- Tytuł:
- Mitogenomic architecture of the multivalent endemic black clam (Villorita cyprinoides) and its phylogenetic implications.
- Autorzy:
- Źródło:
- Scientific reports [Sci Rep] 2020 Sep 22; Vol. 10 (1), pp. 15438. Date of Electronic Publication: 2020 Sep 22.
- Typ publikacji:
- Journal Article; Research Support, Non-U.S. Gov't
- Język:
- English
- Imprint Name(s):
- Original Publication: London : Nature Publishing Group, copyright 2011-
- MeSH Terms:
-
Biological Evolution*
Genes, Mitochondrial*
Genome, Mitochondrial*
Phylogeny*
Bivalvia/*genetics
DNA, Mitochondrial/*analysis
Animals ; DNA, Mitochondrial/genetics ; Gene Order ; Gene Rearrangement ; High-Throughput Nucleotide Sequencing - References:
-
FAO. The State of World Fisheries and Aquaculture (2020).
Aru, V., Khakimov, B., Sørensen, K. M. & Engelsen, S. B. Journal of food composition and analysis the foodome of bivalve molluscs: from hedonic eating to healthy diet. J. Food Compos. Anal. 69, 13–19 (2018).
Butler, P. G., Freitas, P. S., Burchell, M. & Chauvaud, L. Archaeology and sclerochronology of marine bivalves. In Goods and Services of Marine Bivalves 413–444 (Springer International Publishing, 2018). https://doi.org/10.1007/978-3-319-96776-9_21.
Gosling, E. Bivalve Molluscs Biology, Ecology and Culture (Blackwell Publishing, New York, 2003).
National Research Council (U.S.). Committee on Best Practices for Shellfish Mariculture and the Effects of Commercial Activities in Drakes Estero, P. R. N. S. Ecosystem Concepts for Sustainable Bivalve Mariculture. (National Academies Press, 2010).
Vaughn, C. C. & Hoellein, T. J. Bivalve impacts in freshwater and marine ecosystems. Annu. Rev. Ecol. Evol. Syst. 49, 183–208 (2018).
Martijn, J., Vosseberg, J., Guy, L., Offre, P. & Ettema, T. J. G. Deep mitochondrial origin outside the sampled alphaproteobacteria. Nature 557, 101–105 (2018). (PMID: 29695865)
Mitchell, P. Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism. Nature 191, 144–148 (1961). (PMID: 13771349)
Fernández-Pérez, J., Nantón, A., Ruiz-Ruano, F. J., Camacho, J. P. M. & Méndez, J. First complete female mitochondrial genome in four bivalve species genus Donax and their phylogenetic relationships within the Veneroida order. PLoS ONE 12, 1–18 (2017).
Boore, J. L. Animal mitochondrial genomes. Nucleic Acids Res. 27, 1767–1780 (1999). (PMID: 10101183148383)
Boore, J. L. & Brown, W. M. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr. Opin. Genet. Dev. 8, 668–674 (1998). (PMID: 9914213)
Froufe, E. et al. Mesozoic mitogenome rearrangements and freshwater mussel (Bivalvia: Unionoidea) macroevolution. Heredity (Edinb) 124, 182–196 (2020).
Guerra, D. et al. Evolution of sex-dependent mtDNA transmission in freshwater mussels (Bivalvia: Unionida). Sci. Rep. 7, 1–13 (2017).
Lee, Y. et al. A mitochondrial genome phylogeny of Mytilidae (Bivalvia: Mytilida). Mol. Phylogenet. Evol. 139, 106533 (2019). (PMID: 31185299)
Fernández-Pérez, J., Froufe, E., Nantón, A., Gaspar, M. B. & Méndez, J. Genetic diversity and population genetic analysis of Donax vittatus (Mollusca: Bivalvia) and phylogeny of the genus with mitochondrial and nuclear markers. Estuar. Coast. Shelf Sci. 197, 126–135 (2017).
