Different gene rearrangements of the genus Dardanus (Anomura: Diogenidae) and insights into the phylogeny of Paguroidea

  • 1.

    Boore, J. L. Animal mitochondrial genomes. Nucl. Acids Res. 27, 1767–1780 (1999).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 2.

    Gyllensten, U., Wharton, D., Josefsson, A. & Wilson, A. C. Paternal inheritance of mitochondrial DNA in mice. Nature 352, 255–257 (1991).

    ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 3.

    Sato, M. & Sato, K. Maternal inheritance of mitochondrial DNA by diverse mechanisms to eliminate paternal mitochondrial DNA. Biochim. Biophys. Acta (BBA) Mol. Cell Res. 1833, 1979–1984 (2013).

    CAS 
    Article 

    Google Scholar
     

  • 4.

    Sanchez, G. et al. Population genetics of the jumbo squid Dosidicus gigas (Cephalopoda: Ommastrephidae) in the northern Humboldt Current system based on mitochondrial and microsatellite DNA markers. Fish. Res. 175, 1–9. doi.org/10.1016/j.fishres.2015.11.005 (2016).

    Article 

    Google Scholar
     

  • 5.

    Ma, Z. et al. Comparative mitogenomics of the genus Odontobutis (Perciformes: Gobioidei: Odontobutidae) revealed conserved gene rearrangement and high sequence variations. Int. J. Mol. Sci. 16, 25031–25049. doi.org/10.3390/ijms161025031 (2015).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 6.

    Tan, M. H. et al. ORDER within the chaos: Insights into phylogenetic relationships within the Anomura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements. Mol. Phylogenet. Evol. 127, 320–331. doi.org/10.1016/j.ympev.2018.05.015 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 7.

    Ren, L. et al. Comparative analysis of mitochondrial genomes among the subfamily Sarcophaginae (Diptera: Sarcophagidae) and phylogenetic implications. Int. J. Biol. Macromol. 161, 214–222 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 8.

    Chen, L.-P. et al. Comparative analysis of mitogenomes among six species of grasshoppers (Orthoptera: Acridoidea: Catantopidae) and their phylogenetic implications in wing-type evolution. Int. J. Biol. Macromol. 159, 1062–1072 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 9.

    Jiang, L., Kang, L., Wu, C., Chen, M. & Lü, Z. A comprehensive description and evolutionary analysis of 9 Loliginidae mitochondrial genomes. Hydrobiologia 808, 115–124 (2018).

    CAS 
    Article 

    Google Scholar
     

  • 10.

    Wu, X. et al. New features of Asian Crassostrea oyster mitochondrial genomes: A novel alloacceptor tRNA gene recruitment and two novel ORFs. Gene 507, 112–118. doi.org/10.1016/j.gene.2012.07.032 (2012).

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • 11.

    Liu, Q. N. et al. A transfer RNA gene rearrangement in the lepidopteran mitochondrial genome. Biochem. Biophys. Res. Commun. 489, 149–154. doi.org/10.1016/j.bbrc.2017.05.115 (2017).

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • 12.

    Zhang, Y. et al. Gene rearrangements in the mitochondrial genome of Chiromantes eulimene (Brachyura: Sesarmidae) and phylogenetic implications for Brachyura. Int. J. Biol. Macromol. 162, 704–714. doi.org/10.1016/j.ijbiomac.2020.06.196 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • 13.

    Gong, L. et al. Large-scale mitochondrial gene rearrangements in the hermit crab Pagurus nigrofascia and phylogenetic analysis of the Anomura. Gene 695, 75–83. doi.org/10.1016/j.gene.2019.01.035 (2019).

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • 14.

    Yuan, Y., Li, Q., Yu, H. & Kong, L. The complete mitochondrial genomes of six heterodont bivalves (Tellinoidea and Solenoidea): Variable gene arrangements and phylogenetic implications. PLoS ONE 7, e32353 (2012).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 15.

