{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T04:51:59Z","timestamp":1789879919564,"version":"4.0.1"},"reference-count":42,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2008,12]]},"abstract":"Abstract<\/jats:title>\n \n Background<\/jats:title>\n \n Mitochondrial DNA sequences are extensively used as genetic markers not only for studies of population or ecological genetics, but also for phylogenetic and evolutionary analyses. Complete mt-sequences can reveal information about gene order and its variation, as well as gene and genome evolution when sequences from multiple phyla are compared. Mitochondrial gene order is highly variable among mollusks, with bivalves exhibiting the most variability. Of the 41 complete mt genomes sequenced so far, 12 are from bivalves. We determined, in the current study, the complete mitochondrial DNA sequence of\n Crassostrea hongkongensis<\/jats:italic>\n . We present here an analysis of features of its gene content and genome organization in comparison with two other\n Crassostrea<\/jats:italic>\n species to assess the variation within bivalves and among main groups of mollusks.\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n The complete mitochondrial genome of\n C. hongkongensis<\/jats:italic>\n was determined using long PCR and a primer walking sequencing strategy with genus-specific primers. The genome is 16,475 bp in length and contains 12 protein-coding genes (the\n atp8<\/jats:italic>\n gene is missing, as in most bivalves), 22 transfer tRNA genes (including a suppressor tRNA gene), and 2 ribosomal RNA genes, all of which appear to be transcribed from the same strand. A striking finding of this study is that a DNA segment containing four tRNA genes (\n trnk1, trnC, trnQ1<\/jats:italic>\n and\n trnN<\/jats:italic>\n ) and two duplicated or split rRNA gene (\n rrnL5'<\/jats:italic>\n and\n rrnS<\/jats:italic>\n ) are absent from the genome, when compared with that of two other extant\n Crassostrea<\/jats:italic>\n species, which is very likely a consequence of loss of a single genomic region present in ancestor of\n C. hongkongensis<\/jats:italic>\n . It indicates this region seem to be a \"hot spot\" of genomic rearrangements over the\n Crassostrea<\/jats:italic>\n mt-genomes. The arrangement of protein-coding genes in\n C. hongkongensis<\/jats:italic>\n is identical to that of\n Crassostrea gigas<\/jats:italic>\n and\n Crassostrea virginica<\/jats:italic>\n , but higher amino acid sequence identities are shared between\n C. hongkongensis<\/jats:italic>\n and\n C. gigas<\/jats:italic>\n than between other pairs. There exists significant codon bias, favoring codons ending in A or T and against those ending with C. Pair analysis of genome rearrangements showed that the rearrangement distance is great between\n C. gigas<\/jats:italic>\n -\n C. hongkongensis<\/jats:italic>\n and\n C. virginica<\/jats:italic>\n , indicating a high degree of rearrangements within\n Crassostrea<\/jats:italic>\n . The determination of complete mt-genome of\n C. hongkongensis<\/jats:italic>\n has yielded useful insight into features of gene order, variation, and evolution of\n Crassostrea<\/jats:italic>\n and bivalve mt-genomes.\n <\/jats:p>\n <\/jats:sec>\n \n Conclusion<\/jats:title>\n \n The mt-genome of\n C. hongkongensis<\/jats:italic>\n shares some similarity with, and interesting differences to, other\n Crassostrea<\/jats:italic>\n species and bivalves. The absence of\n trnC<\/jats:italic>\n and\n trnN<\/jats:italic>\n genes and duplicated or split rRNA genes from the\n C. hongkongensis<\/jats:italic>\n genome is a completely novel feature not previously reported in\n Crassostrea<\/jats:italic>\n species. The phenomenon is likely due to the loss of a segment that is present in other\n Crassostrea<\/jats:italic>\n species and was present in ancestor of\n C. hongkongensis<\/jats:italic>\n , thus a case of \"tandem duplication-random loss (TDRL)\". The mt-genome and new feature presented here reveal and underline the high level variation of gene order and gene content in\n Crassostrea<\/jats:italic>\n and bivalves, inspiring more research to gain understanding to mechanisms underlying gene and genome evolution in bivalves and mollusks.