Sharma, P. P. et al. Into the deep: a phylogenetic approach to the bivalve subclass Protobranchia. Mol. Phylogenet. Evol. 69, 188–204 (2013). (PMID: 23742885)
Ansari, Z. A., Parulekar, A. H. & Matondkar, S. G. P. seasonal changes in meat weight and biochemical composition in the black clam Villorita cyprinoides. Indian J. Mar. Sci. 10, 128–131 (1981).
Graf, D. L. Patterns of freshwater bivalve global diversity and the state of phylogenetic studies on the unionoida, sphaeriidae, and cyrenidae. Am. Malacol. Bull. 31, 135–153 (2013).
Arun, A. U. Gametogenic cycle in Villorita cyprinoides and the influence of salinity. Aquacul. Aquar. Conserv. Legis. 2, 433–447 (2009).
Lydeard, C. & Cummings, K. S. Freshwater Mollusc of the World: A Distribution Atlas (JHU Press, Baltimore, 2019).
Vijaya Krishna, A. & Ammini, P. Population characteristics of Villorita cyprinoides in Vembanad Lake India. Lake Reserv. Manag. 34, 130–140 (2018).
Joy, M. & Chakraborty, K. Nutritional qualities of the low-value bivalve mollusks Paphia malabarica and Villorita cyprinoides at the estuarine waters of the Southwestern Coast of India. J. Aquat. Food Prod. Technol. 26, 54–70 (2017).
Vipinkumar, V. P. et al. Impact of self-help groups in gender mainstreaming: a case study on clam processing units in Pookaitha village, Kottayam, Kerala m. J. Mar. Biol. Assoc. India. 59, 102–108 (2017).
Joy, M. & Chakraborty, K. Antioxidative and anti-inflammatory pyranoids and isochromenyl analogues from Corbiculid bivalve clam Villorita cyprinoides. Food Chem. 251, 125–134 (2018). (PMID: 29426418)
George, R., Martin, G. D., Nair, S. M. & Chandramohanakumar, N. Biomonitoring of trace metal pollution using the bivalve molluscs, Villorita cyprinoides, from the Cochin backwaters. Environ. Monit. Assess. 185, 10317–10331 (2013). (PMID: 23832233)
Paul, T. T., Salim, S. S., Manoharan, V. S. & Unnithan, U. Identification and evaluation of ecosystem services provided by clam (Villorita cyprinoides) fisheries in wetland. Indian J. Trop. Biodivers. 23, 21–29 (2015).
CMFRI. Annual Report 2017–18. (2018).
Suja, N. & Mohamed, K. S. The black clam, Villorita cyprinoides, fishery in the State of Kerala, India. Mar. Fish. Rev. 72, 48–61 (2010).
Tiemann, J. S., Gillette, D. P., Wildhaber, M. L. & Edds, D. R. Effects of lowhead dams on riffle-dwelling fishes and macroinvertebrates in a midwestern river. Trans. Am. Fish. Soc. 133, 705–717 (2004).
Muehlbauer, F. et al. Ocean & Coastal Management Bivalve aquaculture transfers in Atlantic Europe. Part A : Transfer activities and legal framework. Ocean Coast. Manag. 89, 127–138 (2014).
Muehlbauer, F. et al. Ocean & coastal management bivalve aquaculture transfers in Atlantic Europe. Part B: Environmental impacts of transfer activities. Ocean Coast. Manag. 89, 139–146 (2014).
Kripa, V. et al. Clam fisheries of Vembanad Lake, Kerala with observations on the socio-economic conditions of the clam fisheries. Mar. Fish. Inf. Serv. Tech. Ext. Ser. 179, 14–16 (2004).
Laxmilatha, P. & Appukuttan, K. K. A review of the black clam (Villorita cyprinoides) fishery of the Vembanad Lake. Fish. Res. 49, 85–91 (2002).
Vidya, R. et al. Exploitation of Juvenile Clam, Villorita cyprinoides from Vembanad lake. IFAF (2017).
