The complete mitochondrial genome of Calyptogena marissinica (Heterodonta: Veneroida: Vesicomyidae): Insight into the deep-sea adaptive evolution of vesicomyids
Autoři:
Mei Yang aff001; Lin Gong aff001; Jixing Sui aff001; Xinzheng Li aff001
Působiště autorů:
Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
aff001; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
aff002; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
aff003; University of Chinese Academy of Sciences, Beijing, China
aff004
Vyšlo v časopise:
PLoS ONE 14(9)
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pone.0217952
Souhrn
The deep-sea chemosynthetic environment is one of the most extreme environments on the Earth, with low oxygen, high hydrostatic pressure and high levels of toxic substances. Species of the family Vesicomyidae are among the dominant chemosymbiotic bivalves found in this harsh habitat. Mitochondria play a vital role in oxygen usage and energy metabolism; thus, they may be under selection during the adaptive evolution of deep-sea vesicomyids. In this study, the mitochondrial genome (mitogenome) of the vesicomyid bivalve Calyptogena marissinica was sequenced with Illumina sequencing. The mitogenome of C. marissinica is 17,374 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes (rrnS and rrnL) and 22 transfer RNA genes. All of these genes are encoded on the heavy strand. Some special elements, such as tandem repeat sequences, “G(A)nT” motifs and AT-rich sequences, were observed in the control region of the C. marissinica mitogenome, which is involved in the regulation of replication and transcription of the mitogenome and may be helpful in adjusting the mitochondrial energy metabolism of organisms to adapt to the deep-sea chemosynthetic environment. The gene arrangement of protein-coding genes was identical to that of other sequenced vesicomyids. Phylogenetic analyses clustered C. marissinica with previously reported vesicomyid bivalves with high support values. Positive selection analysis revealed evidence of adaptive change in the mitogenome of Vesicomyidae. Ten potentially important adaptive residues were identified, which were located in cox1, cox3, cob, nad2, nad4 and nad5. Overall, this study sheds light on the mitogenomic adaptation of vesicomyid bivalves that inhabit the deep-sea chemosynthetic environment.
Klíčová slova:
Biology and life sciences – Cell biology – Biochemistry – Nucleic acids – Organisms – Eukaryota – Research and analysis methods – Evolutionary biology – Database and informatics methods – Bioinformatics – Sequence analysis – Animals – Invertebrates – Computer and information sciences – Evolutionary systematics – Phylogenetics – Phylogenetic analysis – Evolutionary processes – Taxonomy – Data management – Cellular structures and organelles – RNA – Non-coding RNA – Sequence motif analysis – Bioenergetics – Energy-producing organelles – Mitochondria – DNA sequence analysis – Ribosomes – Ribosomal RNA – Molluscs – Bivalves – Transfer RNA – Evolutionary adaptation
Zdroje
1. Martijn J, Vosseberg J, Guy L, Offre P, Ettema TJG. Deep mitochondrial origin outside the sampled alphaproteobacteria. Nature. 2018; 557: 101–105. https://doi.org/10.1038/s41586-018-0059-5 29695865
2. Wolstenholme DR. Animal mitochondrial DNA: Structure and evolution. International Review of Cytology. 1992; 141: 173–216. 1452431
3. Boore JL. Animal mitochondrial genomes. Nucleic Acids Research. 1999; 27: 1767–1780. doi: 10.1093/nar/27.8.1767 10101183
4. Hebert P, Cywinska A, Ball S, Waard J. Biological identification through DNA barcodes. Proceedings of the Royal Society B Biological Sciences. 2002; 270: 313–321. https://doi.org/10.1098/rspb.2002.2218 12614582
5. Gissi C, Iannelli F, Pesole G. Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species. Heredity. 2008; 101: 301–320. http://doi.org/10.1038/hdy.2008.62 18612321
6. Tan MH, Gan HM, Lee YP, Linton S, Grandjean F, Bartholomei-Santos ML, et al. ORDER within the chaos: Insights into phylogenetic relationships within the Anomura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements. Molecular Phylogenetics and Evolution. 2018; 127: 320–331. https://doi.org/10.1016/j.ympev.2018.05.015 29800651
7. Schuster A, Vargas S, Knapp IS, Pomponi SA, Toonen RJ, Erpenbeck D, et al. Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model. BMC Evolutionary Biology. 2018; 18: 114. https://dx.doi.org/10.1186/s12862-018-1230-1 30021516
8. Sibuet M, Olu K. Biogeography, biodiversity and fluid dependence of deep-sea cold-seep communities at active and passive margins. Deep-Sea Research II: Topical Studies in Oceanography. 1998; 45: 517–567.