    Smith, M. J., Arndt, A., Gorski, S. & Fajber, E. The phylogeny of echinoderm classes based on mitochondrial gene arrangements. J. Mol. Evol. 36, 545–554 (1993).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 16.

    Morrison, C. et al. Mitochondrial gene rearrangements confirm the parallel evolution of the crab-like form. Proc. R. Soc. Lond. Ser. B Biol. Sci. 269, 345–350 (2002).

    CAS 
    Article 

    Google Scholar
     

  • 17.

    Macey, J. R., Larson, A., Ananjeva, N. B., Fang, Z. & Papenfuss, T. J. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol. Biol. Evol. 14, 91–104 (1997).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 18.

    Thyagarajan, B., Padua, R. A. & Campbell, C. Mammalian mitochondria possess homologous DNA recombination activity. J. Biol. Chem. 271, 27536–27543 (1996).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 19.

    Tsaousis, A. D., Martin, D., Ladoukakis, E., Posada, D. & Zouros, E. Widespread recombination in published animal mtDNA sequences. Mol. Biol. Evol. 22, 925–933 (2005).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 20.

    Zhuang, X. & Cheng, C. H. C. ND6 gene “lost” and found: Evolution of mitochondrial gene rearrangement in Antarctic notothenioids. Mol. Biol. Evol. 27, 1391–1403 (2010).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 21.

    Moritz, C. & Brown, W. M. Tandem duplications in animal mitochondrial DNAs: Variation in incidence and gene content among lizards. Proc. Natl. Acad. Sci. U. S. A. 84, 7183–7187 (1987).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 22.

    Cantatore, P., Gadaleta, M., Roberti, M., Saccone, C. & Wilson, A. Duplication and remoulding of tRNA genes during the evolutionary rearrangement of mitochondrial genomes. Nature 329, 853–855 (1987).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 23.

    Poulton, J. et al. Families of mtDNA re-arrangements can be detected in patients with mtDNA deletions: Duplications may be a transient intermediate form. Hum. Mol. Genet. 2, 23–30 (1993).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 24.

    Lavrov, D. V., Boore, J. L. & Brown, W. M. Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: Duplication and nonrandom loss. Mol. Biol. Evol. 19, 163–169 (2002).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 25.

    De Grave, S. et al. A classification of living and fossil genera of decapod crustaceans. Raffles Bull. Zool. 21 Supplement, 1–109 (2009).

  • 26.

    UDEKEM, D. A. C. D. Inventaire et distribution des crustacés décapodes de l’Atlantique nord-oriental, de la Méditerranée et des eaux continentales adjacentes au nord de 25 N. Collection des Patrimoines Naturels 40, 1–383 (1999).

  • 27.

    Sha, Z., Xiao, L. & Wang, Y. Study on the Taxonomy of the Family Diogenidae (Crustacea: Decapoda: Anomura: Paguridea) from China Seas (Science Press, 2015).


    Google Scholar
     

  • 28.

    McLaughlin, P. A. Illustrated keys to families and genera of the superfamily Paguroidea (Crustacea: Decapoda: Anomura), with diagnoses of genera of Paguridae. Mem. Mus. Vic. 60, 111–144 (2003).

    Article 

    Google Scholar
     

  • 29.

    McLaughlin, P. A. & Lemaitre, R. Carcinization in the Anomura-fact or fiction? I. Evidence from adult morphology. Contrib. Zool. 67, 79–123 (1997).

    Article 

    Google Scholar
     

  • 30.

    McLaughlin, P. A., Lemaitre, R. & Sorhannus, U. Hermit crab phylogeny: A reappraisal and its “fall-out”. J. Crustac. Biol. 27, 97–115 (2007).

    Article 

    Google Scholar
     

  • 31.

    Reshmi, R. & Bijukumar, A. New report of the hermit crabs Dardanus lagopodes (Forskal, 1775), Paguristes miyakei Forest & McLaughlin, 1998 and Oncopagurus monstrosus (Alcock, 1894) (Crustacea: Decapoda: Anomura) from the Indian coast. Rec. Zool. Surv. India 113, 197–201 (2013).


