Molecular phylogeny and divergence time estimates for native giant clams (Cardiidae: Tridacninae) in the Asia-Pacific: Evidence from mitochondrial genomes and nuclear 18S rRNA genes
Giant clams are conspicuous bivalves that inhabit in coral reefs. Among the giant clams, eight species of subfamily Tridacninae are the most common in the Asia-Pacific. However, very little is known about their evolutionary history. Here, we determined the complete mitochondria genome of Hippopus po...
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Frontiers Media S.A.
2022-10-01
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| Series: | Frontiers in Marine Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmars.2022.964202/full |
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| author | Haitao Ma Haitao Ma Haitao Ma Haitao Ma Dongmei Yu Jun Li Jun Li Jun Li Jun Li Yanping Qin Yanping Qin Yanping Qin Yanping Qin Yang Zhang Yang Zhang Yang Zhang Yang Zhang Zhiming Xiang Zhiming Xiang Zhiming Xiang Zhiming Xiang Yuehuan Zhang Yuehuan Zhang Yuehuan Zhang Yuehuan Zhang Ziniu Yu Ziniu Yu Ziniu Yu Ziniu Yu |
| author_facet | Haitao Ma Haitao Ma Haitao Ma Haitao Ma Dongmei Yu Jun Li Jun Li Jun Li Jun Li Yanping Qin Yanping Qin Yanping Qin Yanping Qin Yang Zhang Yang Zhang Yang Zhang Yang Zhang Zhiming Xiang Zhiming Xiang Zhiming Xiang Zhiming Xiang Yuehuan Zhang Yuehuan Zhang Yuehuan Zhang Yuehuan Zhang Ziniu Yu Ziniu Yu Ziniu Yu Ziniu Yu |
| author_sort | Haitao Ma |
| collection | DOAJ |
| description | Giant clams are conspicuous bivalves that inhabit in coral reefs. Among the giant clams, eight species of subfamily Tridacninae are the most common in the Asia-Pacific. However, very little is known about their evolutionary history. Here, we determined the complete mitochondria genome of Hippopus porcellanus, which was 29,434 bp in size and contained 13 protein-coding genes, 2 rRNAs and 23 tRNAs. The A+T composition of protein-coding regions was 57.99%, and the AT composition of the 3rd codon position was 59.33%, of which in agreement with the invertebrate bias favoring codons ending in A or T. Analysis of phylogenetic relationships according to the concatenated nucleotide data set containing 18S rRNA gene and 13 protein-coding genes, the phylogenetic relationship was analyzed by Maximum likelihood and Bayesian inference methods. The results showed that T. maxima was placed with the clade comprising T. noae, T. squamosa, and T. crocea, in which T. squamosa was highly similar to T. crocea and is consistent with the results of the previous studies using15 mitochondrial markers and nuclear 18S rRNA. Moreover, the inferred divergence time of Tridacnidae species is generally consistent with the fossil record of Tridacnidae. The divergence time of H. porcellanus and H. hippopus was about 10.64 Mya, this result is in agreement with the speculation that H. porcellanus also originated in Miocene. The availability of molecular phylogeny and divergence time estimation provides information genetic relationship of Tridacninae, which could be helpful to the ecological research and conservation of giant clams. |
| first_indexed | 2024-04-11T08:37:09Z |
| format | Article |
| id | doaj.art-e96d52e7c8394028a0be8f47cc7dfd36 |
| institution | Directory Open Access Journal |
| issn | 2296-7745 |
| language | English |
| last_indexed | 2024-04-11T08:37:09Z |
| publishDate | 2022-10-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Marine Science |
| spelling | doaj.art-e96d52e7c8394028a0be8f47cc7dfd362022-12-22T04:34:18ZengFrontiers Media S.A.Frontiers in Marine Science2296-77452022-10-01910.3389/fmars.2022.964202964202Molecular phylogeny and divergence time estimates for native giant clams (Cardiidae: Tridacninae) in the Asia-Pacific: Evidence from mitochondrial genomes and nuclear 18S rRNA genesHaitao Ma0Haitao Ma1Haitao Ma2Haitao Ma3Dongmei Yu4Jun Li5Jun Li6Jun Li7Jun Li8Yanping Qin9Yanping Qin10Yanping Qin11Yanping Qin12Yang Zhang13Yang Zhang14Yang Zhang15Yang Zhang16Zhiming Xiang17Zhiming Xiang18Zhiming Xiang19Zhiming Xiang20Yuehuan Zhang21Yuehuan Zhang22Yuehuan Zhang23Yuehuan Zhang24Ziniu Yu25Ziniu Yu26Ziniu Yu27Ziniu Yu28Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaHainan Provincial Key Laboratory of Tropical Marine Biology Technology, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, ChinaSouthern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Department of Science and Technology of Guangdong Province, Guangzhou, ChinaInnovation Academy of South China Sea Ecology an Environmental Engineering, Chinese Academy of Sciences, Guangzhou, ChinaGuangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, ChinaKey Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaHainan Provincial Key Laboratory of Tropical Marine Biology Technology, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, ChinaSouthern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Department of Science and Technology of Guangdong Province, Guangzhou, ChinaInnovation Academy of South China Sea Ecology an Environmental Engineering, Chinese Academy of Sciences, Guangzhou, ChinaKey Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaHainan Provincial Key Laboratory of Tropical Marine Biology Technology, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, ChinaSouthern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Department of Science and Technology of Guangdong Province, Guangzhou, ChinaInnovation Academy of South China Sea Ecology an Environmental Engineering, Chinese Academy of