9. Van Dover CL, German CR, Speer KG, Parson LM, Vrijenhoek RC. Evolution and Biogeography of Deep-Sea Vent and Seep Invertebrates. Science. 2002; 295: 1253–1257. https://doi.org/10.1126/science.1067361 11847331
10. Martin W, Baross J, Kelley D, Russell MJ. Hydrothermal vents and the origin of life. Nature Review Microbiology. 2008; 6: 805–814. https://doi.org/10.1038/nrmicro1991 18820700
11. Vrijenhoek RC. Genetic diversity and connectivity of deep-sea hydrothermal vent metapopulations. Molecular Ecology. 2010; 19: 4391–4411. https://doi.org/10.1111/j.1365-294X.2010.04789.x 20735735
12. Sun J, Zhang Y, Xu T, Zhang Y, Mu H, Zhang Y, et al. Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes. Nature Ecology Evolution. 2017; 1: 121. https://doi.org/10.1038/s41559-017-0121 28812709
13. Zheng P, Wang MX, Li CL, Sun XQ, Wang XC, Sun Y, et al. Insights into deep-sea adaptations and host-symbiont interactions: A comparative transcriptome study on Bathymodiolus mussels and their coastal relatives. Molecular Ecology. 2017; 26: 5133–5148. https://doi.org/10.1111/mec.14160 28437568
14. Hui M, Cheng J, Sha ZL. First comprehensive analysis of lysine acetylation in Alvinocaris longirostris from the deep-sea hydrothermal vents. BMC Genomics. 2018; 19: 352. https://doi.org/10.1186/s12864-018-4745-3 29747590
15. Lan Y, Sun J, Xu T, Chen C, Tian RM, Qiu JW, et al. De novo transcriptome assembly and positive selection analysis of an individual deep-sea fish. BMC Genomics. 2018; 19: 394. https://doi.org/10.1186/s12864-018-4720-z 29793428
16. Sun SE, Hui M, Wang MX, Sha ZL. The complete mitochondrial genome of the alvinocaridid shrimp Shinkaicaris leurokolos (Decapoda, Caridea): Insight into the mitochondrial genetic basis of deep-sea hydrothermal vent adaptation in the shrimp. Comparative Biochemistry and Physiology-Part D. 2018; 25: 42–52. https://doi.org/10.1016/j.cbd.2017.11.002 29145028
17. Wang ZF, Shi XJ, Sun LX, Bai YZ, Zhang DZ, Tang BP. Evolution of mitochondrial energy metabolism genes associated with hydrothermal vent adaption of Alvinocaridid shrimps. Genes Genomics. 2017; 39: 1367–1376. https://doi.org/10.1007/s13258-017-0600-1
18. Plazzi F, Puccio G, Passamonti M. Burrowers from the Past: Mitochondrial Signatures of Ordovician Bivalve Infaunalization. Genome Biology and Evolution. 2017; 9: 956–967. https://doi.org/10.1093/gbe/evx051 28338965
19. Gu ML, Dong XQ, Shi L, Shi L, Lin KQ, Huang XQ, et al. Differences in mtDNA whole sequence between Tibetan and Han populations suggesting adaptive selection to high altitude. Gene. 2012; 496: 37–44. https://doi.org/10.1016/j.gene.2011.12.016 22233893
