Mitogenomics of southern hemisphere blue mussels (Bivalvia: Pteriomorphia): Insights into the evolutionary characteristics of the Mytilus edulis complex

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Gaitán Espitia, Juan Diego ^a,b   Quintero Galvis, Julian F ^a   Mesas, Andres ^a   D'Elía, Guillermo ^a  

^a UNIVERSIDAD AUSTRAL DE CHILE   (Chile)

^b CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; GENETIC SELECTION; GENETICS; GENOMICS; MITOCHONDRIAL GENE; MOLECULAR EVOLUTION; MYTILUS EDULIS; PHYLOGENY; POPULATION GENETICS; SPECIES DIFFERENCE;

ANIMALS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENES, MITOCHONDRIAL; GENETICS, POPULATION; GENOMICS; MYTILUS EDULIS; PHYLOGENY; SELECTION, GENETIC; SPECIES SPECIFICITY;

EID: 84973311126     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep26853     Document Type: Article

References (67)

1. Campbell, D. C. Molecular evidence on the evolution of the Bivalvia. Geol. Soc. London, Spec. Publ. 177, 31-46 (2000).
2. Bayne, B. L. Marine mussels, their ecology and physiology. (Cambridge University Press, 1976).
3. Venier, P. et al. MytiBase: a knowledgebase of mussel (M. galloprovincialis) transcribed sequences. BMC Genomics 10, 72 (2009).
4. Regoli, F., Orlando, E., Regoli, F. & Orlando, E. Accumulation and subcellular distribution of metals (Cu, Fe, Mn, Pb and Zn) in the Mediterranean mussel Mytilus galloprovincialis during a field transplant experiment. Mar. Pollut. Bull. 28, 592-600 (1994).
5. Hilbish, T. J. et al. Origin of the antitropical distribution pattern in marine mussels (Mytilus spp.): routes and timing of transequatorial migration. Mar. Biol. 136, 69-77 (2000).
6. Dellatorre, F. G., Pascual, M. S. & Barón, P. J. Feeding physiology of the Argentine mussel Mytilus edulis platensis (d'Orbigny, 1846): does it feed faster in suspended culture systems? Aquac. Int. 15, 415-424 (2007).
7. Toro, J. PCR-based nuclear and mtDNA markers and shell morphology as an approach to study the taxonomic status of the Chilean bluw mussel, Mytilus chilensis (Bivalvia). Aquat. Living Resour. 11, 347-353 (1998).
8. Wonham, M. Mini-review: distribution of the Mediterranean mussel, Mytilus galloprovincialis (Bivalvia: Mytilidae), and hybrids in the northeast Pacific. J. Shellfish Res. 23, 535-543 (2004).
9. Addison, J. A., Ort, B. S. & Mesa, K. a. & Pogson, G. H. Range-wide genetic homogeneity in the California sea mussel (Mytilus californianus): a comparison of allozymes, nuclear DNA markers, and mitochondrial DNA sequences. Mol. Ecol. 17, 4222-4232 (2008).
10. Borsa, P., Rolland, V. & Daguin-Thiébaut, C. Genetics and taxonomy of Chilean smooth-shelled mussels, Mytilus spp. (Bivalvia: Mytilidae). C. R. Biol. 335, 51-61 (2012).
11. Westfall, K. & Gardner, J. Interlineage Mytilus galloprovincialis Lmk. 1819 hybridization yields inconsistent genetic outcomes in the Southern hemisphere. Biol. Invasions 15, 1493-1506 (2013).
12. Toro, J., Ojeda, J. A., Vergara, A. N. A. M., Castro, G. C. & Alcapán, A. C. Molecular characterization of the Chilean blue mussel (Mytilus chilensis Hupe 1854) demonstrates evidence for the occurrence of Mytilus galloprovincialis in southern. J. Shellfish Res. 24, 1117-1121 (2005).
13. Westfall, K. & Gardner, J. Genetic diversity of Southern hemisphere blue mussels (Bivalvia: Mytilidae) and the identification of nonindigenous taxa. Biol. J. Linn. Soc. 101, 898-909 (2010).
14. Westfall, K., Wimberger, P. & Gardner, J. An RFLP assay to determine if Mytilus galloprovincialis Lmk. (Mytilidae; Bivalvia) is of Northern or Southern hemisphere origin. Mol. Ecol. Resour. 10, 573-575 (2010).
15. Gérard, K., Bierne, N., Borsa, P., Chenuil, A. & Féral, J.-P. Pleistocene separation of mitochondrial lineages of Mytilus spp. mussels from Northern and Southern Hemispheres and strong genetic differentiation among southern populations. Mol. Phylogenet. Evol. 49, 84-91 (2008).
16. Oyarzún, P. A., Toro, J., Garrido, O., Briones, C. & Guinez, R. Differences in sperm ultrastructure between Mytilus chilensis and Mytilus galloprovincialis (Bivalvia, Mytilidae): could be used as a taxonomic trait? Lat. Am. J. Aquat. Res. 42, 172-179 (2014).