    Google Scholar
     

  • 32.

    Deval, M. C. & Froglia, C. New records of deep-sea decapod crustaceans in the Turkish Mediterranean Sea (North Levant Sea). Zool. Middle East 62, 323–330 (2016).

    Article 

    Google Scholar
     

  • 33.

    Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10–12 (2011).

    Article 

    Google Scholar
     

  • 34.

    Dierckxsens, N., Mardulyn, P. & Smits, G. NOVOPlasty: De novo assembly of organelle genomes from whole genome data. Nucl. Acids Res. 45, e18. doi.org/10.1093/nar/gkw955 (2017).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 35.

    Bernt, M. et al. MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol. Phylogenet. Evol. 69, 313–319 (2013).

    PubMed 
    Article 

    Google Scholar
     

  • 36.

    Lowe, T. M. & Chan, P. P. tRNAscan-SE on-line: Integrating search and context for analysis of transfer RNA genes. Nucl. Acids Res 44, W54–W57. doi.org/10.1093/nar/gkw413 (2016).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 37.

    Alikhan, N.-F., Petty, N. K., Zakour, N. L. B. & Beatson, S. A. BLAST Ring Image Generator (BRIG): Simple prokaryote genome comparisons. BMC Genom. 12, 1–10 (2011).

    Article 
    CAS 

    Google Scholar
     

  • 38.

    Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 39.

    Perna, N. T. & Kocher, T. D. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 41, 353–358 (1995).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 40.

    Darling, A. C., Mau, B., Blattner, F. R. & Perna, N. T. Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394–1403 (2004).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 41.

    Bernt, M. et al. CREx: Inferring genomic rearrangements based on common intervals. Bioinformatics 23, 2957–2958 (2007).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 42.

    Hu, F., Lin, Y. & Tang, J. MLGO: Phylogeny reconstruction and ancestral inference from gene-order data. BMC Bioinform. 15, 1–6 (2014).


    Google Scholar
     

  • 43.

    Zhang, D. et al. PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol. Ecol. Resour. 20, 348–355. doi.org/10.1111/1755-0998.13096 (2020).

    Article 
    PubMed 

    Google Scholar
     

  • 44.

    Katoh, K., Misawa, K., Kuma, K. I. & Miyata, T. MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucl. Acids Res. 30, 3059–3066 (2002).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 45.

    Talavera, G. & Castresana, J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564–577 (2007).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 46.

    Nguyen, L.-T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 47.

    Ronquist, F. et al. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542. doi.org/10.1093/sysbio/sys029 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 48.

    Sultana, Z. et al. Molecular phylogeny of ten intertidal hermit crabs of the genus Pagurus inferred from multiple mitochondrial genes, with special emphasis on the evolutionary relationship of Pagurus lanuginosus and Pagurus maculosus. Genetica 146, 369–381 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 49.

    Hickerson, M. & Cunningham, C. Dramatic mitochondrial gene rearrangements in the hermit crab Pagurus longicarpus (Crustacea, Anomura). Mol. Biol. Evol. 17, 639–644 (2000).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 50.

    Gong, L. et al. Novel gene rearrangement in the mitochondrial genome of Coenobita brevimanus (Anomura: Coenobitidae) and phylogenetic implications for Anomura. Genomics 112, 1804–1812. doi.org/10.1016/j.ygeno.2019.10.012 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • 51.

    Veldsman, W. P., Wang, Y., Niu, J., Baeza, J. A. & Chu, K. H. Characterization of the complete mitochondrial genome of a coconut crab, Birgus latro (Linnaeus, 1767) (Decapoda: Anomura: Coenobitidae), from Okinawa, Japan. J. Crustac. Biol. 40, 390–400 (2020).

    Article 

    Google Scholar
     

  • 52.

