The first complete mitogenome of <italic style="font-style: italic">Acharax</italic> sp. (Protobranchia, Solemyida, Solemyidae): comparisons with other Solemyidae bivalves and deep-sea adaptive characteristics

Mei YANG; Jixing SUI; Xinzheng LI

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The first complete mitogenome of Acharax sp. (Protobranchia, Solemyida, Solemyidae): comparisons with other Solemyidae bivalves and deep-sea adaptive characteristics

Biology | Updated：2024-10-12

- The first complete mitogenome of Acharax sp. (Protobranchia, Solemyida, Solemyidae): comparisons with other Solemyidae bivalves and deep-sea adaptive characteristics
- The first complete mitogenome of Acharax sp. (Protobranchia, Solemyida, Solemyidae): comparisons with other Solemyidae bivalves and deep-sea adaptive characteristics
- 海洋湖沼学报(英文) 2023年41卷第6期页码：2374-2390
- Affiliations：
  
  1.Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
  2.Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
  3.University of Chinese Academy of Sciences, Beijing 100049, China
  4.Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Author bio：
  
  lixzh@qdio.ac.cn
- Funds：
  
  the Senior User Project of R/V Kexue(KEXUE2020GZ01);the National Natural Science Foundation of China(42176114)
- DOI：
  中图分类号：
- 收稿：2022-05-07，
  
  录用：2022-07-08，
  
  网络首发：2022-10-17，
  
  纸质出版：2023-11-01
- Accepted：
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The first complete mitogenome of Acharax sp. (Protobranchia, Solemyida, Solemyidae): comparisons with other Solemyidae bivalves and deep-sea adaptive characteristics[J]. 海洋湖沼学报(英文), 2023,41(6):2374-2390.

YANG Mei,SUI Jixing,LI Xinzheng.The first complete mitogenome of Acharax sp. (Protobranchia, Solemyida, Solemyidae): comparisons with other Solemyidae bivalves and deep-sea adaptive characteristics[J].Journal of Oceanology and Limnology,2023,41(06):2374-2390.
The first complete mitogenome of Acharax sp. (Protobranchia, Solemyida, Solemyidae): comparisons with other Solemyidae bivalves and deep-sea adaptive characteristics[J]. 海洋湖沼学报(英文), 2023,41(6):2374-2390. DOI：

YANG Mei,SUI Jixing,LI Xinzheng.The first complete mitogenome of Acharax sp. (Protobranchia, Solemyida, Solemyidae): comparisons with other Solemyidae bivalves and deep-sea adaptive characteristics[J].Journal of Oceanology and Limnology,2023,41(06):2374-2390. DOI：

摘要

Abstract

Solemyidae is an ancient group of protobranch bivalves

and most solemyids are symbiotic with chemoautotrophic and gill-hosted bacteria

enabling them to survive in unusual habitats such as deep-sea chemosynthetic environments. However

evolution of the mitogenomes in this family and their phylogenetic relationships remain poorly understood. The complete mitogenome of

Acharax

sp. was determined and compared with other available mitogenomes of solemyids. The mitogenome of

Acharax

sp. is 18 970 bp in length and consists of 13 protein-coding genes

2 ribosomal RNA genes

and 22 transfer RNA genes. The gene arrangement was identical to those of other sequenced solemyids. For the present five mitogenomes of Solemyidae species

all protein-coding genes were initiated with the typical ATD (ATA

ATG

and ATT) codon and terminated with the TAA/TAG codon. Furthermore

the incomplete termination codon was detected. The Ka/Ks ratio analyses indicated that 13 protein-coding genes of five Solemyidae mitogenomes suffered strong purifying selection. Compared to 45 existing shallow water equivalents

the 18 available mitogenomes from the deep-sea

including the

Acharax

sp. in this study

show significantly more nonpolar amino acids in the 13 protein-coding genes

which indicates the adaptation to the deep-sea environment. The phylogenetic tree based on 48 Bivalvia complete mitogenomes provided further information to support the scientific classification of protobranchs. The relationships among Solemyidae were assessed based on 2 mitochondrial (

16S

rRNA

and

COX1

) and 3 nuclear (

18S

rRNA

28S

rRNA

and

histone

) gene sequences from 17 in-group species. The two genera

Acharax

and

Solemya

formed a monophyletic clade each

and

Acharax

sp. clustered with previously reported

Acharax

bivalves with high support values.