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.1186\/1471-2164-9-477","type":"journal-article","created":{"date-parts":[[2008,10,11]],"date-time":"2008-10-11T14:13:28Z","timestamp":1223734408000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":36,"title":["Complete mitochondrial DNA sequence of oyster Crassostrea hongkongensis-a case of \"Tandem duplication-random loss\" for genome rearrangement in Crassostrea?"],"prefix":"10.1186","volume":"9","author":[{"given":"Ziniu","family":"Yu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhengpeng","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyu","family":"Kong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2008,10,11]]},"reference":[{"key":"1670_CR1","doi-asserted-by":"publisher","first-page":"1767","DOI":"10.1093\/nar\/27.8.1767","volume":"27","author":"JL Boore","year":"1999","unstructured":"Boore JL: Animal mitochondrial genomes. Nucleic Acids Res. 1999, 27: 1767-1780. 10.1093\/nar\/27.8.1767.","journal-title":"Nucleic Acids Res"},{"key":"1670_CR2","doi-asserted-by":"publisher","first-page":"1734","DOI":"10.1093\/oxfordjournals.molbev.a003961","volume":"18","author":"KG Helfenbein","year":"2001","unstructured":"Helfenbein KG, Brown WM, Boore JL: The complete mitochondrial genome of the articulate brachiopod Terebratalia transversa. Mol Biol Evol. 2001, 18: 1734-1744.","journal-title":"Mol Biol Evol"},{"key":"1670_CR3","doi-asserted-by":"publisher","first-page":"1854","DOI":"10.1093\/molbev\/msg218","volume":"20","author":"JM Serb","year":"2003","unstructured":"Serb JM, Lydeard C: Complete mtDNA sequence of the North American freshwater mussel, Lampsilis ornata (Unionidae): An eximination of the evolution and phylogenetic utility of mitochondrial genome organization in Bivalvia (Mollusca). Mol Biol Evol. 2003, 20: 1854-1866. 10.1093\/molbev\/msg218.","journal-title":"Mol Biol Evol"},{"key":"1670_CR4","doi-asserted-by":"publisher","first-page":"1492","DOI":"10.1093\/molbev\/msh090","volume":"21","author":"JL Boore","year":"2004","unstructured":"Boore JL, Medina M, Rosenberg LA: Complete sequences of the highly rearranged molluscan mitochondrial genomes of the scaphopod Graptacme eborea and the bivalve Mytilus edulis. Mol Biol Evol. 2004, 21: 1492-1503. 10.1093\/molbev\/msh090.","journal-title":"Mol Biol Evol"},{"key":"1670_CR5","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1007\/s10126-005-0004-0","volume":"7","author":"CA Milbury","year":"2005","unstructured":"Milbury CA, Gaffney PM: Complete mitochondrial DNA sequence of the eastern oyster Crassostrea virginica. Mar Biotechnol. 2005, 7: 697-712. 10.1007\/s10126-005-0004-0.","journal-title":"Mar Biotechnol"},{"key":"1670_CR6","doi-asserted-by":"publisher","first-page":"645","DOI":"10.1007\/s10126-005-0013-z","volume":"7","author":"BT Maynard","year":"2005","unstructured":"Maynard BT, Kerr LJ, McKiernan JM, Jansen ES, Hanna PJ: Mitochondrial DNA sequence and gene organization in the Australia blacklip abalone Haliotis rubra (Leach). Mar Bioltechnol. 2005, 7: 645-658. 10.1007\/s10126-005-0013-z.","journal-title":"Mar Bioltechnol"},{"key":"1670_CR7","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/1742-9994-3-13","volume":"3","author":"H Dreyer","year":"2006","unstructured":"Dreyer H, Steiner G: The complete sequence and gene organization 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. 