Complete Mitochondrial Genomes of Magallana saidii (Wong & Sigwart, 2021) from Malaysia and Phylogenetic Insight
Article Sidebar
Main Article Content
Abstract
Magallana saidii (Wong & Sigwart, 2021), locally known as the white oyster, is an oyster species endemic to the Muar River, Johor, Malaysia. Although long recognized and exploited by local fishers, it has not been reported elsewhere, making it of conservation concern due to its restricted distribution. Despite its ecological and economic importance, M. saidii has received limited molecular attention since its recent taxonomic description. In this study, two complete mitochondrial genomes (mitogenomes) of M. saidii from Muar, Johor are presented. Whole-genome sequencing was performed using the Illumina NovaSeq6000 platform, and the mitochondrial contigs were assembled using a de novo approach. The mitogenomes measured 21,499 bp (PV711311) and 21,505 bp (PV711312) in length. Each mitogenome comprised 38 genes, including 13 protein-coding genes, 23 transfer RNAs, and two ribosomal RNAs, with largely conserved gene arrangement. Notably, the atp8 gene, which is often unresolved in oyster mitogenomes, was clearly identified. The mitogenome exhibited a strong adenine and thymine bias (A+T content of 66.3%), with nucleotide compositions of 37.3% thymine, 29.0% adenine, 20.6% guanine and 13.0% cytosine. Maximum likelihood phylogenetic analysis based on 13 concatenated protein-coding genes recovered M. saidii as a well-supported clade with another M. saidii mitogenome from GenBank (accession PV564049), and as sister to a clade comprising M. nippona, M. hongkongensis, and M. ariakensis. The complete mitogenome of M. saidii provides a valuable genetic reference to support future phylogenetic studies and conservation management of oysters in Malaysia.
Article Details
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
Copyright Transfer Statement
The copyright of this article is transferred to Current Applied Science and Technology journal with effect if and when the article is accepted for publication. The copyright transfer covers the exclusive right to reproduce and distribute the article, including reprints, translations, photographic reproductions, electronic form (offline, online) or any other reproductions of similar nature.
The author warrants that this contribution is original and that he/she has full power to make this grant. The author signs for and accepts responsibility for releasing this material on behalf of any and all co-authors.
Here is the link for download: Copyright transfer form.pdf
References
Admodisastro, V. A., Ransangan, J., Ilias, N., & Tan, S. H. (2022). Oyster farming potential in Sabah, Malaysia. International Journal of Aquatic Research and Environmental Studies, 2(1), 17-22. https://doi.org/10.70102/IJARES/V2I1/3
Arif, I. A., Khan, H. A., Bahkali, A. H., Al Homaidan, A. A., Al Farhan, A. H., Al Sadoon, M., & Shobrak, M. (2011). DNA marker technology for wildlife conservation. Saudi Journal of Biological Sciences, 18(3), 219-225. https://doi.org/10.1016/j.sjbs.2011.03.002
Bisbal-Pardo, C. I., Río-Portilla, M. A. del, & Rocha-Olivares, A. (2014). Novel gene arrangement in the mitochondrial genome of the Cortés geoduck clam (Panopea globosa). Mitochondrial DNA Part A, 27(3), 1957-1958. https://doi.org/10.3109/19401736.2014.971305
Botta, R., Asche, F., Borsum, J. S., & Camp, E. V. (2020). A review of global oyster aquaculture production and consumption. Marine Policy, 117, Article 103952. https://doi.org/10.1016/j.marpol.2020.103952