关键词

Keywords

references

Anisimova M , Gil M , Dufayard J F et al . 2011 . Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes . Systematic Biology , 60 ( 5 ): 685 - 699 , https://doi.org/10.1093/sysbio/syr041 https://doi.org/10.1093/sysbio/syr041 .

Barrientos A , Barros M H , Valnot I et al . 2002 . Cytochrome oxidase in health and disease . Gene , 286 ( 1 ): 53 - 63 , https://doi.org/10.1016/S0378-1119(01)00803-4 https://doi.org/10.1016/S0378-1119(01)00803-4 .

Bernt M , Donath A , Jühling F et al . 2013 . MITOS: improved de novo metazoan mitochondrial genome annotation . Molecular Phylogenetics and Evolution , 69 ( 2 ): 313 - 319 , https://doi.org/10.1016/j.ympev.2012.08.023 https://doi.org/10.1016/j.ympev.2012.08.023 .

Bernt M , Merkle D , Ramsch K et al . 2007 . CREx: inferring genomic rearrangements based on common intervals . Bioinformatics , 23 ( 21 ): 2957 - 2958 , https://doi.org/10.1093/bioinformatics/btm468 https://doi.org/10.1093/bioinformatics/btm468 .

Bieler R , Mikkelsen P M , Giribet G . 2013 . Bivalvia-A discussion of known unknowns . American Malacological Bulletin , 31 ( 1 ): 123 - 133 , https://doi.org/10.4003/006.031.0105 https://doi.org/10.4003/006.031.0105 .

Boore J L . 1999 . Animal mitochondrial genomes . Nucleic Acids Research , 27 ( 8 ): 1767 - 1780 , https://doi.‍org/10.1093/nar/27.8.1767 https://doi.‍org/10.1093/nar/27.8.1767 . https://do 10.1093/nar/27.8.1767 http://dx.doi.org/10.1093/nar/27.8.1767

Chan P P , Lowe T M . 2019 . tRNAscan-SE: searching for tRNA genes in genomic sequences . In: Kollmar M ed . Gene Prediction : Methods and Protocols. Humana, New York. p . 1 - 14 , https://doi.‍org/10.1007/978-1-4939-9173-0_1 https://doi.‍org/10.1007/978-1-4939-9173-0_1 . https://do 10.1007/978-1-4939-9173-0_1 http://dx.doi.org/10.1007/978-1-4939-9173-0_1

Conway N M , Howes B L , McDowell Capuzzo J E et al . 1992 . Characterization and site description of Solemya borealis (Bivalvia; Solemyidae), another bivalve-bacteria symbiosis . Marine Biology , 112 ( 4 ): 601 - 613 , https://doi.org/10.1007/BF00346178 https://doi.org/10.1007/BF00346178 .

Cunha R L , Grande C , Zardoya R . 2009 . Neogastropod phylogenetic relationships based on entire mitochondrial genomes . BMC Evolutionary Biology , 9 : 210 , https://doi.org/10.1186/1471-2148-9-210 https://doi.org/10.1186/1471-2148-9-210 .

da Fonseca R R , Johnson W E , O'Brien S J et al . 2008 . The adaptive evolution of the mammalian mitochondrial genome . BMC Genomics , 9 : 119 , https://doi.org/10.1186/1471-2164-9-119 https://doi.org/10.1186/1471-2164-9-119 .

Dreyer H , Steiner G . 2006 . The complete sequences and gene organisation of the mitochondrial genomes 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 , 3 : 13 , https://doi.org/10.1186/1742-9994-3-13 https://doi.org/10.1186/1742-9994-3-13 .

Fisher C R , Childress J J . 1986 . Translocation of fixed carbon from symbiotic bacteria to host tissues in the gutless bivalve Solemya reidi . Marine Biology , 93 ( 1 ): 59 - 68 , https://doi.org/10.1007/BF00428655 https://doi.org/10.1007/BF00428655 .

Fujiwara Y . 2003 . Symbiotic adaptation for deeper habitats in chemosynthetic environments . Journal of Geography (Chigaku Zasshi) , 112 ( 2 ): 302 - 308 , https://doi.org/10.5026/jgeography.112.2_302 https://doi.org/10.5026/jgeography.112.2_302 .

Fukasawa Y , Matsumoto H , Beppu S et al . 2017 . Molecular phylogenetic analysis of chemosymbiotic Solemyidae and Thyasiridae . Open Journal of Marine Science , 7 ( 1 ): 124 - 141 , https://doi.org/10.4236/ojms.2017.71010 https://doi.org/10.4236/ojms.2017.71010 .