20. Yu L, Wang XP, Ting N, Zhang YP. Mitogenomic analysis of Chinese snub-nosed monkeys: Evidence of positive selection in NADH dehydrogenase genes in high-altitude adaptation. Mitochondrion. 2011; 11: 497–503. https://doi.org/10.1016/j.mito.2011.01.004 21292038
21. Xu SQ, Yang YZ, Zhou J, Jin GE, Chen YT, Wang J, et al. A mitochondrial genome sequence of the Tibetan antelope (Pantholops hodgsonii). Genomics, proteomics & bioinformatics. 2005; 3: 5–17. doi: 10.1016/S1672-0229(05)03003-2 16144518
22. Ning T, Xiao H, Li J, Hua S, Zhang YP. Adaptive evolution of the mitochondrial ND6 gene in the domestic horse. Genetics and Molecular Research. 2010; 9: 144–150. https://doi.org/10.4238/vol9-1gmr705 20198570
23. Wang ZF, Yonezawa T, Liu B, Ma T, Shen X, Su JP, et al. Domestication relaxed selective constraints on the yak mitochondrial genome. Molecular Biology and Evolution. 2011; 28:1553–1556. https://doi.org/10.1093/molbev/msq336 21156878
24. Zhou TC, Shen XJ, Irwin DM, Shen YY, Zhang YP. Mitogenomic analyses propose positive selection in mitochondrial genes for high-altitude adaptation in galliform birds. Mitochondrion. 2014; 18: 70–75. https://doi.org/10.1016/j.mito.2014.07.012 25110061
25. Wang Y, Shen YJ, Feng CG, Zhao K, Song ZB, Zhang YP, et al. Mitogenomic perspectives on the origin of Tibetan loaches and their adaptation to high altitude. Scientific Reports. 2016; 6: 29690. https://doi.org/10.1038/srep29690 27417983
26. Boss KJ, Turner RD. The giant white clam from the Galapagos Rift, Calyptogena magnifica species novum. Malacologia. 1980; 20: 161–194.
27. Bennett BA, Smith CR, Glaser B, Maybaum HL. Faunal community structure of achemoautortophic assemblage on whale bones in the deep northeast Pacific Ocean. Marine Ecology Progress. 1994; 108: 205–223.
28. Cosel RV, Salas C, Høisæter T. Vesicomyidae (Mollusca: Bivalvia) of the genera Vesicomya, Wais-iuconcha, Isorropodon and Callogonia in the eastern Atlantic and the Mediterranean. Sarsia, 86(4–5): 333–366. https://doi.org/10.1080/00364827.2001.10425523.
29. Krylova EM, Sahling H. Vesicomyidae (bivalvia): Current taxonomy and distribution. PLoS One. 2010; 5: e9957. https://doi.org/10.1371/journal.pone.0009957 20376362
30. Fisher CR. Chemoautotrophic and methanotrophic symbioses in marine invertebrates. Reviews in Aquatic Sciences. 1990; 2: 399–436.
31. Krylova EM, Drozdov AL, Mironov AN. Presence of bacteria in gills of hadal bivalve “Vesicomya” sergeevi Filatova, 1971. Ruthenica. 2000; 10: 76–79.
32. Chen C, Okutani T, Liang QY, Qiu JW. A Noteworthy New Species of the Family Vesicomyidae from the South China Sea (Bivalvia: Glossoidea). Venus. 2018; 76: 29–37.