Law, R. Fishing, selection, and phenotypic evolution. ICES J. Mar. Sci. 57, 659–668 (2000).
Suja, N. & Mohamed, K. S. Use of minimum legal size in managing black clam (Villorita cyprinoides) fishery in India. Int. J. Aquat. Biol. 1, 306–315 (2014).
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). (PMID: 223842273285693)
Wolstenholme, D. R. Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol. 141, 173–216 (1992). (PMID: 1452431)
Dreyer, H. & Steiner, G. 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. Front. Zool. 3, 1–14 (2006).
Yuan, Y., Li, Q., Kong, L. & Yu, H. The complete mitochondrial genome of the grand jackknife clam, Solen grandis (Bivalvia: Solenidae): a novel gene order and unusual non-coding region. Mol. Biol. Rep. 39, 1287–1292 (2012). (PMID: 21598108)
Zhang, T. et al. The complete mitogenome of clam Corbicula fluminea determined using next-generation and PacBio sequencing. Mitochondrial DNA Part B Resour. 4, 1660–1661 (2019).
Ojala, D., Montoya, J. & Attardi, G. tRNA punctuation model of RNA processing in human mitochondria. Nature 290, 470–474 (1981). (PMID: 7219536)
Boore, J. L. & Brown, W. M. 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. Mol. Biol. Evol. 17, 87–106 (2000). (PMID: 10666709)
Lv, C., Li, Q. & Kong, L. Comparative analyses of the complete mitochondrial genomes of Dosinia clams and their phylogenetic position within Veneridae. PLoS ONE 13, 1–18 (2018).
Imanishi, Y., Tanaka, M. & Fujiwara, M. Complete mitochondrial genome sequence of Japanese cockle Fulvia mutica (Cardiidae). Fish. Sci. 79, 949–957 (2013).
Plazzi, F., Ribani, A. & Passamonti, M. The complete mitochondrial genome of Solemya velum (Mollusca: Bivalvia) and its relationships with Conchifera. BMC Genomics 14, 409 (2013). (PMID: 237773153704766)
Yu, H. & Li, Q. Mutation and selection on the wobble nucleotide in tRNA anticodons in marine bivalve mitochondrial genomes. PLoS ONE 6, e16147 (2011). (PMID: 212674623022732)
Xu, X., Wu, X. & Yu, Z. The mitogenome of Paphia euglypta (Bivalvia: Veneridae) and comparative mitogenomic analyses of three venerids. Genome. 53, 1041–1052 (2010). (PMID: 21164537)
Sun, S., Kong, L., Yu, H. & Li, Q. The complete mitochondrial DNA of Tegillarca granosa and comparative mitogenomic analyses of three Arcidae species. Gene 557, 61–70 (2015). (PMID: 25499696)
He, C. B. et al. The complete mitochondrial genome of the hard clam Meretrix meretrix. Mol. Biol. Rep. 38, 3401–3409 (2011). (PMID: 21086173)
Wang, H., Zhang, S., Xiao, G. & Liu, B. Complete mtDNA of the Meretrix lamarckii (Bivalvia: Veneridae) and molecular identification of suspected M. lamarckii based on the whole mitochondrial genome. Mar. Genomics 4, 263–271 (2011). (PMID: 22118638)
Boore, J. L., Lavrov, D. V. & Brown, W. M. Gene translocation links insects and crustaceans. Nature 392, 667–668 (1998). (PMID: 9565028)
Yu, Z., Wei, Z., Kong, X. & Shi, W. Complete mitochondrial DNA sequence of oyster Crassostrea hongkongensis-a case of "Tandem duplication-random loss" for genome rearrangement in Crassostrea?. BMC Genomics. 9, 477 (2008). (PMID: 188475022576254)
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). (PMID: 211891473040558)
Belda, E., Moya, A. & Silva, F. J. Genome rearrangement distances and gene order phylogeny in γ-proteobacteria. Mol. Biol. Evol. 22, 1456–1467 (2005). (PMID: 15772379)
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).
