1
|
Ma P, Liu Y, Wang J, Chen Y, Zhang Z, Zhang T, Wang H. Comparative analysis of the mitochondrial genomes of the family Mactridae (Mollusca: Venerida) and their phylogenetic implications. Int J Biol Macromol 2023; 249:126081. [PMID: 37536404 DOI: 10.1016/j.ijbiomac.2023.126081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/05/2023]
Abstract
Taxonomy and phylogenetic relationships within the family Mactridae have remained debatable because of the plasticity of morphological characteristics and the lack of accurate molecular data, thereby resulting in abundant synonyms and taxa rearrangements. Mitochondrial genomes (mitogenomes) have been widely used as powerful tools to reconstruct phylogenies of various groups of mollusks; however, they have not been used for studying the phylogeny of mactrids specifically. In the present study, mitogenomes of seven Mactridae species, namely Mactra chinensis, Mactra cygnus, Mactra quadrangularis, Mactra cumingii, Mactrinula dolabrata, Raeta pulchella, and Raeta sp., were sequenced by Illumina high-throughput sequencing, and a comparative mitochondrial genomic analysis was conducted. The newly sequenced mitogenomes were double-stranded circular molecules, with all functional genes encoded on the heavy strand. All the new mactrid mitogenomes had two rRNA genes (12S and 16S), 13 protein-coding genes (PCGs) (atp6, cox1, cox2, cox3, cytb, nad1, nad2, nad3, nad4, nad4l, nad5, nad6, and atp8), and 22 tRNAs. The mitogenomes showed considerable variation in AT content, GC skew, and AT skew. The results of the phylogenetic analysis confirmed monophyly of the family Mactridae and suggested that genera Mactrinula, Spisula, Rangia, and Mulinia should not be placed under subfamily Mactrinae. Our results supported that potential cryptic species existed in Mactra antiquata. We also proposed subfamily Kymatoxinae should belong to the family Mactridae rather than Anatinellidae and Mactra alta in China should be Mactra cygnus. Additionally, conservation in functional gene arrangement was found in genera Mactra, Raeta, and Lutraria. But gene orders in S. sachalinensis and S. solida were quite different, questioning their congeneric relationship. Our results further suggested that the taxonomy within the family Mactridae requires an integrative revision.
Collapse
Affiliation(s)
- Peizhen Ma
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yumeng Liu
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jiahui Wang
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Ya Chen
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Zhang
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Haiyan Wang
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| |
Collapse
|
2
|
Sun Y, Liu X, Xie X, Bai Y, Wang S, Teng W, Li D, Li H, Yu Z, Zhang M, Zhou Z, Liu X, Nie H, Du S, Li X, Li Q, Wang Q. A high-quality chromosome-level genome assembly of the bivalve mollusk Mactra veneriformis. G3 (BETHESDA, MD.) 2022; 12:jkac229. [PMID: 36165708 PMCID: PMC9635629 DOI: 10.1093/g3journal/jkac229] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/16/2022] [Indexed: 06/16/2023]
Abstract
Mactra veneriformis (Bivalvia: Mactridae) is a bivalve mollusk of major economic importance in China. Decreased natural yields of M. veneriformis have led to an urgent need for genomic resources. To address this problem and the currently limited knowledge of molecular evolution in this genus, we here report a high-quality chromosome-level genome assembly of M. veneriformis. Our approach yielded a 939.32 Mb assembled genome with an N50 contig length of 7,977.84 kb. Hi-C scaffolding of the genome resulted in assembly of 19 pseudochromosomes. Repetitive elements made up ∼51.79% of the genome assembly. A total of 29,315 protein-coding genes (PCGs) were predicted in M. veneriformis. Construction of a genome-level phylogenetic tree demonstrated that M. veneriformis and Ruditapes philippinarum diverged around 231 million years ago (MYA). Inter-species comparisons revealed that 493 gene families have undergone expansion and 449 have undergone contraction in the M. veneriformis genome. Chromosome-based macrosynteny analysis revealed a high degree of synteny between the 19 chromosomes of M. veneriformis and those of Patinopecten yessoensis. These results suggested that M. veneriformis has a similar karyotype to that of P. yessoensis, and that a highly conserved 19-chromosome karyotype was formed in the early differentiation stages of bivalves. In summary, the genomic resources generated in this work serve as a valuable reference for investigating the molecular mechanisms underlying biological functions in M. veneriformis and will facilitate future genetic improvement and disease treatment in this economically important species. Furthermore, the assembled genome greatly improves our understanding of early genomic evolution of the Bivalvia.
