Mitochondrial gene rearrangement and phylogenetic relationships in the Amphilepidida and Ophiacanthida (Echinodermata, Ophiuroidea)

References

• Arndt A, Smith MJ. 1998. Mitochondrial gene rearrangement in the sea cucumber genus Cucumaria. Molecular Biology and Evolution. 15:1009–1016. doi: 10.1093/oxfordjournals.molbev.a025999
   Google Scholar
• Barr CM, Neiman M, Taylor DR. 2005. Inheritance and recombination of mitochondrial genomes in plants, fungi, and animals. New Phytologist. 168:39–50. doi: 10.1111/j.1469-8137.2005.01492.x
   Google Scholar
• Bauza-Ribot MM, Jaume D, Juan C, Pons J. 2009. The complete mitochondrial genome of the subterranean crustacean Metacrangonyx longipes (Amphipoda): A unique gene order and extremely short control region. Mitochondrial DNA. 20:88–99. doi: 10.1080/19401730902964417
   Google Scholar
• Bensch S, Harlid S. 2000. Mitochondrial genomic re-arrangements in songbirds. Molecular Biology and Evolution. 17:107–113. doi: 10.1093/oxfordjournals.molbev.a026223
   Google Scholar
• 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 (oxford, England). 23:2957–2958. doi: 10.1093/bioinformatics/btm468
   Google Scholar
• Boissin E, Hoareau TB, Paulay G, Bruggemann JH. 2017. DNA barcoding of reef brittle stars (Ophiuroidea, Echinodermata) from the southwestern Indian Ocean evolutionary hot spot of biodiversity. Ecology and Evolution. 7:11197–11203. doi: 10.1002/ece3.3554
   Google Scholar
• Boore JL. 1999. Animal mitochondrial genomes. Nucleic Acids Research. 27:1767–1780. doi: 10.1093/nar/27.8.1767
   Google Scholar
• Boore JL, Brown WM. 1998. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Current Opinion in Genetics & Development. 8:668–674. doi: 10.1016/S0959-437X(98)80035-X
   Google Scholar
• Boore JL, Brown WM. 2000. Mitochondrial genomes of Galathealinum, Helobdella, and Platynereis: sequence and gene arrangement comparisons indicate that Pogonophora is not a phylum and Annelida and Arthropoda are not sister taxa. Molecular Biology and Evolution. 17:87–106. doi: 10.1093/oxfordjournals.molbev.a026241
   Google Scholar
• Cameron SL. 2014. Insect mitochondrial genomics: Implications for evolution and phylogeny. Annual Review of Entomology. 59:95–117. doi: 10.1146/annurev-ento-011613-162007
   Google Scholar
• Chen L, Chen PY, Xue XF, Hua HQ, Li YX, Zhang F, Wei SJ. 2018. Extensive gene rearrangements in the mitochondrial genomes of two egg parasitoids, Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae). Scientific Reports. 8:1–11. doi: 10.1038/s41598-017-17765-5
   Google Scholar
• Chen ZQ, McNamara KJ. 2006. End-Permian extinction and subsequent recovery of the Ophiuroidea (Echinodermata). Palaeogeography, Palaeoclimatology, Palaeoecology. 236:321–344. doi: 10.1016/j.palaeo.2005.11.014
   Google Scholar
• Cox CJ, Li B, Foster PG, Embley TM, Civáň P. 2014. Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions. Systematic Biology. 63:272–279. doi: 10.1093/sysbio/syt109
   Google Scholar
• Curole JP, Kocher TD. 1999. Mitogenomics: Digging deeper with complete mitochondrial genomes. Trends in Ecology & Evolution. 14:394–398. doi: 10.1016/S0169-5347(99)01660-2
   Google Scholar
• Darriba D, Taboada GL, Doallo R, Posada D. 2011. Prottest 3: fast selection of best-fit models of protein evolution. Bioinformatics (oxford, England). 27:1164–1165. doi: 10.1093/bioinformatics/btr088
   Google Scholar
• Darriba D, Taboada GL, Doallo R, Posada D. 2012. Jmodeltest 2: more models, new heuristics, and parallel computing. Nature Methods. 9:772. doi: 10.1038/nmeth.2109
   Google Scholar
• Dowton M, Austin AD. 1999. Evolutionary dynamics of a mitochondrial rearrangement “hot spot” in the Hymenoptera. Molecular Biology and Evolution. 16:298–309. doi: 10.1093/oxfordjournals.molbev.a026111
   Google Scholar