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). (PMID: 20817110)
Bieler, R. et al. Investigating the bivalve tree of life—an exemplar-based approach combining molecular and novel morphological characters. Invertebr. Syst. 28, 32 (2014).
González, V. L. et al. A phylogenetic backbone for Bivalvia: an RNA-seq approach. Proc. R. Soc. B Biol. Sci. 282, 20142332 (2015).
Park, J. & Foighil, O. D. Sphaeriid and corbiculid clams represent separate heterodont. Mol. Phylogenet. Evol. 14, 75–88 (2000). (PMID: 10631043)
Canapa, A., Barucca, M., Marinelli, A. & Olmo, E. A molecular phylogeny of heterodonta (Bivalvia) based on small ribosomal subunit RNA sequences. Mol. Phylogenet. Evol. 21, 156–161 (2001). (PMID: 11603945)
Taylor, J. D., Williams, S. T., Glover, E. A. & Dyal, P. A molecular phylogeny of heterodont bivalves (Mollusca: Bivalvia: Heterodonta): new analyses of 18S and 28S rRNA genes. Zool. Scr. 36, 587–606 (2007).
Mikkelsen, P. M., Bieler, R., Kappner, I. & Rawlings, T. A. Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules. Zool. J. Linn. Soc. 148, 439–521 (2006).
Gardner, R. N. Middle-Late Jurassic bivalves of the superfamily Veneroidea from New Zealand and New Caledonia. New Zeal. J. Geol. Geophys. 48, 325–376 (2005).
Canapa, A., Schiaparelli, S., Marota, I. & Barucca, M. Molecular data from the 16S rRNA gene for the phylogeny of Veneridae (Mollusca: Bivalvia). Mar. Biol. 142, 1125–1130 (2003).
Combosch, D. J. et al. A family-level tree of life for bivalves based on a Sanger-sequencing approach. Mol. Phylogenet. Evol. 107, 191–208 (2017). (PMID: 27840226)
Campbell, D. C. Molecular evidence on the evolution of the Bivalvia. Geol Soc. Lond. Spec. Publ. 177, 31–46 (2000).
Poulton, T. P. Hettangian through Aalenian (Jurassic) guide fossils and biostratigraphy, Northern Yukon and adjacent Northwest Territories. Bull. Geol. Sur. Can.410, 1–95 (1991).
Johnson, S. B., Krylova, E. M., Audzijonyte, A., Sahling, H. & Vrijenhoek, R. C. Phylogeny and origins of chemosynthetic vesicomyid clams. Syst. Biodivers. 15, 346–360 (2017).
Gallardi, S. B. Effects of bivalve aquaculture on the environment and their possible mitigation: a review. Syst. Biodivers. https://doi.org/10.4172/2150-3508.1000105 (2014). (PMID: 10.4172/2150-3508.1000105)
Beaumont, A. Genetic considerations in transfers and introductions of scallops. Aquac. Int. 8, 493–512 (2000).
Breton, S., Beaupré, H. D., Stewart, D. T., Hoeh, W. R. & Blier, P. U. The unusual system of doubly uniparental inheritance of mtDNA: isn’t one enough?. Trends Genet. 23, 465–474 (2007). (PMID: 17681397)
Rao, N. V. S. Handbook Freshwater Molluscs of India (Zoological Survey of India, Kolkatta, 1989).
Rao, N. V. S. Indian Seashells: Part-2 Bivalvia (Zoological Survey of India, Kolkatta, 2017).
Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3, 294–299 (1994). (PMID: 7881515)
Capt, C. et al. Unorthodox features in two venerid bivalves with doubly uniparental inheritance of mitochondria. Sci. Rep. 10, 1–13 (2020).
Medlin, L., Elwood, H. J., Stickel, S. & Sogin, M. L. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71, 491–499 (1988). (PMID: 3224833)
Colgan, D. J. et al. Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution. Aust. J. Zool. 46, 419–437 (1998).
