Published February 18, 2026
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New mitochondrial genomes of Saccostrea (Mollusca, Ostreidae) specimens from Hainan Island
Authors/Creators
- 1. School of Marine Biology and Fisheries, Hainan University, Haikou, China|College of Innovation and Entrepreneurship of Hainan University, Haikou, China
- 2. School of Marine Biology and Fisheries, Hainan University, Haikou, China
- 3. School of Marine Biology and Fisheries, Hainan University, Haikou, China|College of Innovation and Entrepreneurship of Hainan University, Haikou, China|Sanya Nanfan Research Institute, Hainan University, Sanya, China
Description
The taxonomic classification of oysters, particularly within the genus Saccostrea, remains poorly resolved due to limitations in traditional morphological and single-gene approaches. To address this, we sequenced the mitochondrial genomes of four Saccostrea specimens (Saccostrea MBSR 211-214) from Hainan Island. The complete mitochondrial genomes (16,280–16,289 bp) revealed a conserved gene arrangement, including 12 protein-coding genes (PCGs), 23 transfer RNA (tRNA), and two ribosomal RNA (rRNA) genes on a single strand, with a fragmented 16S rRNA gene as a distinctive feature. Different OTU delimitation methods consistently identified these four lineages as two novel operational taxonomic units (OTUs). Within one of the OTUs, there are high levels of intraspecific divergence, exhibiting the potential for independent evolution. Our analysis reclassified the publicly available mitochondrial genomes of Saccostrea into nine OTUs, further revealing significant mislabeling on GenBank as indicated by previous studies. The study adds new mitogenomic resources for Saccostrea and provides data useful for future integrative taxonomic work.
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References
- Amaral VS, Simone LRL (2016) Comparative anatomy of five species of Saccostrea Dollfus & Dautzenberg, 1920 (Bivalvia: Ostreidae) from the Pacific Ocean. The Nautilus 130(2): 53–71. https://doi.org/10.5281/zenodo.15938620
- Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF (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
- Chen S, Zhou Y, Chen Y, Gu J (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34(17): i884–i890. https://doi.org/10.1093/bioinformatics/bty560
- Chen Y, Li C, Lu R, Wang H (2024) Morphological and molecular analysis identified a subspecies of Crassostrea ariakensis (Fujita, 1913) along the coast of Asia. Genes 15(5): 644. https://doi.org/10.3390/genes15050644
- Crocetta F, Mariottini P, Salvi D, Oliverio M (2015) Does GenBank provide a reliable DNA barcode reference toidentify small alien oysters invading the Mediterranean Sea? Journal of the Marine Biological Association of the United Kingdom 95(1): 111–122. https://doi.org/10.1017/S0025315414001027
- Cui Z, Hu L, Li C, Zhang Z, Guo X, Wang H (2021) Identification of Saccostrea mordax and a new species Saccostrea mordoides sp. nov. (Bivalvia: Ostreidae) from China. Journal of Shellfish Research 40(1): 63–75. https://doi.org/10.2983/035.040.0107
- Darty K, Denise A, Ponty Y (2009) VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics: 25(15): 1974–1975. https://doi.org/10.1093/bioinformatics/btp250
- Delcour N, Garzia M, Oliver PG, Berrilli E, Toso A, Bariche M, Albano PG, Mariottini P, Salvi D (2025) High genetic diversity and lack of structure underlie the invasion history of the non-indigenous oyster Dendostrea cf. crenulifera (Mollusca, Ostreida, Ostreidae) spreading in the eastern Mediterranean Sea. NeoBiota 101: 277–302. https://doi.org/10.3897/neobiota.101.154917
- Guo X, Li C, Wang H, Xu Z (2018) Diversity and evolution of living oysters. Journal of Shellfish Research 37(4): 755–771. https://doi.org/10.2983/035.037.0407
- Hamaguchi M, Shimabukuro H, Usuki H, Hori M (2014) Occurrences of the Indo-West Pacific rock oyster Saccostrea cucullata in mainland Japan. Marine Biodiversity Records 7: e84. https://doi.org/10.1017/S1755267214000864
- Harry HW (1985) Synopsis of the supraspecific classification of living oysters (Bivalvia: Gryphaeidae and Ostreidae). The Veliger 28(2): 121–158. https://doi.org/10.5281/zenodo.16667686