Guerra D , Bouvet K , Breton S . 2018 . Mitochondrial gene order evolution in Mollusca: inference of the ancestral state from the mtDNA of Chaetopleura apiculata (polyplacophora, chaetopleuridae) . Molecular Phylogenetics and Evolution , 120 : 233 - 239 , https://doi.org/10.1016/j.ympev.2017.12.013 https://doi.org/10.1016/j.ympev.2017.12.013 .

Hao J S , Sun Q Q , Zhao H B et al . 2012 . The complete mitochondrial genome of Ctenoptilum vasava (Lepidoptera: Hesperiidae: Pyrginae) and its phylogenetic implication . Comparative and Functional Genomics , 2012 : 328049 , https://doi.org/10.1155/2012/328049 https://doi.org/10.1155/2012/328049 .

Hassanin A , Ropiquet A , Couloux A et al . 2009 . Evolution of the mitochondrial genome in mammals living at high altitude: new insights from a study of the tribe Caprini (Bovidae, Antilopinae) . Journal of Molecular Evolution , 68 ( 4 ): 293 - 310 , https://doi.org/10.1007/s00239-009-9208-7 https://doi.org/10.1007/s00239-009-9208-7 .

Hoang D T , Chernomor O , von Haeseler A et al . 2018 . UFBoot2: improving the ultrafast bootstrap approximation . Molecular Biology and Evolution , 35 ( 2 ): 518 - 522 , https://doi.org/10.1093/molbev/msx281 https://doi.org/10.1093/molbev/msx281 .

Kamenev G M . 2009 . North Pacific species of the genus Solemya Lamarck, 1818 (Bivalvia: Solemyidae) , with notes on Acharax johnsoni (Dall , 1891 ). Malacologia, 51 ( 2 ): 233 - 261 , https://doi.org/10.4002/040.051.0202 https://doi.org/10.4002/040.051.0202 .

Katoh K , Rozewicki J , Yamada K D . 2019 . MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization . Briefings in Bioinformatics , 20 ( 4 ): 1160 - 1166 , https://doi.org/10.1093/bib/bbx108 https://doi.org/10.1093/bib/bbx108 .

Kou Q , Xu P , Poore G C B et al . 2020 . A new species of the deep-sea sponge-associated genus Eiconaxius (Crustacea: Decapoda: Axiidae), with new insights into the distribution, speciation, and mitogenomic phylogeny of axiidean shrimps . Frontiers in Marine Science , 7 : 469 , https://doi.org/10.3389/fmars.2020.00469 https://doi.org/10.3389/fmars.2020.00469 .

Kück P , Meid S A , Groß C et al . 2014 . AliGROOVE-visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support . BMC Bioinformatics , 15 ( 1 ): 294 , https://doi.org/10.1186/1471-2105-15-294 https://doi.org/10.1186/1471-2105-15-294 .

Kumar S , Stecher G , Tamura K . 2016 . MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets . Molecular Biology and Evolution , 33 ( 7 ): 1870 - 1874 , https://doi.org/10.1093/molbev/msw054 https://doi.org/10.1093/molbev/msw054 .

Lanfear R , Frandsen P B , Wright A M et al . 2016 . PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses . Molecular Biology and Evolution , 34 : 772 - 773 , https://doi.org/10.1093/molbev/msw260 https://doi.org/10.1093/molbev/msw260 .

Lavrov D V , Brown W M , Boore J L . 2000 . 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 , 97 ( 25 ): 13738 - 13742 , https://doi.org/10.1073/pnas.250402997 https://doi.org/10.1073/pnas.250402997 .

Lemer S , Bieler R , Giribet G . 2019 . Resolving the relationships of clams and cockles: dense transcriptome sampling drastically improves the bivalve tree of life . Proceedings of the Royal Society B: Biological Sciences , 286 ( 1896 ): 20182684 , https://doi.org/10.1098/rspb.2018.2684 https://doi.org/10.1098/rspb.2018.2684 .

Letunic I , Bork P . 2007 . Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation . Bioinformatics , 23 ( 1 ): 127 - 128 , https://doi.org/10.1093/bioinformatics/btl529 https://doi.org/10.1093/bioinformatics/btl529 .