Bridge, D., Cunningham, C. W., Schierwater, B., DeSalle, R., & Buss, L. W. (1992). Class-level relationships in the phylum Cnidaria: evidence from mitochondrial genome structure. Proceedings of the National Academy of Sciences of the United States of America, 89(18), 8750-8753. https://doi.org/10.1073/pnas.89.18.8750
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
Doinsing, J. W., Al-Azad, S., & Ransangan, J. (2024). Reproductive biology and spawning pattern of oyster Magallana bilineata in Mengkabong Bay, Sabah, Malaysia. Croatian Journal of Fisheries, 82(1), 19-32. https://doi.org/10.2478/cjf-2024-0003
Edgar, R. C. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792-1797. https://doi.org/10.1093/nar/gkh340
Ghiselli, F., Iannello, M., Piccinini, G., & Milani, L. (2021). Bivalve molluscs as model systems for studying mitochondrial biology. Integrative and Comparative Biology, 61(5), 1699-1714. https://doi.org/10.1093/icb/icab057
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
Jin, J. J., Yu, W. B., Yang, J. B., Song, Y., dePamphilis, C. W., Yi, T. S., & Li, D. Z. (2020). GetOrganelle: A fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology, 21, Article 241. https://doi.org/10.1186/s13059-020-02154-5
Krzywinski, M., Schein, J., Birol, İ., Connors, J., Gascoyne, R., Horsman, D., Jones, S. J., & Marra, M. A. (2009). Circos: An information aesthetic for comparative genomics. Genome Research, 19(9), 1639-1645. https://doi.org/10.1101/gr.092759.109
Li, C., Kou, Q., Zhang, Z., Hu, L., Huang, W., Cui, Z., Liu, Y., Ma, P. & Wang, H. (2021a). Reconstruction of the evolutionary biogeography reveal the origins and diversification of oysters (Bivalvia: Ostreidae). Molecular Phylogenetics and Evolution, 164, Article 107268. https://doi.org/10.1016/j.ympev.2021.107268
Li, Y., Xu, L., Wang, X., Huang, D., Wang, L., Ning, J., Liu, S & Du, F. (2021b). The complete mitochondrial genome of the tropical oyster Saccostrea echinata (Bivalvia: Ostreidae) from the South China Sea. Mitochondrial DNA Part B, 6(2), 384-386. https://doi.org/10.1080/23802359.2020.1869610
Liao, X., Zhu, X., & Yang, M. (2020). Complete mitochondrial DNA genomes for Geloina erosa (Veneroida: Corbiculidae). Mitochondrial DNA Part B, 5(2), 1590-1591. https://doi.org/10.1080/23802359.2020.1742616
Marková, S., Filipi, K., Searle, J. B., & Kotlík, P. (2015). Mapping 3′ transcript ends in the bank vole (Clethrionomys glareolus) mitochondrial genome with RNA-Seq. BMC Genomics, 16, Article 870. https://doi.org/10.1186/s12864-015-2103-2
McDougall, C., Nenadic, N., Richardson, M., & Healy, J. M. (2024). Molecular identification of intertidal rock oyster species in north-eastern Australia reveals new candidates for aquaculture. Aquaculture, 587, Article 740838. https://doi.org/10.1016/j.aquaculture.2024.740838
Meng, G., Li, Y., Yang, C., & Liu, S. (2019). MitoZ: A toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Research, 47(11), Article e63. https://doi.org/10.1093/nar/gkz173
Mu, W. (2022). The complete mitochondrial genome of Saccostrea malabonensis (Ostreida: Ostreidae): Characterization and phylogenetic position. Mitochondrial DNA Part B, 7(11), 1945-1947. https://doi.org/10.1080/23802359.2022.2139160
Nawrocki, E. P., & Eddy, S. R. (2013). Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics, 29(22), 2933-2935. https://doi.org/10.1093/bioinformatics/btt509
Nei, M., & Kumar, S. (2000). Molecular evolution and phylogenetics. Oxford University Press.