33. Liu HL, Cai SY, Zhang HB, Vrijenhoek RC. Complete mitochondrial genome of hydrothermal vent clam Calyptogena magnifica. Mitochondrial DNA Part A DNA Mapping, Sequencing, and Analysis. 2015; 27: 4333–4335. https://doi.org/10.3109/19401736.2015.1089488 26462964
34. Liu HL, Cai SY, Liu J, Zhang HB. Comparative mitochondrial genomic analyses of three chemosynthetic vesicomyid clams from deep-sea habitats. Ecology and Evolution. 2018; 8: 7261–7272. https://doi.org/10.1002/ece3.4153 30151147
35. Ozawa G, Shimamura S, Takaki Y, Takishita K, Ikuta T, Barry JP, et al. Ancient occasional host switching of maternally transmitted bacterial symbionts of chemosynthetic vesicomyid clams. Genome Biology and Evolution. 2017; 9: 2226–2236. https://doi.org/10.1093/gbe/evx166 28922872
36. Ozawa G, Shimamura S, Takaki Y, Yokobori SI, Ohara Y, Takishita K, et al. Updated mitochondrial phylogeny of Pteriomorph and Heterodont Bivalvia, including deep-sea chemosymbiotic Bathymodiolus mussels, vesicomyid clams and the thyasirid clam Conchocele cf. bisecta. Marine Genomics. 2017; 31: 43–52. https://doi.org/10.1016/j.margen.2016.09.003 27720682
37. Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology. 2008; 9: R7. https://doi.org/10.1186/gb-2008-9-1-r7 18190707
38. Lagesen K, Hallin P, Rødland EA, Stærfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Research. 2007; 35: 3100–3108. https://doi.org/10.1093/nar/gkm160 17452365
39. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research. 1997; 25: 955–964. https://doi.org/10.1093/nar/25.5.0955 9023104
40. Lohse M, Drechsel O, Bock R. OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Current Genetics. 2007; 52: 267–274. https://doi.org/10.1007/s00294-007-0161-y 17957369
41. Librado P, Rozas J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009; 25: 1451–1452. https://doi.org/10.1093/bioinformatics/btp187 19346325
42. Perna NT, Kocher TD. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. Journal of Molecular Evolution. 1995; 41: 353–358. doi: 10.1007/bf00186547 7563121
43. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research. 1999; 27: 573–580. https://doi.org/10.1093/nar/27.2.573 9862982
44. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research. 2003; 31: 3406–3415. https://doi.org/10.1093/nar/gkg595 12824337
45. Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology. 2007; 56: 564–577. https://doi.org/10.1080/10635150701472164 17654362
46. Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods. 2012; 9: 772. https://doi.org/10.1038/nmeth.2109 22847109
47. Darriba D, Taboada GL, Doallo R, Posada D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics. 2011; 27: 1164–1165. https://doi.org/10.1093/bioinformatics/btr088 21335321
48. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30: 1312–1313. https://doi.org/10.1093/bioinformatics/btu033 24451623
49. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hӧhna S. MrBayes 3.2: efficient bayesian phylogenetic inference and model choice across a large model space. Systematic Biology. 2012; 61: 539–542. https://doi.org/10.1093/sysbio/sys029 22357727
50. Ohta T. The nearly neutral theory of molecular evolution. Annual Review of Ecology and Systematics. 1992; 23: 263–286. https://www.jstor.org/stable/2097289
51. Yang Z. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Molecular Biology and Evolution. 1998; 15: 568–573. https://doi.org/10.1093/oxfordjournals.molbev.a025957 9580986
52. Yang Z. PAML 4: a program package for phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution. 2007; 24: 1586–1591. https://doi.org/10.1093/molbev/msm088 17483113
53. Yang Z, Nielsen R, Goldman N, Pedersen AM. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics. 2000; 155: 431–449. 10790415
54. Nielsen R, Yang Z. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics. 1998; 148: 929–936. 9539414
55. Yang Z, Wong WS, Nielsen R. Bayes empirical bayes inference of amino acid sites under positive selection. Molecular Biology and Evolution. 2005; 22: 1107–1118. https://doi.org/10.1093/molbev/msi097 15689528
56. Xu X, Wu X, Yu Z. The mitogenome of Paphia euglypta (Bivalvia: Veneridae) and comparative mitogenomic analyses of three venerids. Genome. 2010; 53: 1041–1052. https://doi.org/10.1139/G10-096 21164537
57. Liao F, Wang L, Wu S, Li YP, Zhao L, Huang GM, et al. The complete mitochondrial genome of the fall webworm, Hyphantria cunea (Lepidoptera: Arctiidae). International Journal of Biological Sciences. 2010; 6: 172–186. doi: 10.7150/ijbs.6.172 20376208
58. Wang ZL, Chao L, Fang WY, Yu XP. The Complete Mitochondrial Genome of two Tetragnatha Spiders (Araneae: Tetragnathidae): Severe Truncation of tRNAs and Novel Gene Rearrangements in Araneae. International Journal of Biological Sciences. 2016; 12: 109–119. https://doi.org/10.7150/ijbs.12358 26722222
59. Ojala D, Montoya J, Attardi G. tRNA punctuation model of RNA processing in human mitochondria. Nature. 1981; 290: 470–474. doi: 10.1038/290470a0 7219536
60. Dreyer H, Steiner G. The complete sequences and gene organisation of the mitochondrial genome of the heterodont bivalves Acanthocardia tuberculata and Hiatella arctica– and the first record for a putative Atpase subunit 8 gene in marine bivalves. Frontiers in Zoology. 2006; 3: 13. https://dx.doi.org/10.1186/1742-9994-3-13 16948842
61. Salvato P, Simonato M, Battisti A, Negrisolo E. The complete mitochondrial genome of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae). BMC Genomics. 2008; 9: 331. https://dx.doi.org/10.1186/1471-2164-9-331 18627592
62. Yu H, Li Q. Complete mitochondrial DNA sequence of Crassostrea nippona: comparative and phylogenomic studies on seven commercial Crassostrea species. Molecular Biology Reports. 2012; 39: 999–1009. https://doi.org/10.1007/s11033-011-0825-z 21562763.