- Heng X, Li F, Xie D, Wang A, Liu C, Yang Y (2025) Species diversity of oysters (Mollusca, Bivalvia) in the intertidal zone of Hainan Island revealed by DNA barcoding analysis. ZooKeys 1241: 247–260. https://doi.org/10.3897/zookeys.1241.139908
- Hu L, Wang H, Zhang Z, Li C, Guo X (2019) Classification of small flat oysters of Ostrea stentina species complex and a new species Ostrea neostentina sp. nov. (Bivalvia: Ostreidae). Journal of Shellfish Research 38(2): 295–308. https://doi.org/10.2983/035.038.0210
- Hurst LD (2002) The Ka/Ks ratio: diagnosing the form of sequence evolution. TRENDS in Genetics 18(9): 486–487. https://doi.org/10.1016/S0168-9525(02)02722-1
- Kapli P, Lutteropp S, Zhang J, Kobert K, Pavlidis P, Stamatakis A, Flouri T (2017) Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics 33(11): 1630–1638. https://doi.org/10.1093/bioinformatics/btx025
- Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28(12): 1647–1649. https://doi.org/10.1093/bioinformatics/bts199
- Lam K, Morton B (2006) Morphological and mitochondrial-DNA analysis of the Indo-West Pacific rock oysters (Ostreidae: Saccostrea species). Journal of Molluscan Studies 72(3): 235–245. https://doi.org/10.1093/mollus/eyl002
- Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B (2016) PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and Evolution 34(3): 772–773. https://doi.org/10.1093/molbev/msw260
- Laslett D, Canbäck B (2008) ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 24(2): 172–175. https://doi.org/10.1093/bioinformatics/btm573
- Li C, Haws M, Wang H, Guo X (2017) Taxonomic classification of three oyster (Ostreidae) species from Myanmar. Journal of Shellfish Research 36(2): 365–371. https://doi.org/10.2983/035.036.0209
- Li C, Kou Q, Zhang Z, Hu L, Huang W, Cui Z, Liu Y, Ma P, Wang H (2021) Reconstruction of the evolutionary biogeography reveal the origins and diversification of oysters (Bivalvia: Ostreidae). Molecular Phylogenetics and Evolution 164: 107268. https://doi.org/10.1016/j.ympev.2021.107268
- Li S, Qin Y, Shi G, Wan W, Liao Q, Ma H, Li J, Yu Z, Pan Y, Zhang Y (2023) Feasibility of interspecific hybridization between Iwagaki oyster, Crassostrea nippona and Portuguese oyster, Crassostrea angulata. Aquaculture 563: 739002. https://doi.org/10.1016/j.aquaculture.2022.739002
- Liu J, Li Q, Kong L, Yu H, Zheng X (2011) Identifying the true oysters (Bivalvia: Ostreidae) with mitochondrial phylogeny and distance-based DNA barcoding. Molecular Ecology Resources 11(5): 820–830. https://doi.org/10.1111/j.1755-0998.2011.03025.x
- Lohan KMP, Hill-Spanik KM, Torchin ME, Strong EE, Fleischer RC, Ruiz GM (2015) Molecular phylogenetics reveals first record and invasion of Saccostrea species in the Caribbean. Marine Biology 162(5): 957–968. https://doi.org/10.1007/s00227-015-2637-5
- Lu R, Chen Y, Ma P, Li C, Zhang Z, Zang G, Liu Z, Wang H (2024) Species composition and distribution of common Crassostrea and Saccostrea oysters along the coast of Hainan Island. Journal of Oceanology and Limnology 42(5): 1609–1620. https://doi.org/10.1007/s00343-024-3213-y
- McDougall C, Nenadic N, Richardson M, Healy JM (2024) Molecular identification of intertidal rock oyster species in north-eastern Australia reveals new candidates for aquaculture. Aquaculture 587: 740838. https://doi.org/10.1016/j.aquaculture.2024.740838
- Milbury CA, Lee JC, Cannone JJ, Gaffney PM, Gutell RR (2010) Fragmentation of the large subunit ribosomal RNA gene in oyster mitochondrial genomes. BMC Genomics 11: 485. https://doi.org/10.1186/1471-2164-11-485
- Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ (2014) 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
- Oliver PG, Garzia M, Paulay G, Salvi D (2025) On the species identity of a tropical oyster (Bivalvia, Ostreidae, Dendostrea) invading the eastern Mediterranean Sea. ZooKeys 1243: 207–224. https://doi.org/10.3897/zookeys.1243.152856
- Puillandre N, Brouillet S, Achaz G (2021) ASAP: Assemble Species by Automatic Partitioning. Molecular Ecology Resources 21(2): 609–620. https://doi.org/10.1111/1755-0998.13281
