprella mutica (Amphipoda: Caprellidea) reveals a unique gene order and shared apomorphic translocations with Gammaridea. Mitochondrial DNA. 21(3-4):77–86.
  • Knox GA, Lowry JK. 1977. A comparison between the benthos of the Southern Ocean and the North Polar Ocean with special reference to the Amphipoda and the Polychaeta. Polar oceans. Calgary: Arctic Institute of North America; p. 423–462.
  • Krebes L, Bastrop R. 2012. The mitogenome of Gammarus duebeni (Crustacea Amphipoda): a new gene order and non-neutral sequence evolution of tandem repeats in the control region. Comp Biochem Physiol D Genomics Proteomics. 7(2):201–211.
  • Lan Y, Sun J, Bartlett DH, Rouse GW, Tabata HG, Qian PY. 2016. The deepest mitochondrial genome sequenced from Mariana Trench Hirondellea gigas (Amphipoda). Mitochondrial DNA B Resour. 1(1):802–803.
  • Laslett D, Canbäck B. 2008. ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics. 24(2):172–175.
  • Li JY, Song ZL, Yan GY, He LS. 2019b. The complete mitochondrial genome of the largest amphipod, Alicella gigantea: insight into its phylogenetic relationships and deep sea adaptive characters. Int J Biol Macromol. 141:570–577.
  • Li JY, Zeng C, Yan GY, He LS. 2019a. Characterization of the mitochondrial genome of an ancient amphipod Halice sp. MT-2017 (Pardaliscidae) from 10,908 m in the Mariana Trench. Sci Rep. 9(1):1–15.
  • Lin CP, Danforth BN. 2004. How do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian analyses of combined datasets. Mol Phylogenet Evol. 30(3):686–702.
  • López-López A, Vogler AP. 2017. The mitogenome phylogeny of Adephaga (Coleoptera). Mol Phylogenet Evol. 114:166–174.
  • Lowry JK, Myers AA. 2017. A phylogeny and classification of the Amphipoda with the establishment of the new order Ingolfiellida (Crustacea: Peracarida). Zootaxa. 4265(1):1–89.
  • Macey JR, Larson A, Ananjeva NB, Papenfuss TJ. 1997. Replication slippage may cause parallel evolution in the secondary structures of mitochondrial transfer RNAs. Mol Biol Evol. 14(1):30–39.
  • Perna NT, Kocher TD. 1995. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol. 41(3):353–358.
  • Pilar Cabezas M, Cabezas P, Machordom A, Guerra‐García JM. 2013. Hidden diversity and cryptic speciation refute cosmopolitan distribution in Caprella penantis (Crustacea: Amphipoda: Caprellidae). J Zool Syst Evol Res. 51(2):85–99.
  • Pons J, Bauzà-Ribot MM, Jaume D, Juan C. 2014. Next-generation sequencing, phylogenetic signal and comparative mitogenomic analyses in Metacrangonyctidae (Amphipoda: Crustacea). BMC Genomics. 15(1):566.
  • Ritchie H, Jamieson AJ, Piertney SB. 2015. Phylogenetic relationships among hadal amphipods of the Superfamily Lysianassoidea: implications for taxonomy and biogeography. Deep Sea Res Part I. 105:119–131.
  • Romanova EV, Aleoshin VV, Kamaltynov RM, Mikhailov KV, Logacheva MD, Sirotinina EA, Gornov AY, Anikin AS, Sherbakov DY. 2016. Evolution of mitochondrial genomes in Baikalian amphipods. BMC Genomics. 17(Suppl 14):1016.
  • Ronquist F, Huelsenbeck JP. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19(12):1572–1574.
  • Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol. 34(12):3299–3302.
  • Shin SC, Cho J, Lee JK, Ahn DH, Lee H, Park H. 2012. Complete mitochondrial genome of the Antarctic amphipod Gondogeneia antarctica (Crustacea, amphipod). Mitochondrial DNA. 23(1):25–27.
  • Sun S, Wu Y, Ge X, Jakovlić I, Zhu J, Mahboob S, Al-Ghanim KA, Al-Misned F, Fu H. 2020. Disentangling the interplay of positive and negative selection forces that shaped mitochondrial genomes of Gammarus pisinnus and Gammarus lacustris. R Soc Open Sci. 7(1):190669.
  • Tang Y, Zheng X, Liu H, Sunxie F. 2020. Population genetics and comparative mitogenomic analyses reveal cryptic diversity of Amphioctopus neglectus (Cephalopoda: Octopodidae). Genomics. 112(6):3893–3902.
  • Väinölä R, Witt JDS, Grabowski M, Bradbury JH, Jazdzewski K, Sket B. 2008. Global diversity of amphipods (Amphipoda; Crustacea) in freshwater. Hydrobiologia 595:241–255.
  • Verheye ML, D’Udekem D’Acoz C. 2021. Integrative taxonomy of giant crested Eusirus in the Southern Ocean, including the description of a new species (Crustacea: Amphipoda: Eusiridae. Zool J Linn Soc. 193(1):31–77.
  • Watanabe YI, Suematsu T, Ohtsuki T. 2014. Losing the stem-loop structure from metazoan mitochondrial tRNAs and co-evolution of interacting factors. Front Genet. 5:109.
  • Wilson K, Cahill V, Ballment E, Benzie J. 2000. The complete sequence of the mitochondrial genome of the crustacean Penaeus monodon: are malacostracan crustaceans more closely related to insects than to branchiopods? Mol Biol Evol. 17(6):863–874.
  • Witt JD, Threloff DL, Hebert PD. 2006. DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation. Mol Ecol. 15(10):3073–3082.
  • Yamazaki N, Ueshima R, Terrett JA, Yokobori S, Kaifu M, Segawa R, Kobayashi T, Numachi K, Ueda T, Nishikawa K. 1997. Evolution of pulmonate gastropod mitochondrial genomes: comparisons of gene organizations of Euhadra, Cepaea and Albinaria and implications of unusual tRNA secondary structures. Genetics. 145(3):749–758.
  • Zhang D, Li WX, Zou H, Wu SG, Li M, Jakovlić I, Zhang J, Chen R, Wang GT. 2018. Mitochondrial genomes of two diplectanids (Platyhelminthes: Monogenea) expose paraphyly of the order Dactylogyridea and extensive tRNA gene rearrangements. Parasit Vectors. 11(1):1–13.
  • Zhang DX, Hewitt GM. 1997. Insect mitochondrial control region: a review of its structure, evolution and usefulness in evolutionary studies. Biochem Syst Ecol. 25(2):99–120.
  • Zhang Z, Xing Y, Cheng J, Pan D, Lv L, Cumberlidge N, Sun H. 2020. Phylogenetic implications of mitogenome rearrangements in East Asian potamiscine freshwater crabs (Brachyura: Potamidae). Mol Phylogenet Evol. 143:106669.