63. Sun SE, Sha ZL, Wang YR. Complete mitochondrial genome of the first deep-sea spongicolid shrimp Spongiocaris panglao (Decapoda: Stenopodidea): Novel gene arrangement and the phylogenetic position and origin of Stenopodidea. Gene. 2018; 676: 123–138. https://doi.org/10.1016/j.gene.2018.07.026 30021129
64. Brown WM. The mitochondrial genome of animals. In: Molecular Evolutionary Genetics. New York: Plenum Press; 1985.
65. Chai HN, Du YZ, Zhai BP. Characterization of the complete mitochondrial genome of Cnaphalocrocis medinalis and Chilo suppressalis (Lepidoptera: Pyralidae). International Journal of Biological Sciences. 2012; 8: 561–579. https://doi.org/10.1007/s10126-005-0004-0 22532789
66. Zhang B, Zhang YH, Wang X, Zhang HX, Lin Q. The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the seep-sea environment. Ecology and Evolution. 2017; 7: 4951–4962. https://doi.org/10.1002/ece3.3067 28690821
67. Plazzi F, Ribani A, Passamonti M. The complete mitochondrial genome of Solemya velum (Mollusca: Bivalvia) and its relationships with conchifera. BMC Genomics. 2013; 14: 409. https://doi.org/10.1186/1471-2164-14-409 23777315
68. Okimoto R, Macfarlane JL, Clary DO, Wolstenholme DR. The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics. 1992; 130: 471–498. 1551572
69. Ohtsuki T, Kawai G, Watanabe K. The minimal tRNA: unique structure of Ascaris suum mitochondrial tRNA(Ser)(UCU) having a short T arm and lacking the entire D arm. FEBS Letter. 2002; 514: 37–43. doi: 10.1016/s0014-5793(02)02328-1 11904178
70. Chimnaronk S, Gravers Jeppesen M, Suzuki T, Nyborg J, Watanabe K. Dualmode recognition of noncanonical tRNAs(Ser) by seryl-tRNA synthetase in mammalian mitochondria. Embo Journal. 2005; 24: 3369–3379. https://doi.org/10.1038/sj.emboj.7600811 16163389
71. Lavrov DV, Brown WM, Boore JL. A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus. Proceedings of the National Academy of Sciences of the United States of America. 2000; 97: 13738–13742. https://doi.org/10.1073/pnas.250402997 11095730
72. Miller AD, Murphy NP, Burridge CP, Austin CM. Complete mitochondrial DNA sequences of the decapod crustaceans Pseudocarcinus gigas (Menippidae) and Macrobrachium rosenbergii (Palaemonidae). Marine Biotechnology. 2005; 7: 339–349. https://doi.org/10.1007/s10126-004-4077-y 15902543
73. Aquadro CF, Greenberg BD. Human mitochondrial DNA variation and evolution: Analysis of nucleotide sequences from seven individuals. Genetics. 1983; 103: 287–312. 6299878
74. Marshall HD, Baker AJ. Structural conservation and variation in the mitochondrial control region of fringilline finches (Fringilla spp.) and the greenfinch (Carduelis chloris). Molecular Biology and Evolution. 1997; 14: 173–184. https://doi.org/10.1093/oxfordjournals.molbev.a025750 9029795
75. Flot JF, Tillier S. The mitogenome of Pocillopora (Cnidaria: Scleractinia) contains two variable regions: The putative D-loop and a novel ORF of unknown function. Gene. 2007; 401: 80–87. https://doi.org/10.1016/j.gene.2007.07.006 17716831
76. Stanton DJ, Daehler LL, Moritz CC, Brown WM. Sequences with the potential to form stem-and-loop structures are associated with coding-region duplications in animal mitochondrial DNA. Genetics. 1994; 137: 233–241. 8056313