Andrews, S. FastQC: a quality control tool for high throughput sequence data. Available online at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc . (2010).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014). (PMID: 2469540424695404)
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).
Bernt, M. et al. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol. Phylogenet. Evol. 69, 313–319 (2013). (PMID: 22982435)
Lowe, T. M. & Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964 (1997). (PMID: 9023104146525)
Laslett, D. & Canback, B. ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 24, 172–175 (2008). (PMID: 18033792)
Byun, Y. & Han, K. PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures. Nucleic Acids Res. 34, W416–W422 (2006). (PMID: 168450391538805)
Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406–3415 (2003). (PMID: 12824337169194)
Kumar, S., Stecher, G. & Tamura, K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874 (2016). (PMID: 27004904)
Carver, T., Thomson, N., Bleasby, A., Berriman, M. & Parkhill, J. DNAPlotter : circular and linear interactive genome visualization. Bioinformatics 25, 119–120 (2009). (PMID: 18990721)
Kearse, M. et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649 (2012). (PMID: 2254336722543367)
Librado, P. & Rozas, J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451–1452 (2009).
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). (PMID: 7563121)
Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680 (1994). (PMID: 7984417308517)
Talavera, G. & Castresana, J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564–577 (2007). (PMID: 17654362)
Lanfear, R., Calcott, B., Ho, S. Y. & Guindon, S. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol. Biol. Evol. 29, 1695–1701 (2012). (PMID: 22319168)
Nguyen, L., Schmidt, H. A., Haeseler, A. V. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2014). (PMID: 253714304271533)
Ronquist, F. et al. MrBayes 3.2 efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542 (2012). (PMID: 223577273329765)
Yang, Z. & Rannala, B. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 23, 212–226 (2006). (PMID: 16177230)
Rannala, B. & Yang, Z. Inferring speciation tunes under an episodic molecular clock. Syst. Biol. 56, 453–466 (2007). (PMID: 17558967)
Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007). (PMID: 17483113)
Landing, E. D. Upper precambrian through lower cambrian of Cape Breton Island: Faunas, paleoenvironments and stratigraphic revision. J. Paleontol. 65, 570–595 (1991).
Brasier, M. D., Hewitt, R. A. & Brasier, C. J. On the late precambrian-early cambrian hartshill formation of warwickshire. Geol. Mag. 115, 21–36 (1978).
Devaere, L, Clausen, S, Sosa-Leon, J. P, Palafox-Reyes, J. J, Buitron-Sanchez, B .E and Vachard, D. Early cambrian small shelly fossils from northwest Mexico: Biostratigraphic implications for Laurentia. Palaeontol. Electron. 22, 1–60 (2019).
Fang, Z. J. et al. Supraspecific Taxa of the Bivalvia first named, described, and published in China (1927–2007). Univ. Kansas Paleontol. Contrib. 17, 1–157 (2009).
Hayami, I. A systematic survey of the Mesozoic Bivalvia from Japan. Univ. Mus. Univ. Tokyo Bull. 10, http://umdb.um.u-tokyo.ac.jp/DKankoub/Bulletin/no10/no10000.html (1975).
Elias, M. Late Mississippian fauna from the redoak hollow formation of southern Oklahom Part I. J. Paleontol. 31, 370–342 (1957).
Paleobiology Database. The Paleobiology Database. (2018). Available at: https://paleobiodb.org/classic/checkTaxonInfo?taxon_no=281202 . - Substance Nomenclature:
- 0 (DNA, Mitochondrial)
- Entry Date(s):
- Date Created: 20200923 Date Completed: 20201215 Latest Revision: 20210922
- Update Code:
- 20240105
- PubMed Central ID:
- PMC7508841
- DOI:
- 10.1038/s41598-020-72194-1
- PMID:
- 32963308
- Czasopismo naukowe
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