17. Tarifeno, E. et al. Erroneous identification of the mussel, Mytilus galloprovincialis (Lamarck 1819) as the specie, Mytilus chilensis (Hupe 1854) in the Bay of Concepcion, Chile. Gayana 76, 167-172 (2012).
18. McDonald, J., Seed, R. & Koehn, R. Allozymes and morphometric characters of three species of Mytilus in the Northern and Southern Hemispheres. Mar. Biol. 111, 323-333 (1991).
19. Seed, R. Systematics evolution and distribution of mussels belonging to the genus Mytilus: an overview. Am. Malacol. Bull. 9, 123-137 (1992).
20. De Moreno, J. E. A., Pollero, R. J., Moreno, V. J. & Brenner, R. R. Lipids and fatty acids of the mussel (Mytilus Platensis d'Orbigny) from South Atlantic waters. J. Exp. Mar. Bio. Ecol. 48, 263-276 (1980).
21. Breton, S., Burger, G., Stewart, D. & Blier, P. U. Comparative analysis of gender-associated complete mitochondrial genomes in marine mussels (Mytilus spp.). Genetics 172, 1107-1119 (2006).
22. Zbawicka, M., Wenne, R. & Burzyński, A. Mitogenomics of recombinant mitochondrial genomes of Baltic Sea Mytilus mussels. Mol. Genet. Genomics MGG 289, 1275-1287 (2014).
23. Smietanka, B., Burzynski, A. & Wenne, R. Comparative genomics of marine mussels (Mytilus spp.) gender associated mtDNA: rapidly evolving atp8. J. Mol. Evol. 71, 385-400 (2010).
24. Stewart, D., Kenchington, E. R., Singh, R. K. & Zonros, E. Degree of selective constraint as an explanation of the different rates of evolution of gender-specific mitochondrial DNA lineages in the mussel Mytilus. Genetics 143, 1349-1357 (1996).
25. Hoffmann, R. J., Boore, J. L. & Brownt, W. M. A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics 131, 397-412 (1992).
26. Mizi, A., Zouros, E., Moschonas, N. & Rodakis, G. C. The complete maternal and paternal mitochondrial genomes of the Mediterranean mussel Mytilus galloprovincialis: implications for the doubly uniparental inheritance mode of mtDNA. Mol. Biol. Evol. 22, 952-967 (2005).
27. Passamonti, M. & Ghiselli, F. Doubly uniparental inheritance: two mitochondrial genomes, one precious model for organelle DNA inheritance and evolution. DNA Cell Biol. 28, 79-89 (2009).
28. Quesada, H., Warren, M. & Skibinski, D. O. Nonneutral evolution and differential mutation rate of gender-associated mitochondrial DNA lineages in the marine mussel Mytilus. Genetics 149, 1511-1526 (1998).
29. Ort, B. S. & Pogson, G. H. Molecular population genetics of the male and female mitochondrial DNA molecules of the California Sea Mussel, Mytilus californianus. Genetics 177, 1087-1099 (2007).
30. Breton, S., Stewart, D. & Blier, P. U. Role-reversal of gender-associated mitochondrial dna affects mitochondrial function in mytilus edulis (bivalvia: mytilidae). J. Exp. Zool. Part B Mol. Dev. Evol. 312, 108-117 (2009).
31. Stager, M., Cerasale, D. J., Dor, R., Winkler, D. W. & Cheviron, Z. A. Signatures of natural selection in the mitochondrial genomes of Tachycineta swallows and their implications for latitudinal patterns of the 'pace of life'. Gene 546, 104-111 (2014).
32. Lesser, M. P. Oxidative stress in marine environments: biochemistry and physiological ecology. Annu. Rev. Physiol. 68, 253-278 (2006).
33. Kowaltowski, A. J. & Vercesi, A. E. Mitochondrial damage induced by conditions of oxidative stress. Free Radic. Biol. Med. 26, 463-471 (1999).
34. Blier, P. U., Dufresne, F. & Burton, R. S. Natural selection and the evolution of mtDNA-encoded peptides: evidence for intergenomic co-adaptation. Trends Genet. 17, 400-406 (2001).
35. Wu, X., Xu, X., Yu, Z., Wei, Z. & Xia, J. Comparison of seven Crassostrea mitogenomes and phylogenetic analyses. Mol. Phylogenet. Evol. 57, 448-454 (2010).
36. Boore, J. L. Animal mitochondrial genomes. Nucleic Acids Res. 27, 1767-1780 (1999).
37. Breton, S. et al. Novel protein genes in animal mtDNA: A new sex determination system in freshwater mussels (Bivalvia: Unionoida)? Mol. Biol. Evol. 28, 1645-1659 (2011).
38. Stöger, I. & Schrödl, M. Mitogenomics does not resolve deep molluscan relationships (yet?). Mol. Phylogenet. Evol. 69, 376-392 (2013).
39. Breton, S., Stewart, D. & Hoeh, W. R. Characterization of a mitochondrial ORF from the gender-associated mtDNAs of Mytilus spp. (Bivalvia: Mytilidae): identification of the 'missing' ATPase 8 gene. Mar. Genomics 3, 11-18 (2010).