77. Fernández-Silva P, Enriquez JA, Montoya J. Replication and transcription of mammalian mitochondrial DNA. Experimental Physiology. 2003; 88: 41–56. 12525854
78. Serb JM, Lydeard C. Complete mtDNA sequence of the north American freshwater mussel, Lampsilis ornata (Unionidae): an examination of the evolution and phylogenetic utility of mitochondrial genome organization in Bivalvia (Mollusca). Molecular Biology and Evolution. 2003; 20: 1854–1866. https://doi.org/10.1093/molbev/msg218 12949150
79. Ren J, Shen X, Jiang F, Liu B. The mitochondrial genomes of two scallops, Argopecten irradians and Chlamys farreri (Mollusca: Bivalvia): the most highly rearranged gene order in the family Pectinidae. Journal of Molecular Evolution. 2009; 70: 57–68. https://doi.org/10.1007/s00239-009-9308-4 20013337
80. Milbury CA, Gaffney PM. Complete mitochondrial DNA sequence of the eastern oyster Crassostrea virginica. Marine Biotechnology. 2005; 7: 697–712. https://doi.org/10.1007/s10126-005-0004-0 16132463
81. Kumazawa Y, Miura S, Yamada C, Hashiguchi Y. Gene rearrangements in gekkonid mitochondrial genomes with shuffling, loss, and reassignment of tRNA genes. BMC Genomics. 2014; 15: 930. https://doi.org/10.1186/1471-2164-15-930 25344428
82. Sahyoun AH, Hӧlzer M, Jühling F, Hӧlzer zu Siederdissen C, Al-Arab M, Tout K, et al. Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes. Nucleic Acids Research. 2015; 43: 8044–8056. https://doi.org/10.1093/nar/gkv746 26227972
83. Boore JL, Brown WM. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Current Opinion in Genetics and Development. 1998; 8: 668–674. 9914213
84. Perseke M, Bernhard D, Fritzsch G, Brümmer F, Stadler PF, Schlegel M. Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: insights in phylogenetic relationships of Echinodermata. Molecular Phylogenet Evolution. 2010; 56:201–211. https://doi.org/10.1016/j.ympev.2010.01.035 20152912
85. Krylova EM, Sahling H. Recent bivalve molluscs of the genus Calyptogena (Vesicomyidae). Journal of Molluscan Studies. 2006; 72: 359–395. https://doi.org/10.1093/mollus/eyl022
86. Decker C, Olu K, Cunha RL, Arnaud-Haond S. Phylogeny and diversifcation patterns among vesicomyid bivalves. PLoS ONE. 2012; 7: e33359. https://doi.org/10.1371/journal.pone.0033359 22511920
87. Johnson SB, Krylova EM, Audzijonyte A, Sahling H, Vrijenhoek RC. Phylogeny and origins of chemosynthetic vesicomyid clams. Systematics and Biodiversity. 2017; 15: 346–360. https://doi.org/10.1080/14772000.2016.1252438
88. Shen YY, Liang L, Zhu ZH, Zhou WP, Irwin DM, Zhang YP. Adaptive evolution of energy metabolism genes and the origin of flight in bats. Proceedings of the National Academy of Sciences of the United States of America. 2010; 107: 8666–8671. https://doi.org/10.1073/pnas.0912613107 20421465
89. Tomasco IH, Lessa EP. The evolution of mitochondrial genomes in subterranean caviomorph rodents: adaptation against a background of purifying selection. Molecular Phylogenetics and Evolution. 2011; 61: 64–70. https://doi.org/10.1016/j.ympev.2011.06.014 21723951
90. Plazzi F, Puccio G, Passamonti M. Burrowers from the past: mitochondrial signatures of Ordovician bivalve infaunalization. Genome Biology and Evolution. 2017; 9: 956–967. https://doi.org/10.1093/gbe/evx051 28338965