2006, 3: 13-10.1186\/1742-9994-3-13.","journal-title":"Front Zool"},{"key":"1670_CR8","doi-asserted-by":"publisher","first-page":"668","DOI":"10.1016\/S0959-437X(98)80035-X","volume":"8","author":"JL Boore","year":"1998","unstructured":"Boore JL, Brown WM: Big trees from little genome: Mitochondrial gene order as a phylogenetic tool. Curr Opin Gent Dev. 1998, 8: 668-674. 10.1016\/S0959-437X(98)80035-X.","journal-title":"Curr Opin Gent Dev"},{"key":"1670_CR9","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0044-8486(03)00215-1","volume":"228","author":"K Lam","year":"2003","unstructured":"Lam K, Morton B: Mitochondrial DNA and morphological identification of a new species of Crassostrea (Bivalvia: Ostreidae) cultured for centuries in the Pearl River Delta, Hong Kong, China. Aquaculture. 2003, 228: 1-13. 10.1016\/S0044-8486(03)00215-1.","journal-title":"Aquaculture"},{"key":"1670_CR10","first-page":"51","volume-title":"Proceedings of Marine Biology of South China Sea","author":"G Li","year":"1988","unstructured":"Li G, Hu Y, Qing N: Population gene pools of big size cultured oysters (Crassostrea) along the Guangdong and Fujian coast of China. Proceedings of Marine Biology of South China Sea. 1988, Guangzhou, China Ocean Press, 51-70."},{"issue":"2","key":"1670_CR11","first-page":"100","volume":"15","author":"T Su","year":"2005","unstructured":"Su T, Jiang S, Zhou F, Zhu C, Chen P: Mitochondrial 16S rRNA gene fragment sequence analysis in populations of Crassostrea rivularis. High Technol Lett. 2005, 15 (2): 100-103.","journal-title":"High Technol Lett"},{"issue":"3","key":"1670_CR12","first-page":"3","volume":"26","author":"M Xue","year":"2006","unstructured":"Xue M, Du X, Huang R, Wang Q: Biochemical genetic variation in Chinese oyster Ostea rivularis. J Zhanjiang Ocean Univ. 2006, 26 (3): 3-7.","journal-title":"J Zhanjiang Ocean Univ"},{"key":"1670_CR13","doi-asserted-by":"publisher","first-page":"1604","DOI":"10.1093\/oxfordjournals.molbev.a003949","volume":"18","author":"T Rawlings","year":"2001","unstructured":"Rawlings T, Collins T, Bieler R: A major mitochondrial gene rearrangement among closely related species. Mol Biol Evol. 2001, 18: 1604-1609.","journal-title":"Mol Biol Evol"},{"key":"1670_CR14","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1093\/genetics\/145.3.749","volume":"145","author":"N Yamazaki","year":"1997","unstructured":"Yamazaki N, Ueshima R, Terrett JA, Yokobori SI, Kaifu M, Segawa R, Kobayashi T, Numachi KI, Ueda T, Nishikawa K, Watanabe K, Thomas RH: Evolution of pulmonate gastropod mitochondrial genomes: comparisons of gene organizations of Euhadra, Cepaea and Albinaria and implications of unusual tRNA secondary structure. Genetics. 1997, 145: 749-758.","journal-title":"Genetics"},{"key":"1670_CR15","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1113\/eph8802514","volume":"88","author":"P Fern\u00e1ndez-Silva","year":"2003","unstructured":"Fern\u00e1ndez-Silva P, Enriquez JA, Montoya J: Replication and transcription of mammalian mitochondrial DNA. Exp Physiol. 2003, 88: 41-56. 10.1113\/eph8802514.","journal-title":"Exp Physiol"},{"key":"1670_CR16","doi-asserted-by":"publisher","first-page":"470","DOI":"10.1038\/290470a0","volume":"290","author":"D Ojala","year":"1981","unstructured":"Ojala D, Montoya J, Attardi J: tRNA punctuation model of RNA processing in human mitochondria. Nature. 1981, 290: 470-474. 10.1038\/290470a0.","journal-title":"Nature"},{"key":"1670_CR17","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1007\/BF01215182","volume":"41","author":"NT Perna","year":"1995","unstructured":"Perna NT, Kocher TD: Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol. 1995, 41: 353-358. 10.1007\/BF01215182.","journal-title":"J Mol Evol"},{"key":"1670_CR18","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1007\/s00239-007-9030-z","volume":"65","author":"C Papetti","year":"2007","unstructured":"Papetti C, Li\u00f2 P, R\u00fcber L, Patarnello T, Zardoya R: Antarctic fish mitochondrial genomes lack ND6 gene. J Mol Evol. 2007, 65: 519-528. 