40. 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. J. Mol. Evol. 70, 57-68 (2010).
41. Ren, J., Liu, X., Jiang, F., Guo, X. & Liu, B. Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia. BMC Evol. Biol. 10, 394 (2010).
42. Li, X., Wu, X. & Yu, Z. Complete mitochondrial genome of the Asian green mussel Perna viridis (Bivalvia, Mytilidae). Mitochondrial DNA 23, 358-360 (2012).
43. Gaitán-Espitia, J. D., Nespolo, R. F. & Opazo, J. C. The Complete Mitochondrial Genome of the Land Snail Cornu aspersum (Helicidae: Mollusca): Intra-Specific Divergence of Protein-Coding Genes and Phylogenetic Considerations within Euthyneura. PLos One 8, e67299 (2013).
44. Cea, G., Gaitán-Espitia, J. D. & Cárdenas, L. Complete mitogenome of the edible sea urchin Loxechinus albus: genetic structure and comparative genomics within Echinozoa. Mol. Biol. Rep. 42, 1081-1089 (2015).
45. Cao, L., Kenchington, E., Zouros, E. & Rodakis, G. C. Evidence that the large noncoding sequence is the main control region of maternally and paternally transmitted mitochondrial genomes of the marine mussel (Mytilus spp.). Genetics 167, 835-850 (2004).
46. Lee, Y. & Lee, Y. The F type mitochondrial genome of hard-shelled mussel: Mytilus coruscus (Mytiloida, Mytilidae). Mitochondrial DNA 1736, 1-2 (2014).
47. Cao, L. et al. The Control Region of Maternally and Paternally Inherited Mitochondrial Genomes of Three Species of the Sea Mussel Genus Mytilus. Genetics 181, 1045-1056 (2009).
48. Poon, A. F. Y., Frost, S. D. W. & Pond, S. In Bioinforma. DNA Seq. Anal. (Posada, D.) 163-183, doi: 10.1007/978-1-59745-251-9-8 (Humana Press, 2009).
49. Masters, B. C., Fan, V. & Ross, H. A. Species delimitation-a geneious plugin for the exploration of species boundaries. Mol. Ecol. Resour. 11, 154-157 (2011).
50. Carcamo, C., Comesana, A., Winkler, F. M. & Sanjuan, A. Allozyme identification of mussels (Bivalvia: Mytilus) on the Pacific coast of South America. J. Shellfish Res. 24, 1101-1115 (2005).
51. Toro, J. & Castro, G. Allozymic variation and differentiation in the chilean blue mussel, Mytilus chilensis, along its natural distribution. Genet. Mol. Biol. 179, 174-179 (2006).
52. Plazzi, F. & Passamonti, M. Towards a molecular phylogeny of Mollusks: bivalves' early evolution as revealed by mitochondrial genes. Mol. Phylogenet. Evol. 57, 641-657 (2010).
53. Giribet, G. & Wheeler, W. On bivalve phylogeny: a high-level analysis of the Bivalvia (Mollusca) based on combined morphology and DNA sequence data. Invertebr. Biol. 121, 271-324 (2005).
54. Matsumoto, M. Phylogenetic analysis of the subclass Pteriomorphia (Bivalvia) from mtDNA COI sequences. Mol. Phylogenet. Evol. 27, 429-440 (2003).
55. Kocot, K. M. et al. Phylogenomics reveals deep molluscan relationships. Nature 477, 452-456 (2011).
56. Andrade, C. S. et al. A phylogenetic backbone for Bivalvia: an RNA-seq approach. Proc. R. Soc. B Biol. Sci. 282, 20142332 (2015).
57. Altschul, S. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
58. Laslett, D. & Canbäck, B. ARWEN, a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 24, 172-175 (2008).
59. Schattner, P., Brooks, A. N. & Lowe, T. M. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33, W686-W689 (2005).
60. Bernt, M. et al. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol. Phylogenet. Evol. 69, 313-319 (2013).
61. Abascal, F., Zardoya, R. & Telford, M. TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Res. 38, W7-13 (2010).
62. Tamura, K. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739 (2011).
63. Delport, W., Poon, A. F. Y., Frost, S. D. W. & Pond, S. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 26, 2455-2457 (2010).
64. Lanfear, R., Calcott, B., Ho, S. Y. W. & Guindon, S. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol. Biol. Evol. 29, 1695-1701 (2012).
65. Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690 (2006).
66. Silvestro, D. & Michalak, I. Raxml GUI: a graphical front-end for RAxML. Org. Divers. Evol. 12, 335-337 (2012).
67. Ronquist, F. & Huelsenbeck, J. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574 (2003).