• Dowton M, Cameron SL, Dowavic JI, Austin AD, Whiting MF. 2009. Characterization of 67 mitochondrial tRNA gene rearrangements in the Hymenoptera suggests that mitochondrial tRNA gene position is selectively neutral. Molecular Biology and Evolution. 26:1607–1617. doi: 10.1093/molbev/msp072
   Google Scholar
• Foster PG, de Oliveira TMP, Bergo ES, Conn JE, Sant’Ana DC, Nagaki SS, Nihei S, Lamas CE, González C, Moreira CC, Sallum M. 2017. Phylogeny of Anophelinae using mitochondrial protein coding genes. Royal Society Open Science. 4:170758. doi: 10.1098/rsos.170758
   Google Scholar
• Foster PG, Hickey DA. 1999. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. Journal of Molecular Evolution. 48:284–290. doi: 10.1007/PL00006471
   Google Scholar
• Galaska MP, Li Y, Kocot KM, Mahon AR, Halanych KM. 2019. Conservation of mitochondrial genome arrangements in brittle stars (Echinodermata, Ophiuroidea). Molecular Phylogenetics and Evolution. 130:115–120. doi: 10.1016/j.ympev.2018.10.002
   Google Scholar
• Grande C, Templado J, Zardoya R. 2008. Evolution of gastropod mitochondrial genome arrangements. BMC Evolutionary Biology. 8:1–15. doi: 10.1186/1471-2148-8-61
   Google Scholar
• Guindon S, Gascuel O. 2003. A simple, fast, and accurate method to estimate large phylogenies by maximum-likelihood. Systematic Biology. 52:696–704. doi: 10.1080/10635150390235520
   Google Scholar
• Hemery LG, Eléaume M, Roussel V, Améziane N, Gallut C, Steinke D, Cruaud C, Couloux A, Wilson NG. 2012. Comprehensive sampling reveals circumpolarity and sympatry in seven mitochondrial lineages of the Southern Ocean crinoid species Promachocrinus kerguelensis (Echinodermata). Molecular Ecology. 21:2502–2518. doi: 10.1111/j.1365-294X.2012.05512.x
   Google Scholar
• Hickerson MJ, Cunningham CW. 2000. Dramatic mitochondrial gene rearrangements in the hermit crab Pagurus longicarpus (Crustacea, Anomura). Molecular Biology and Evolution. 17:639–644. doi: 10.1093/oxfordjournals.molbev.a026342
   Google Scholar
• Hoareau TB, Boissin E. 2010. Design of phylum-specific hybrid primers for DNA barcoding: Addressing the need for efficient COI amplification in the Echinodermata. Molecular Ecology Resources. 10:960–967. doi: 10.1111/j.1755-0998.2010.02848.x
   Google Scholar
• Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics (oxford, England). 17:754–755. doi: 10.1093/bioinformatics/17.8.754
   Google Scholar
• Hugall AF, O’Hara TD, Hunjan S, Nilsen R, Moussalli A. 2016. An exon-capture system for the entire class Ophiuroidea. Molecular Biology and Evolution. 33:281–294. doi: 10.1093/molbev/msv216
   Google Scholar
• Irisarri I, Eernisse DJ, Zardoya R. 2014. Molecular phylogeny of Acanthochitonina (Mollusca: Polyplacophora: Chitonida): three new mitochondrial genomes, rearranged gene orders and systematics. Journal of Natural History. 48:2825–2853. doi: 10.1080/00222933.2014.963721
   Google Scholar
• Janies DA, Voight JR, Daly M. 2011. Echinoderm phylogeny including Xyloplax, a progenetic asteroid. Systematic Biology. 60:420–438. doi: 10.1093/sysbio/syr044
   Google Scholar
• Kurabayashi A, Sumida M, Yonekawa H, Glaw F, Vences M, Hasegawa M. 2008. Phylogeny, recombination, and mechanisms of stepwise mitochondrial genome reorganization in mantellid frogs from Madagascar. Molecular Biology and Evolution. 25:874–891. doi: 10.1093/molbev/msn031
   Google Scholar
• Kurabayashi A, Yoshikawa N, Sato N, Hayashi Y, Oumi S, Fujii T, Sumida M. 2010. Complete mitochondrial DNA sequence of the endangered frog Odorrana ishikawae (family Ranidae) and unexpected diversity of mt gene arrangements in ranids. Molecular Phylogenetics and Evolution. 56:543–553. doi: 10.1016/j.ympev.2010.01.022
   Google Scholar
• Laslett D, Canbäck B. 2008. ARWEN: A program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics (Oxford, England). 24:172–175. doi: 10.1093/bioinformatics/btm573
   Google Scholar
• Layton KKS, Corstorphine EA, Hebert PDN. 2016. Exploring Canadian Echinoderm diversity through DNA Barcodes. PLoS One. 11(e0166118):1–16.