Li J , Zhao Y Q , Lin R R et al . 2019a . Mitochondrial genome characteristics of Somena scintillans (Lepidoptera: Erebidae) and comparation with other Noctuoidea insects . Genomics , 111 ( 6 ): 1239 - 1248 , https://doi.org/10.1016/j.ygeno.2018.08.003 https://doi.org/10.1016/j.ygeno.2018.08.003 .

Li J Y , Song Z L , Yan G Y et al . 2019b . The complete mitochondrial genome of the largest amphipod, Alicella gigantea : insight into its phylogenetic relationships and deep sea adaptive characters . International Journal of Biological Macromolecules , 141 : 570 - 577 , https://doi.org/10.1016/j.ijbiomac.2019.09.050 https://doi.org/10.1016/j.ijbiomac.2019.09.050 .

Liu H Y , Yang Y , Sun S E et al . 2020 . Mitogenomic phylogeny of the Naticidae (Gastropoda: Littorinimorpha) reveals monophyly of the Polinicinae . Zoologica Scripta , 49 ( 3 ): 295 - 306 , https://doi.‍org/10.1111/zsc.12412 https://doi.‍org/10.1111/zsc.12412 . https://do 10.1111/zsc.12412 http://dx.doi.org/10.1111/zsc.12412

Lohse M , Drechsel O , Bock R . 2007 . OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes . Current Genetics , 52 ( 5 ): 267 - 274 , https://doi.org/10.1007/s00294-007-0161-y https://doi.org/10.1007/s00294-007-0161-y .

Luo Y J , Gao W X , Gao Y Q et al . 2008 . Mitochondrial genome analysis of Ochotona curzoniae and implication of cytochrome c oxidase in hypoxic adaptation . Mitochondrion , 8 ( 5-6 ): 352 - 357 , https://doi.org/10.1016/j.mito.2008.07.005 https://doi.org/10.1016/j.mito.2008.07.005 .

Lü Z M , Zhu K H , Jiang H et al . 2019 . Complete mitochondrial genome of Ophichthus brevicaudatus reveals novel gene order and phylogenetic relationships of Anguilliformes . International Journal of Biological Macromolecules , 135 : 609 - 618 , https://doi.org/10.1016/j.ijbiomac.2019.05.139 https://doi.org/10.1016/j.ijbiomac.2019.05.139 .

Metpally R P R , Reddy B V B . 2009 . Comparative proteome analysis of psychrophilic versus mesophilic bacterial species: insights into the molecular basis of cold adaptation of proteins . BMC Genomics , 10 : 11 , https://doi.org/10.1186/1471-2164-10-11 https://doi.org/10.1186/1471-2164-10-11 .

Mu W D , Liu J , Zhang H B . 2018 . 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 , 8 ( 22 ): 10673 - 10686 , https://doi.org/10.1002/ece3.4427 https://doi.org/10.1002/ece3.4427 .

Neulinger S C , Sahling H , Süling J et al . 2006 . Presence of two phylogenetically distinct groups in the deep-sea mussel Acharax (Mollusca: Bivalvia: Solemyidae) . Marine Ecology Progress Series , 312 : 161 - 168 , https://doi.org/10.3354/meps312161 https://doi.org/10.3354/meps312161 .

Nguyen L T , Schmidt H A , von Haeseler A et al . 2015 . IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies . Molecular Biology and Evolution , 32 ( 1 ): 268 - 274 , https://doi.org/10.1093/molbev/msu300 https://doi.org/10.1093/molbev/msu300 .

Oliver G , Rodrigues C F , Cunha M R . 2011 . Chemosymbiotic bivalves from the mud volcanoes of the Gulf of Cadiz, NE Atlantic, with descriptions of new species of Solemyidae, Lucinidae and Vesicomyidae . ZooKeys , 113 : 1 - 38 , https://doi.org/10.3897/zookeys.113.1402 https://doi.org/10.3897/zookeys.113.1402 .

Perna N T , Kocher T D . 1995 . Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes . Journal of Molecular Evolution , 41 ( 3 ): 353 - 358 , https://doi.org/10.1007/BF00186547 https://doi.org/10.1007/BF00186547 .

Plazzi F , Ribani A , Passamonti M . 2013 . The complete mitochondrial genome of Solemya velum (Mollusca: Bivalvia) and its relationships with Conchifera . BMC Genomics 14 : 409 , https://doi.org/10.1186/1471-2164-14-409 https://doi.org/10.1186/1471-2164-14-409 .