91. da Fonseca RR, Johnson WE, O’Brien SJ, Ramos MJ, Antunes A. The adaptive evolution of the mammalian mitochondrial genome. BMC Genomics. 2008; 9: 119. https://doi.org/10.1186/1471-2164-9-119 18318906
92. Yang YX, Xu SX, Xu JX, Guo Y, Yang G. Adaptive evolution of mitochondrial energy metabolism genes associated with increased energy demand in flying insects. Plos ONE. 2014; 9: e99120. https://doi.org/10.1371/journal.pone.0099120 24918926
93. Das J. The role of mitochondrial respiration in physiological and evolutionary adaptation. BioEssays. 2006; 28: 890–901. https://doi.org/10.1002/bies.20463 16937356
94. Zhang J, Nielsen R, Yang Z. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Molecular Biology and Evolution. 2005; 22: 247 2–2479. https://doi.org/10.1093/molbev/msi237 16107592
95. Trumpower BL. The protonmotive Q cycle. Energy transduction by coupling of proton translocation to electron transfer by the cytochrome bc1 complex. Journal of Biological Chemistry. 1990; 265:11409–11412. 2164001
96. Silva G, Lima FP, Martel P, Caastilho R. Thermal adaptation and clinal mitochondrial DNA variation of European anchovy. Proceedings Biological Sciences. 2014; 281: 1792. https://doi.org/10.1098/rspb.2014.1093 25143035
97. Luo YJ, Gao WX, Gao YQ, Tang S, Huang QY, Tan XL, et al. Mitochondrial genome analysis of Ochotona curzoniae and implication of cytochrome c oxidase in hypoxic adaptation. Mitochondrion. 2008; 8: 352–357. https://doi.org/10.1016/j.mito.2008.07.005 18722554
98. Mahalingam S, McClelland GB, Scott GR. Evolved changes in the intracellular distribution and physiology of muscle mitochondria in high-altitude native deer mice. The Journal of Physiology. 2017; 595: 4785–4801. https://doi.org/10.1113/JP274130 28418073
99. Chandel NS, Maltepe E, Goldwasser E, Mathieu CE, Simon MC, Schumacker PT. Mitochondrial reactive oxygen species trigger hypoxia-induced transcription. Proceedings of the National Academy of Sciences of the United States of America. 1998; 95: 11715–11720. https://doi.org/10.1073/pnas.95.20.11715 9751731
100. Dirmeier R, O’Brien KM, Engle M, Dodd A, Spears E, Poyton RO. Exposure of yeast cells to anoxia induces transient oxidative stress. Implications for the induction of hypoxic genes. Journal of Biological Chemistry. 2002; 277: 34773–34784. https://doi.org/10.1074/jbc.M203902200 12089150
101. Levin LA. Ecology of cold seep sediments: interactions of fauna with flow, chemistry and microbes. Oceanography and Marine Biology. 2005; 43:1–46.
102. Mu WD, Liu J, Zhang HB. Complete mitochondrial genome of Benthodytes marianensis (Holothuroidea: Elasipodida: Psychropotidae): Insight into deep sea adaptation in the sea cucumber. PLoS ONE. 2018; 13: e0208051. https://doi.org/10.1371/journal.pone.0208051 30500836
103. Mu WD, Liu J, Zhang HB. The first complete mitochondrial genome of the Mariana Trench Freyastera benthophila (Asteroidea: Brisingida: Brisingidae) allows insights into the deep-sea adaptive evolution of Brisingida. Ecology and Evolution. 2018; 8: 10673–10686. https://doi.org/10.1002/ece3.4427 30519397
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