   Google Scholar
• Lee T, Shin S. 2018. Complete mitochondrial genome analysis of Distolasterias nipon (Echinodermata, Asteroidea, Forcipulatida). Mitochondrial DNA Part B. 3:1290–1291. doi: 10.1080/23802359.2018.1501313
   Google Scholar
• Li Q, Chen C, Xiong C, Chen Z, Huang W. 2018. Comparative mitogenomics reveals large-scale gene rearrangement in the mitochondrial genome of two Pleurotus species. Applied Microbiology and Biotechnology. 102:6143–6153. doi: 10.1007/s00253-018-9082-6
   Google Scholar
• Li Q, Wei SJ, Tang P, Wu Q, Shi M, Sharkey MJ, Chen XX. 2016. Multiple lines of evidence from mitochondrial genomes resolve phylogenetic relationships of parasitic wasps in Braconidae. Genome Biology and Evolution. 8:2651–2662. doi: 10.1093/gbe/evw184
   Google Scholar
• Li Y, Kocot KM, Schander C, Santos SR, Thornhill DJ, Halanych KM. 2015. Mitogenomics reveals phylogeny and repeated motifs in control regions of the deep-sea family Siboglinidae (Annelida). Molecular Phylogenetics and Evolution. 85:221–229. doi: 10.1016/j.ympev.2015.02.008
   Google Scholar
• Littlewood DT, Smith AB, Clough KA, Emson RH. 1997. The interrelationships of the echinoderm classes: morphological and molecular evidence. Biological Journal of the Linnean Society. 61:409–438. doi: 10.1111/j.1095-8312.1997.tb01799.x
   Google Scholar
• Liu H, Li H, Song F, Gu W, Feng J, Cai W, Shao R. 2017. Novel insights into mitochondrial gene rearrangement in thrips (Insecta: Thysanoptera) from the grass thrips, Anaphothrips obscurus. Scientific Reports. 7:4284. doi: 10.1038/s41598-017-04617-5
   Google Scholar
• López-Márquez V, Acevedo I, Manjón-Cabeza ME, García-Jiménez R, Templado J, Machordom A. 2018. Looking for morphological evidence of cryptic species in Asterina Nardo, 1834 (Echinodermata: Asteroidea). The redescription of Asterina pancerii (Gasco, 1870) and the description of two new species. Invertebrate Systematics. 32:505–523. doi: 10.1071/IS17024
   Google Scholar
• Lowe TM, Chan PP. 2016. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Research. 44:W54–W57. doi: 10.1093/nar/gkw413
   Google Scholar
• Matsumoto Y, Yanase T, Tsuda T, Noda H. 2009. Species-specific mitochondrial gene rearrangements in biting midges and vector species identification. Medical and Veterinary Entomology. 23:47–55. doi: 10.1111/j.1365-2915.2008.00789.x
   Google Scholar
• O’Hara TD, Hugall AF, Thuy B, Stöhr S, Martynov AV. 2017. Restructuring higher taxonomy using broad-scale phylogenomics: the living Ophiuroidea. Molecular Phylogenetics and Evolution. 107:415–430. doi: 10.1016/j.ympev.2016.12.006
   Google Scholar
• O’Hara TD, Stöhr S, Hugall AF, Thuy B, Martynov A. 2018. Morphological diagnoses of higher taxa in Ophiuroidea (Echinodermata) in support of a new classification. European Journal of Taxonomy. 416:1–35.
   Google Scholar
• Okanishi M, O’Hara TD, Fujita T. 2011. Molecular phylogeny of the order Euryalida (Echinodermata: Ophiuroidea), based on mitochondrial and nuclear ribosomal genes. Molecular Phylogenetics and Evolution. 61:392–399. doi: 10.1016/j.ympev.2011.07.003
   Google Scholar
• Park HJ. 2013. Complete mitochondrial genome of Korean endangered species Ophiacantha linea and Pseudomaretia alta. Korea: Graduate School of Education, Kyungpook National University, 1–53.