Pojeta J J . 1988 . The origin and Paleozoic diversification of Solemyoid Pelecypods . New Mexico Bureau of Mines and Mineral Resources, Memoir , 44 : 201 - 271 .

Rahuman S , Jeena N S , Asokan P K et al . 2020 . Mitogenomic architecture of the multivalent endemic black clam ( Villorita cyprinoides ) and its phylogenetic implications . Scientific Reports , 10 ( 1 ): 15438 , https://doi.org/10.1038/s41598-020-72194-1 https://doi.org/10.1038/s41598-020-72194-1 .

Rex M A . 1981 . Community structure in the deep-sea Benthos . Annual Review of Ecology and Systematics , 12 : 331 - 353 . https://do 10.1146/annurev.es.12.110181.001555 http://dx.doi.org/10.1146/annurev.es.12.110181.001555

Rodrigues C F , Webster G , Cunha M R et al . 2010 . Chemosynthetic bacteria found in bivalve species from mud volcanoes of the Gulf of Cadiz . FEMS Microbiology Ecology , 73 ( 3 ): 486 - 499 , https://doi.‍org/10.1111/j.1574-6941.2010.00913.x https://doi.‍org/10.1111/j.1574-6941.2010.00913.x . https://do 10.1111/j.1574-6941.2010.00913.x http://dx.doi.org/10.1111/j.1574-6941.2010.00913.x

Ronquist F , Teslenko M , van der Mark P et al . 2012 . MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space . Systematic Biology , 61 ( 3 ): 539 - 542 , https://doi.‍org/10.1093/sysbio/sys029 https://doi.‍org/10.1093/sysbio/sys029 . https://do 10.1093/sysbio/sys029 http://dx.doi.org/10.1093/sysbio/sys029

Rozas J , Ferrer-Mata A , Sánchez-DelBarrio J C et al . 2017 . DnaSP 6: DNA sequence polymorphism analysis of large data sets . Molecular Biology and Evolution , 34 ( 12 ): 3299 - 3302 , https://doi.org/10.1093/molbev/msx248 https://doi.org/10.1093/molbev/msx248 .

Russell S L , McCartney E , Cavanaugh C M . 2018 . Transmission strategies in a chemosynthetic symbiosis: detection and quantification of symbionts in host tissues and their environment . Proceedings of the Royal Society B: Biological Sciences , 285 ( 1890 ): 20182157 , https://doi.org/10.1098/rspb.2018.2157 https://doi.org/10.1098/rspb.2018.2157 .

Saether K P , Sha J G , Little C T S et al . 2016 . New records and a new species of bivalve (Mollusca: Bivalvia) from Miocene hydrocarbon seep deposits, North Island, New Zealand . Zootaxa , 4154 ( 1 ): 1 - 26 , https://doi.org/10.11646/zootaxa.4154.1.1 https://doi.org/10.11646/zootaxa.4154.1.1 .

Salvato P , Simonato M , Battisti A et al . 2008 . The complete mitochondrial genome of the bag-shelter m oth Ochrogaster lunifer (Lepidoptera, Notodontidae) . BMC Genomics , 9 : 331 , https://doi.org/10.1186/1471-2164-9-33 https://doi.org/10.1186/1471-2164-9-33 .

Sato K , Kano Y , Setiamarga D H E et al . 2020 . Molecular phylogeny of protobranch bivalves and systematic implications of their shell microstructure . Zoologica Scripta , 49 ( 4 ): 458 - 472 , https://doi.org/10.1111/zsc.12419 https://doi.org/10.1111/zsc.12419 .

Sato K , Nakashima R , Majima R et al . 2013 . Shell microstructures of five recent solemyids from Japan (Mollusca: Bivalvia) . Paleontological Research , 17 ( 1 ): 69 - 90 , https://doi.org/10.2517/1342-8144-17.1.69 https://doi.org/10.2517/1342-8144-17.1.69 .

Satoh T P , Miya M , Mabuchi K et al . 2016 . Structure and variation of the mitochondrial genome of fishes . BMC Genomics , 17 : 719 , https://doi.org/10.1186/s12864-016-3054-y https://doi.org/10.1186/s12864-016-3054-y .