Sciences, Guangzhou, ChinaKey Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaHainan Provincial Key Laboratory of Tropical Marine Biology Technology, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, ChinaSouthern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Department of Science and Technology of Guangdong Province, Guangzhou, ChinaInnovation Academy of South China Sea Ecology an Environmental Engineering, Chinese Academy of Sciences, Guangzhou, ChinaKey Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaHainan Provincial Key Laboratory of Tropical Marine Biology Technology, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, ChinaSouthern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Department of Science and Technology of Guangdong Province, Guangzhou, ChinaInnovation Academy of South China Sea Ecology an Environmental Engineering, Chinese Academy of Sciences, Guangzhou, ChinaKey Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaHainan Provincial Key Laboratory of Tropical Marine Biology Technology, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, ChinaSouthern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Department of Science and Technology of Guangdong Province, Guangzhou, ChinaInnovation Academy of South China Sea Ecology an Environmental Engineering, Chinese Academy of Sciences, Guangzhou, ChinaKey Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaHainan Provincial Key Laboratory of Tropical Marine Biology Technology, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, ChinaSouthern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Department of Science and Technology of Guangdong Province, Guangzhou, ChinaInnovation Academy of South China Sea Ecology an Environmental Engineering, Chinese Academy of Sciences, Guangzhou, ChinaGiant clams are conspicuous bivalves that inhabit in coral reefs. Among the giant clams, eight species of subfamily Tridacninae are the most common in the Asia-Pacific. However, very little is known about their evolutionary history. Here, we determined the complete mitochondria genome of Hippopus porcellanus, which was 29,434 bp in size and contained 13 protein-coding genes, 2 rRNAs and 23 tRNAs. The A+T composition of protein-coding regions was 57.99%, and the AT composition of the 3rd codon position was 59.33%, of which in agreement with the invertebrate bias favoring codons ending in A or T. Analysis of phylogenetic relationships according to the concatenated nucleotide data set containing 18S rRNA gene and 13 protein-coding genes, the phylogenetic relationship was analyzed by Maximum likelihood and Bayesian inference methods. The results showed that T. maxima was placed with the clade comprising T. noae, T. squamosa, and T. crocea, in which T. squamosa was highly similar to T. crocea and is consistent with the results of the previous studies using15 mitochondrial markers and nuclear 18S rRNA. Moreover, the inferred divergence time of Tridacnidae species is generally consistent with the fossil record of Tridacnidae. The divergence time of H. porcellanus and H. hippopus was about 10.64 Mya, this result is in agreement with the speculation that H. porcellanus also originated in Miocene. The availability of molecular phylogeny and divergence time estimation provides information genetic relationship of Tridacninae, which could be helpful to the ecological research and conservation of giant clams.https://www.frontiersin.org/articles/10.3389/fmars.2022.964202/fullTridacninaemitochondrial genome18Sgene arrangementphylogenymolecular clock |
| spellingShingle | Haitao Ma Haitao Ma Haitao Ma Haitao Ma Dongmei Yu Jun Li Jun Li Jun Li Jun Li Yanping Qin Yanping Qin Yanping Qin Yanping Qin Yang Zhang Yang Zhang Yang Zhang Yang Zhang Zhiming Xiang Zhiming Xiang Zhiming Xiang Zhiming Xiang Yuehuan Zhang Yuehuan Zhang Yuehuan Zhang Yuehuan Zhang Ziniu Yu Ziniu Yu Ziniu Yu Ziniu Yu Molecular phylogeny and divergence time estimates for native giant clams (Cardiidae: Tridacninae) in the Asia-Pacific: Evidence from mitochondrial genomes and nuclear 18S rRNA genes Frontiers in Marine Science Tridacninae mitochondrial genome 18S gene arrangement phylogeny molecular clock |
| title | Molecular phylogeny and divergence time estimates for native giant clams (Cardiidae: Tridacninae) in the Asia-Pacific: Evidence from mitochondrial genomes and nuclear 18S rRNA genes |
| title_full | Molecular phylogeny and divergence time estimates for native giant clams (Cardiidae: Tridacninae) in the Asia-Pacific: Evidence from mitochondrial genomes and nuclear 18S rRNA genes |
| title_fullStr | Molecular phylogeny and divergence time estimates for native giant clams (Cardiidae: Tridacninae) in the Asia-Pacific: Evidence from mitochondrial genomes and nuclear 18S rRNA genes |
| title_full_unstemmed | Molecular phylogeny and divergence time estimates for native giant clams (Cardiidae: Tridacninae) in the Asia-Pacific: Evidence from mitochondrial genomes and nuclear 18S rRNA genes |
| title_short | Molecular phylogeny and divergence time estimates for native giant clams (Cardiidae: Tridacninae) in the Asia-Pacific: Evidence from mitochondrial genomes and nuclear 18S rRNA genes |
| title_sort | molecular phylogeny and divergence time estimates for native giant clams cardiidae tridacninae in the asia pacific evidence from mitochondrial genomes and nuclear 18s rrna genes |
| topic | Tridacninae mitochondrial genome 18S gene arrangement phylogeny molecular clock |
| url | https://www.frontiersin.org/articles/10.3389/fmars.2022.964202/full |
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