- Raith M, Zacherl DC, Pilgrim EM, Eernisse DJ (2016) Phylogeny and species diversity of Gulf of California oysters (Ostreidae) inferred from mitochondrial DNA. American Malacological Bulletin 33(2): 263–283. https://doi.org/10.4003/006.033.0206
- Reece KS, Cordes JF, Stubbs JB, Hudson KL, Francis EA (2008) Molecular phylogenies help resolve taxonomic confusion with Asian Crassostrea oyster species. Marine Biology 153(4): 709–721. https://doi.org/10.1007/s00227-007-0846-2
- Ren J, Liu X, Jiang F, Guo X, Liu B (2010) Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia. BMC Evolutionary Biology 10(1): 394. https://doi.org/10.1186/1471-2148-10-394
- Rombel IT, Sykes KF, Rayner S, Johnston SA (2002) ORF-FINDER: a vector for high-throughput gene identification. Gene 282(1–2): 33–41. https://doi.org/10.1016/S0378-1119(01)00819-8
- Ronquist F, Teslenko M, Van Der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (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
- Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A (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
- Salvi D, Mariottini P (2016) Molecular taxonomy in 2D: A novel ITS2 rRNA sequence-structure approach guides the description of the oysters' subfamily Saccostreinae and the genus Magallana (Bivalvia: Ostreidae). Zoological Journal of the Linnean Society 178(3): 651–670. https://doi.org/10.1111/zoj.12455
- Salvi D, Macali A, Mariottini P (2014) Molecular phylogenetics and systematics of the bivalve family Ostreidae based on rRNA sequence-structure models and multilocus species tree. PLoS ONE 9(9): e108696. https://doi.org/10.1371/journal.pone.0108696
- Sekino M, Yamashita H (2013) Mitochondrial DNA barcoding for Okinawan oysters: a cryptic population of the Portuguese oyster Crassostrea angulata in Japanese waters. Fisheries Science 79(1): 61–76. https://doi.org/10.1007/s12562-012-0577-2
- Sekino M, Yamashita H (2016) Mitochondrial and nuclear DNA analyses of Saccostrea oysters in Japan highlight the confused taxonomy of the genus. Journal of Molluscan Studies 82(4): 492–506. https://doi.org/10.1093/mollus/eyw022
- Sigwart JD, Wong NL WS, Esa Y (2021) Global controversy in oyster systematics and a newly described species from SE Asia (Bivalvia: Ostreidae: Crassostreinae). Marine Biodiversity 51: 83. https://doi.org/10.1007/s12526-021-01203-x
- Stenzel HB (1971) Oysters. In: Moore RC (Ed.) Treatise on Invertebrate Paleontology, Part N, Mollusca Vol. 3, Bivalvia 6. Geological Society of America, Boulder, N953–N1224.
- Tamura K, Stecher G, Kumar S (2021) MEGA11: Molecular Evolutionary Genetics Analysis version 11. Molecular Biology and Evolution 38(7): 3022–3027. https://doi.org/10.1093/molbev/msab120
- Torstrom SM, Pangle KL, Swanson BJ (2014) Shedding subspecies: the influence of genetics on reptile subspecies taxonomy. Molecular Phylogenetics and Evolution 76: 134–143. https://doi.org/10.1016/j.ympev.2014.03.011
- Wu X, Xu X, Yu Z, Wei Z, Xia J (2010) Comparison of seven Crassostrea mitogenomes and phylogenetic analyses. Molecular Phylogenetics and Evolution 57(1): 448–454. https://doi.org/10.1016/j.ympev.2010.05.029
- Xiao S, Wu X, Li L, Yu Z (2015) Complete mitochondrial genome of the Olympia oyster Ostrea lurida (Bivalvia, Ostreidae). Mitochondrial DNA 26(3): 471–472. https://doi.org/10.3109/19401736.2013.834428
- Yu H, Li Q (2012) Complete mitochondrial DNA sequence of Crassostrea nippona: comparative and phylogenomic studies on seven commercial Crassostrea species. Molecular Biology Reports 39(2): 999–1009. https://doi.org/10.1007/s11033-011-0825-z
- Zhan X, Zhang S, Gu Z, Wang A (2018) Complete mitochondrial genomes of two pearl oyster species (Bivalvia: Pteriomorphia) reveal novel gene arrangements. Journal of Shellfish Research 37(5): 1039–1050. https://doi.org/10.2983/035.037.0515
- Zhou Z, Song Y, Zheng Z, Liu Y, Yao H, Rao X, Lin G (2024) The complete mitochondrial genome and phylogenetic analysis of the freshwater shellfish Novaculina chinensis (Bivalvia: Pharidae). International Journal of Molecular Sciences 25(1): 67. https://doi.org/10.3390/ijms25010067