    Gan, H. Y., Gan, H. M., Tan, M. H., Lee, Y. P. & Austin, C. M. The complete mitogenome of the hermit crab Clibanarius infraspinatus (Hilgendorf, 1869), (Crustacea; Decapoda; Diogenidae)—A new gene order for the Decapoda. Mitochondrial DNA Part A 27, 4099–4100 (2016).

    CAS 
    Article 

    Google Scholar
     

  • 53.

    Wang, Q. et al. Comparative mitochondrial genomic analysis of Macrophthalmus pacificus and insights into the phylogeny of the Ocypodoidea & Grapsoidea. Genomics 112, 82–91 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 54.

    Kim, M. I. et al. Complete nucleotide sequence and organization of the mitogenome of the red-spotted apollo butterfly, Parnassius bremeri (Lepidoptera: Papilionidae) and comparison with other lepidopteran insects. Mol. Cells 28, 347–363 (2009).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 55.

    Hao, J. et al. The complete mitochondrial genome of Ctenoptilum vasava (Lepidoptera: Hesperiidae: Pyrginae) and its phylogenetic implication. Comp. Funct. Genom. 2012, 328049 (2012).

    Article 
    CAS 

    Google Scholar
     

  • 56.

    Boore, J. L., Lavrov, D. V. & Brown, W. M. Gene translocation links insects and crustaceans. Nature 392, 667–668 (1998).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 57.

    Richter, S. & Scholz, G. Morphological evidence for a hermit crab ancestry of lithodids (Crustace, Decapoda, Anomala, Paguroidea). Zool. Anz. 233, 187–187 (1994).


    Google Scholar
     

  • 58.

    Lemaitre, R., Mclaughlin, P. A. & Sorhannus, U. Phylogenetic relationships within the Pylochelidae (Decapoda: Anomura: Paguroidea): A cladistic analysis based on morphological characters. Zootaxa 2022, 1–14 (2009).

    Article 

    Google Scholar
     

  • 59.

    Lemaitre, R. & McLaughlin, P. A. Recent advances and conflicts in concepts of anomuran phylogeny (Crustacea: Malacostraca). Arthropod Syst. Phylogeny. 67, 119–135 (2009).

  • 60.

    Forest, J. Crustacea Decapoda Anomura: Révision du genre Trizopagurus Forest, 1952 (Diogenidae), avec rétablissement de deux genres nouveaux. Mémoires du Muséum national d’Histoire naturelle. Série A, Zoologie. 163, 9–149 (1995).

  • 61.

    Forest, J. Révision du genre Aniculus (Decapoda Diogenidae). Crustaceana 8, 1–91 (1984).


    Google Scholar
     

  • 62.

    Tsang, L., Ma, K., Ahyong, S., Chan, T.-Y. & Chu, K. Phylogeny of Decapoda using two nuclear protein-coding genes: Origin and evolution of the Reptantia. Mol. Phylogenet. Evol. 48, 359–368 (2008).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 63.

    Landschoff, J. & Gouws, G. DNA barcoding as a tool to facilitate the taxonomy of hermit crabs (Decapoda: Anomura: Paguroidea). J. Crustac. Biol. 38, 780–793 (2018).

    Article 

    Google Scholar
     

  • 64.

    Sun, S. E., Sha, Z. & Wang, Y. The complete mitochondrial genomes of two vent squat lobsters, Munidopsis lauensis and M. verrilli: Novel gene arrangements and phylogenetic implications. Ecol. Evol. 9, 12390–12407 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 65.

    Akasaki, T. et al. Extensive mitochondrial gene arrangements in coleoid Cephalopoda and their phylogenetic implications. Mol. Phylogenet. Evol. 38, 648–658 (2006).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 66.

    Zhang, Z. et al. Phylogenetic implications of mitogenome rearrangements in East Asian potamiscine freshwater crabs (Brachyura: Potamidae). Mol. Phylogenet. Evol. 143, 106669 (2020).

    PubMed 
    Article 

    Google Scholar
     

  • Read more here: Source link