   Google Scholar
• Perseke M, Bernhard D, Fritzsch G, Brümmer F, Stadler PF, Schlegel M. 2010. Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: insights in phylogenetic relationships of Echinodermata. Molecular Phylogenetics and Evolution. 56:201–211. doi: 10.1016/j.ympev.2010.01.035
   Google Scholar
• Perseke M, Fritzsch G, Ramsch K, Bernt M, Merkle D, Middendorf M, Bernhard D, Stadler PF, Schlegel M. 2008. Evolution of mitochondrial gene orders in echinoderms. Molecular Phylogenetics and Evolution. 47:855–864. doi: 10.1016/j.ympev.2007.11.034
   Google Scholar
• Rawlings TA, Collins TM, Bieler R. 2001. A major mitochondrial gene rearrangement among closely related species. Molecular Biology and Evolution. 18:1604–1609. doi: 10.1093/oxfordjournals.molbev.a003949
   Google Scholar
• Rokas A, Holland PWH. 2000. Rare genomic changes as a tool for phylogenetics. Trends in Ecology & Evolution. 15:454–459. doi: 10.1016/S0169-5347(00)01967-4
   Google Scholar
• Rota-Stabelli O, Lartillot N, Philippe H, Pisani D. 2013. Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study. Systematic Biology. 62:121–133. doi: 10.1093/sysbio/sys077
   Google Scholar
• Scouras A, Beckenbach K, Arndt A, Smith MJ. 2004. Complete mitochondrial genome DNA sequence for two ophiuroids and a holothuroid: the utility of protein gene sequence and gene maps in the analyses of deep deuterostome phylogeny. Molecular Phylogenetics and Evolution. 31:50–65. doi: 10.1016/j.ympev.2003.07.005
   Google Scholar
• Scouras A, Smith MJ. 2001. A novel mitochondrial gene order in the crinoid echinoderm Florometra serratissima. Molecular Biology and Evolution. 18:61–73. doi: 10.1093/oxfordjournals.molbev.a003720
   Google Scholar
• Smith MJ, Arndt A, Gorski S, Fajber E. 1993. The phylogeny of echinoderm classes based on mitochondrial gene arrangements. Journal of Molecular Evolution. 36:545–554. doi: 10.1007/BF00556359
   Google Scholar
• Song F, Li H, Jiang P, Zhou X, Liu J, Sun C, Vogler AP, Cai W. 2016. Capturing the phylogeny of Holometabola with mitochondrial genome data and Bayesian site-heterogeneous mixture models. Genome Biology and Evolution. 8:1411–1426. doi: 10.1093/gbe/evw086
   Google Scholar
• Stamatakis A. 2014. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics (oxford, England). 30:1312–1313. doi: 10.1093/bioinformatics/btu033
   Google Scholar
• Stokkan M, Jurado-Rivera JA, Juan C, Jaume D, Pons J. 2015. Mitochondrial genome rearrangements at low taxonomic levels: three distinct mitogenome gene orders in the genus Pseudoniphargus (Crustacea: Amphipoda). Mitochondrial DNA Part A. 27:3579–3589. doi: 10.3109/19401736.2015.1079821
   Google Scholar
• Tang M, Tan M, Meng G, Yang S, Su X, Liu S, Song W, Li Y, Wu Q, Zhang A, Zhou X. 2014. Multiplex sequencing of pooled mitochondrial genomes—a crucial step toward biodiversity analysis using mito-metagenomics. Nucleic Acids Research. 42:e166. doi: 10.1093/nar/gku917
   Google Scholar
• Tsang LM, Schubart CD, Ahyong ST, Lai JCY, Au EYC, Chan TY, Ng PKL, Chu KH. 2014. Evolutionary history of true crabs (crustacea: Decapoda: brachyura) and the origin of freshwater crabs. Molecular Biology and Evolution. 31:1173–1187. doi: 10.1093/molbev/msu068
   Google Scholar
• Uthicke S, Byrne M, Conand C. 2010. Genetic barcoding of commercial bêche-de-mer species (Echinodermata: Holothuroidea). Molecular Ecology Resources. 10:634–646. doi: 10.1111/j.1755-0998.2009.02826.x
   Google Scholar
• Vawter L, Brown WM. 1986. Nuclear and mitochondrial DNA comparisons reveal extreme rate variation in the molecular clock. Science. 234:194–196. doi: 10.1126/science.3018931
   Google Scholar
• Ward RD, Holmes BH, O’Hara TD. 2008. DNA barcoding discriminates echinoderm species. Molecular Ecology Resources. 8:1202–1211. doi: 10.1111/j.1755-0998.2008.02332.x
   Google Scholar
• Wyman SK, Jansen RK, Boore JL. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics (oxford, England). 20:3252–3255. doi: 10.1093/bioinformatics/bth352
   Google Scholar
• Zhong M, Struck TH, Halanych KM. 2008. Phylogenetic information from three mitochondrial genomes of Terebelliformia (Annelida) worms and duplication of the methionine tRNA. Gene. 416:11–21. doi: 10.1016/j.gene.2008.02.020
   Google Scholar