10.1007\/s00239-007-9030-z.","journal-title":"J Mol Evol"},{"key":"1670_CR19","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1093\/nar\/26.4.865","volume":"26","author":"MW Gray","year":"1998","unstructured":"Gray MW, Lang BF, Cedergren R, Golding GB, Lemieux C, Sankoff D, Turmel M, Brossard N, Delage E, Littlejohn TG, Plante I, Rioux P, Saint-Louis D, Zhu Y, Burger G: Genome structure and gene content in protist mitochondrial DNAs. Nucleic Acids Res. 1998, 26: 865-878. 10.1093\/nar\/26.4.865.","journal-title":"Nucleic Acids Res"},{"key":"1670_CR20","first-page":"909","volume-title":"Escherichia coli and Salmonella: Cellular and molecular biology","author":"H Engelberg-Kulka","year":"1996","unstructured":"Engelberg-Kulka H, Schoulaker-Schwarz R: Suppression of termination codons. Escherichia coli and Salmonella: Cellular and molecular biology. Edited by: Neidhardt F. 1996, Washington, DC, ASM Press, 909-921. 2","edition":"2"},{"key":"1670_CR21","doi-asserted-by":"publisher","first-page":"5368","DOI":"10.1073\/pnas.91.12.5368","volume":"91","author":"JR Valverde","year":"1994","unstructured":"Valverde JR, Marco R, Garesse R: A conserved heptamer motif for ribosomal RNA transcription termination in animal mitochondria. Proc Natl Acad Sci USA. 1994, 91: 5368-5371. 10.1073\/pnas.91.12.5368.","journal-title":"Proc Natl Acad Sci USA"},{"key":"1670_CR22","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1093\/genetics\/138.2.423","volume":"138","author":"JL Boore","year":"1994","unstructured":"Boore JL, Brown WM: The complete DNA sequence of the mitochondrial genome of the black chiton Katharina tunicata. Genetics. 1994, 138: 423-443.","journal-title":"Genetics"},{"key":"1670_CR23","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1146\/annurev.es.18.110187.001413","volume":"18","author":"C Moritz","year":"1987","unstructured":"Moritz C, Dowling TE, Brown WM: Evolution of animal mitochondrial DNA: Relevance for population biology and systematics. Annu Rev Ecol Syst. 1987, 18: 269-292. 10.1146\/annurev.es.18.110187.001413.","journal-title":"Annu Rev Ecol Syst"},{"key":"1670_CR24","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1093\/oxfordjournals.molbev.a025706","volume":"14","author":"JR Macey","year":"1997","unstructured":"Macey JR, Larson A, Ananjeva NB, Fang Z, Papenfuss TJ: Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol Biol Evol. 1997, 14: 91-104.","journal-title":"Mol Biol Evol"},{"key":"1670_CR25","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1038\/387247a0","volume":"387","author":"DH Lunt","year":"1997","unstructured":"Lunt DH, Hyman BC: Animal mitochondrial DNA recombination. Nature. 1997, 387: 247-10.1038\/387247a0.","journal-title":"Nature"},{"key":"1670_CR26","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1007\/s00239-002-2420-3","volume":"56","author":"M Dowton","year":"2003","unstructured":"Dowton M, Castro LR, Campbell SL, Bargon SD, Austin AD: Frequent mitochondrial gene rearrangements at the Hymenopteran nad3-nad5 junction. J Mol Evol. 2003, 56: 517-526. 10.1007\/s00239-002-2420-3.","journal-title":"J Mol Evol"},{"key":"1670_CR27","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1093\/genetics\/130.3.471","volume":"130","author":"R Okimoto","year":"1992","unstructured":"Okimoto R, Macfarlane JL, Clary DO, Wolstenholme DR: The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics. 1992, 130: 471-498.","journal-title":"Genetics"},{"key":"1670_CR28","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1093\/genetics\/131.2.397","volume":"131","author":"RJ Hoffman","year":"1992","unstructured":"Hoffman RJ, Boore JL, Brown WM: A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics. 1992, 131: 397-412.","journal-title":"Genetics"},{"key":"1670_CR29","volume-title":"Crassostrea gigas mitochondrial DNA","author":"SH Kim","year":"1999","unstructured":"Kim SH, Je EY, Park DW: Crassostrea gigas mitochondrial DNA. 1999, GenBank accession number AF177226"},{"key":"1670_CR30","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1016\/S1055-7903(03)00194-5","volume":"29","author":"KL Adams","year":"2003","unstructured":"Adams KL, Palmer JD: Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol Phylogenet Evol. 2003, 29: 380-395. 