Seike K , Jenkins R G , Watanabe H et al . 2012 . Novel use of burrow casting as a research tool in deep-sea ecology . Biology Letters , 8 ( 4 ): 648 - 651 , https://doi.org/10.1098/rsbl.2011.1111 https://doi.org/10.1098/rsbl.2011.1111 .

Sharma P P , Zardus J D , Boyle E E et al . 2013 . Into the Deep: a phylogenetic approach to the bivalve subclass Protobranchia . Molecular Phylogenetics and Evolution , 69 ( 1 ): 188 - 204 , https://doi.org/10.1016/j.ympev.2013.05.018 https://doi.org/10.1016/j.ympev.2013.05.018 .

Sun S E , Sha Z L , Wang Y R . 2018 . 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 , 676 : 123 - 138 , https://doi.org/10.1016/j.gene.2018.07.026 https://doi.org/10.1016/j.gene.2018.07.026 .

Talavera G , Castresana J . 2007 . Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments . Systematic Biology , 56 ( 4 ): 564 - 577 , https://doi.‍org/10.1080/10635150701472164 https://doi.‍org/10.1080/10635150701472164 . https://do 10.1080/10635150701472164 http://dx.doi.org/10.1080/10635150701472164

Taylor J D , Glover E A , Williams S T . 2008 . Ancient chemosynthetic bivalves: systematics of Solemyidae from eastern and southern Australia (Mollusca: Bivalvia) . Memoirs Queensland Museum-Nature , 54 ( 1 ): 75 - 104 .

Tomasco I H , Lessa E P . 2011 . The evolution of mitochondrial genomes in subterranean caviomorph rodents: adaptation against a background of purifying selection . Molecular Phylogenetics and Evolution , 61 ( 1 ): 64 - 70 , https://doi.org/10.1016/j.ympev.2011.06.014 https://doi.org/10.1016/j.ympev.2011.06.014 .

Uribe J E , Zardoya R , Puillandre N . 2018 . Phylogenetic relationships of the conoidean snails (Gastropoda: Caenogastropoda) based on mitochondrial genomes . Molecular Phylogenetics and Evolution , 127 : 898 - 906 , https://doi.org/10.1016/j.ympev.2018.06.037 https://doi.org/10.1016/j.ympev.2018.06.037 .

Walton K . 2015 . New Zealand living Solemyidae (Bivalvia: Protobranchia) . Molluscan Research , 35 ( 4 ): 246 - 261 , https://doi.org/10.1080/13235818.2015.1053168 https://doi.org/10.1080/13235818.2015.1053168 .

Wang K , Shen Y J , Yang Y Z et al . 2019 . Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation . Nature Ecology & Evolution , 3 ( 5 ): 823 - 833 , https://doi.‍org/10.1038/s41559-019-0864-8 https://doi.‍org/10.1038/s41559-019-0864-8 . https://do 10.1038/s41559-019-0864-8 http://dx.doi.org/10.1038/s41559-019-0864-8

Wang Y , Shen Y J , Feng C G et al . 2016a . Mitogenomic perspectives on the origin of Tibetan loaches and their adaptation to high altitude . Scientific Reports , 6 : 29690 , https://doi.org/10.1038/srep29690 https://doi.org/10.1038/srep29690 .

Wang Z L , Li C , Fang W Y et al . 2016b . 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 , 12 ( 1 ): 109 - 119 , https://doi.org/10.7150/ijbs.12358 https://doi.org/10.7150/ijbs.12358 .

Wei S J , Shi M , Chen X X et al . 2010 . New views on strand asymmetry in insect mitochondrial genomes . PLoS One , 5 ( 9 ): e12708 , https://doi.org/10.1371/journal.pone.0012708 https://doi.org/10.1371/journal.pone.0012708 .

Xu F S . 1999 . Fauna Sinica: Phylum Mollusca: Class Bivalvia: Subclass Protobranchia and Anomalodesmata. Science Press, Beijing, China . p. 1 - 244 . (in Chinese)

Xu S Q , Luosang J , Hua S et al . 2007 . High altitude adaptation and phylogenetic analysis of Tibetan horse based on the mitochondrial genome . Journal of Genetics and Genomics , 34 ( 8 ): 720 - 729 , https://doi.‍org/10.1016/S1673-8527(07)60081-2 https://doi.‍org/10.1016/S1673-8527(07)60081-2 . https://do 10.1016/s1673-8527(07)60081-2 http://dx.doi.org/10.1016/s1673-8527(07)60081-2

Xu S Q , Yang Y Z , Zhou J et al . 2005 . A mitochondrial genome sequence of the Tibetan antelope ( Pantholops hodgsonii ) . Genomics, Proteomics & Bioinformatics , 3 ( 1 ): 5 - 17 , https://doi.org/10.1016/S1672-0229(05)03003-2 https://doi.org/10.1016/S1672-0229(05)03003-2 .