Quek, Z. B. R., Chang, J. J. M., Ip, Y. C. A., Chan, Y. K. S., & Huang, D. (2021). Mitogenomes reveal alternative initiation codons and lineage-specific gene order conservation in echinoderms. Molecular Biology and Evolution, 38(3), 981-985. https://doi.org/10.1093/molbev/msaa262
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, Article 394. https://doi.org/10.1186/1471-2148-10-394
Salvi, D., & Mariottini, P. (2021). Revision shock in Pacific oyster taxonomy: The genus Magallana (formerly Crassostrea in part) is well-founded and necessary. Zoological Journal of the Linnean Society, 192(1), 43-58. https://doi.org/10.1093/zoolinnean/zlaa112
Salvi, D., Berrilli, E., Garzia, M., & Mariottini, P. (2021). Yet another mitochondrial genome of the Pacific cupped oyster: The published mitogenome of Alectryonella plicatula (Ostreinae) is based on a misidentified Magallana gigas (Crassostreinae). Frontiers in Marine Science, 8, Article 741455. https://doi.org/10.3389/fmars.2021.741455
Santhi, V. V., Chaube, S. K., & Antony, M. M. (2025). A novel mitochondrial gene rearrangement delineate Magallana gryphoides species from other Magallana crassostreine oysters. Molecular Biology Reports, 52(1), Article 247. https://doi.org/10.1007/s11033-025-10335-3
Sigwart, J., Wong, N. L. W. S., & Esa, Y. (2021). Global controversy in oyster systematics and a newly described species from SE Asia (Bivalvia: Ostreidae: Crassostreinae). Marine Biodiversity, 51, Article 83. https://doi.org/10.1007/s12526-021-01203-x
Sun, S., Li, Q., & Kong, L. (2021). Relaxation of selective constraint on the ultra-large mitochondrial genomes of Arcidae (Mollusca: Bivalvia). Journal of Ocean University of China, 20(5), 1157-1166. https://doi.org/10.1007/s11802-021-4707-2
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
Tan, S.-H. A., Chang, G.-O., Yen, P. K., & Teh, C. P. (2014). Oyster culture in Malaysia: Opportunities and challenges. Journal of Science and Technology in the Tropics, 10(2), 99-108.
Tavaré, S. (1986). Some probabilistic and statistical problems in the analysis of DNA sequences. In Lectures on mathematics in the life sciences (Vol. 17, pp. 57-86). American Mathematical Society.
Thornlow, B. P., Hough, J., Roger, J. M., Gong, H., Lowe, T. M., & Corbett-Detig, R. B. (2018). Transfer RNA genes experience exceptionally elevated mutation rates. Proceedings of the National Academy of Sciences of the United States of America, 115(36), 8996-9001. https://doi.org/10.1073/pnas.1801240115
Venton, D. (2014). Highlight: Not like a textbook-Nuclear genes in Blastocystis use mRNA polyadenylation for stop codons. Genome Biology and Evolution, 6(8), 1962-1963. https://doi.org/10.1093/gbe/evu167
World Register of Marine Species. (2025). Magallana bilineata (Röding, 1798). https://www.marinespecies.org/aphia.php?p=taxdetails&id=836036
Xu, M., Yang, X., Song, X., Xu, K., & Yang, L. (2021). Seasonal analysis of artificial oyster reef ecosystems: Implications for sustainable fisheries management. Aquaculture International, 29(1), 167-192. https://doi.org/10.1007/s10499-020-00617-x
Yu, H., & Li, Q. (2011). Mutation and selection on the wobble nucleotide in tRNA anticodons in marine bivalve mitochondrial genomes. PLoS ONE, 6(1), Article e16147. https://doi.org/10.1371/journal.pone.0016147
Zhao, B., Gao, S., Zhao, M., Lv, H., Song, J., Wang, H., Zeng, Q., & Liu, J. (2022). Mitochondrial genomic analyses provide new insights into the “missing” atp8 and adaptive evolution of Mytilidae. BMC Genomics, 23(1), Article 738. https://doi.org/10.1186/s12864-022-08940-8
Zhu, L., Zhu, Z., Zhu, L., Wang, D., Wang, J., & Lin, Q. (2021). The complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) with implication of phylogenomics and population genetics. PLoS ONE, 16(11), Article e0255547. https://doi.org/10.1371/journal.pone.0255547