10.1016\/S1055-7903(03)00194-5.","journal-title":"Mol Phylogenet Evol"},{"key":"1670_CR31","first-page":"49","volume-title":"Ribosomal RNA: Structure, Evolution, Processing, and Function in Protein Biosynthesis","author":"MW Gary","year":"1996","unstructured":"Gary MW, Schnare MN: Evolution of rRNA gene organization. Ribosomal RNA: Structure, Evolution, Processing, and Function in Protein Biosynthesis. Edited by: Zimmermann RA, Dahlberg AE. 1996, Boca Raton, FL, CRC Press, 49-69."},{"key":"1670_CR32","volume-title":"Cold Spring Harbor","author":"JE Sambrook","year":"1989","unstructured":"Sambrook JE, Fritsch EF, Maniatis T: Molecular Cloning, A laboratory Manual. Cold Spring Harbor. 1989, New York, Cold Spring Harbor Laboratory, 2","edition":"2"},{"key":"1670_CR33","unstructured":"The Basic Local Alignment Search Tool (BLAST). [http:\/\/www.ncbi.nlm.nih.gov\/BLAST\/]"},{"key":"1670_CR34","unstructured":"NCBI Open Reading Frame Finder. [http:\/\/www.ncbi.nlm.nih.gov\/gorf\/gorf.html]"},{"key":"1670_CR35","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1093\/nar\/25.5.0955","volume":"25","author":"TM Lowe","year":"1997","unstructured":"Lowe TM, Eddy SR: A program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res. 1997, 25: 955-964. 10.1093\/nar\/25.5.955.","journal-title":"Nucl Acids Res"},{"key":"1670_CR36","unstructured":"tRNAscan-SE Search Server. [http:\/\/selab.janelia.org\/tRNAscan-SE\/]"},{"key":"1670_CR37","unstructured":"GenBank. [http:\/\/www.ncbi.nlm.nih.gov\/]"},{"key":"1670_CR38","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1093\/nar\/gkg077","volume":"31","author":"D Jameson","year":"2003","unstructured":"Jameson D, Gibson AP, Hudelot C, Higgs PG: OGRe: a relational database for comparative analysis of mitochondrial genomes. Nucl Acids Res. 2003, 31: 202-206. 10.1093\/nar\/gkg077.","journal-title":"Nucl Acids Res"},{"key":"1670_CR39","unstructured":"OGRe (the Organellar Genome Retrieval system). [http:\/\/drake.physics.mcmaster.ca\/ogre\/index.shtml]"},{"key":"1670_CR40","doi-asserted-by":"crossref","unstructured":"Lin YC, Lu CL, Liu YC, Tang CY: SPRING: a tool for the analysis of genome rearrangement using reversals and block-Interchanges. Nucl Acids Res. 2006, W696-W699. 10.1093\/nar\/gkl169. 34 Web Server","DOI":"10.1093\/nar\/gkl169"},{"key":"1670_CR41","unstructured":"SPRING: Sorting Permutation by Reversals and block-Interchanges. [http:\/\/algorithm.cs.nthu.edu.tw\/tools\/SPRING\/]"},{"key":"1670_CR42","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1093\/bioinformatics\/bti054","volume":"21","author":"P Stothard","year":"2005","unstructured":"Stothard P, Wishart DS: Circular genome visualization and exploration using CGView. Bioinformatics. 2005, 21: 537-539. 10.1093\/bioinformatics\/bti054.","journal-title":"Bioinformatics"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2164-9-477.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,31]],"date-time":"2021-08-31T23:29:49Z","timestamp":1630452589000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/1471-2164-9-477"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,10,11]]},"references-count":42,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["1670"],"URL":"https:\/\/doi.org\/10.1186\/1471-2164-9-477","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,10,11]]},"assertion":[{"value":"18 February 2008","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 October 2008","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 October 2008","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"477"}}