Yang L L , Tang S K , Huang Y et al . 2015 . Low temperature adaptation is not the opposite process of high temperature adaptation in terms of changes in amino acid composition . Genome Biology and Evolution , 7 ( 12 ): 3426 - 3433 , https://doi.org/10.1093/gbe/evv232 https://doi.org/10.1093/gbe/evv232 .

Yang M , Dong D , Li X Z . 2021 . The complete mitogenome of Phymorhynchus sp. (Neogastropoda, Conoidea, Raphitomidae) provides insights into the deep-sea adaptive evolution of Conoidea . Ecology and Evolution , 11 ( 12 ): 7518 - 7531 , https://doi.org/10.1002/ece3.7582 https://doi.org/10.1002/ece3.7582 .

Yang M , Gong L , Sui J X et al . 2019 . The complete mitochondrial genome of Calyptogena marissinica (Heterodonta: Venero ida: Vesicomyidae): insight into the deep-sea adaptive evolution of vesicomyids . PLoS One , 14 ( 9 ): e0217952 , https://doi.org/10.1371/journal.pone.0217952 https://doi.org/10.1371/journal.pone.0217952 .

Yang Z H , Bielawski J P . 2000 . Statistical methods for detecting molecular adaptation . Trends in Ecology & Evolution , 15 ( 12 ): 496 - 503 , https://doi.org/10.1016/S0169-5347(00)01994-7 https://doi.org/10.1016/S0169-5347(00)01994-7 .

Yu L , Wang X P , Ting N et al . 2011 . Mitogenomic analysis of Chinese snub-nosed monkeys: evidence of positive selection in NADH dehydrogenase genes in high-altitude adaptation . Mitochondrion , 11 ( 3 ): 497 - 503 , https://doi.org/10.1016/j.mito.2011.01.004 https://doi.org/10.1016/j.mito.2011.01.004 .

Zardus J D . 2002 . Protobranch bivalves . Advances in Marine Biology , 42 : 1 - 65 , https://doi.org/10.1016/S0065-2881(02)42012-3 https://doi.org/10.1016/S0065-2881(02)42012-3 .

Zhang B , Wu Y Y , Wang X et al . 2020a . Comparative analysis of mitochondrial genome of a deep-sea crab Chaceon granulates reveals positive selection and novel genetic features . Journal of Oceanology and Limnology , 38 ( 2 ): 427 - 437 , https://doi.org/10.1007/s00343-019-8364-x https://doi.org/10.1007/s00343-019-8364-x .

Zhang B , Zhang Y H , Wang X et al . 2017a . The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep-sea environment . Ecology and Evolution , 7 ( 13 ): 4951 - 4962 , https://doi.org/10.1002/ece3.3067 https://doi.org/10.1002/ece3.3067 .

Zhang D , Gao F L , Jakovlić I et al . 2020b . PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies . Molecular Ecology Resources , 20 ( 1 ): 348 - 355 , https://doi.org/10.1111/1755-0998.13096 https://doi.org/10.1111/1755-0998.13096 .

Zhang K , Sun J , Xu T et al . 2021 . Phylogenetic relationships and adaptation in deep-sea mussels: insights from mitochondrial genomes . International Journal of Molecular Sciences , 22 ( 4 ): 1900 , https://doi.org/10.3390/ijms22041900 https://doi.org/10.3390/ijms22041900 .

Zhang Y J , Sun J , Chen C et al . 2017b . Adaptation and evolution of deep-sea scale worms (Annelida: Polynoidae): insights from transcriptome comparison with a shallow-water species . Scientific Reports , 7 : 46205 , https://doi.org/10.1038/srep46205 https://doi.org/10.1038/srep46205 .

Zhu K C , Liang Y Y , Wu N et al . 2017 . Sequencing and characterization of the complete mitochondrial genome of Japanese Swellshark ( Cephalloscyllium umbratile ) . Scientific Reports , 7 : 15299 , https://doi.org/10.1038/s41598-017-15702-0 https://doi.org/10.1038/s41598-017-15702-0 .

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