Collapse
Affiliation(s)
| | | | | | | | - Shuo Wang
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Weiming Teng
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Dacheng Li
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Hualin Li
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Zuoan Yu
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Ming Zhang
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Zunchun Zhou
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Xu Liu
- Panjin Guanghe Crab Industry Co., LTD, Panjin 124299, China
| | - Hongtao Nie
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Shaojun Du
- Department of Biochemistry and Molecular Biology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD 21202, USA
| | - Xiaodong Li
- Key Laboratory of Zoonosis, Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Qi Li
- Corresponding author: Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
| | - Qingzhi Wang
- Corresponding author: Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China.
| |
Collapse
|
3
|
Feng JT, Guo YH, Yan CR, Ye YY, Li JJ, Guo BY, Lü ZM. Comparative analysis of the complete mitochondrial genomes in two limpets from Lottiidae (Gastropoda: Patellogastropoda): rare irregular gene rearrangement within Gastropoda. Sci Rep 2020; 10:19277. [PMID: 33159159 PMCID: PMC7648102 DOI: 10.1038/s41598-020-76410-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/21/2020] [Indexed: 01/15/2023] Open
Abstract
To improve the systematics and taxonomy of Patellogastropoda within the evolution of gastropods, we determined the complete mitochondrial genome sequences of Lottia goshimai and Nipponacmea fuscoviridis in the family Lottiidae, which presented sizes of 18,192 bp and 18,720 bp, respectively. In addition to 37 common genes among metazoa, we observed duplication of the trnM gene in L. goshimai and the trnM and trnW genes in N. fuscoviridis. The highest A + T contents of the two species were found within protein-coding genes (59.95% and 54.55%), followed by rRNAs (56.50% and 52.44%) and tRNAs (56.42% and 52.41%). trnS1 and trnS2 could not form the canonical cloverleaf secondary structure due to the lack of a dihydrouracil arm in both species. The gene arrangements in all Patellogastropoda compared with those of ancestral gastropods showed different levels of gene rearrangement, including the shuffling, translocation and inversion of single genes or gene fragments. This kind of irregular rearrangement is particularly obvious in the Lottiidae family. The results of phylogenetic and gene rearrangement analyses showed that L. goshimai and Lottia digitalis clustered into one group, which in turn clustered with N. fuscoviridis in Patellogastropoda. This study demonstrates the significance of complete mitogenomes for phylogenetic analysis and enhances our understanding of the evolution of Patellogastropoda.
Collapse
Affiliation(s)
- Jian-Tong Feng
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Ya-Hong Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Cheng-Rui Yan
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Ying-Ying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Ji-Ji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Bao-Ying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Zhen-Ming Lü
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China
| |
Collapse
|
4
|
Ao J, Gu J, Yuan T, Li D, Ma Y, Shen Z. Applying molecular modelling and experimental studies to develop molecularly imprinted polymer for domoic acid enrichment from both seawater and shellfish. CHEMOSPHERE 2018; 199:98-106. [PMID: 29433033 DOI: 10.1016/j.chemosphere.2018.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 06/08/2023]
Abstract
A highly selective sample cleanup method using molecularly imprinted polymers (MIP) was developed for the enrichment of domoic acid (DA, an amnesic shellfish toxin) from both seawater and shellfish samples. Molecular modelling was firstly applied to screening a suitable functional monomer and optimize the polymer preparation. Theoretical results were in a good agreement with those of the experimental studies. MIP was prepared by precipitation polymerization using 1, 3, 5-pentanetricarboxylic acid and 2-(Trifluoromethyl)acrylic acid as the template molecule and functional monomer, respectively. The morphology and molecular structure of MIP were revealed by scanning electron microscope (SEM) and fourier transform infrared spectroscopy (FTIR), respectively. The obtained MIP showed high affinity and selectivity for DA with binding site numbers of 0.875 mg g-1 and an average association constant of 0.219 L mg-1 evaluated by adsorption experiments. The developed molecularly imprinted solid-phase extraction (MISPE) column achieved satisfied adsorption rate (99.2%) and recovery (71.2%) with relative standard deviation (RSD) less than 1.0%, which is more stable and precise than the C18, SAX, and HLB columns. Finally, the determination method for DA in both seawater and shellfish samples was then successfully established and validated using MISPE coupled with high-performance liquid chromatography-ultraviolet detection (HPLC-UV). The method limit of detection was 20 μg L-1 and 50 μg kg-1 for seawater and shellfish, respectively. This study demonstrates that molecular modelling is a useful tool to screening functional monomer and optimize polymer preparation. It provides an innovative polymer for trace DA monitoring in both seawater and shellfish.
Collapse
Affiliation(s)
- Junjie Ao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiaping Gu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Tao Yuan
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Dan Li
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuning Ma
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhemin Shen
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| |
Collapse
|
5
|
Shen X, Meng XP, Chu KH, Zhao NN, Tian M, Liang M, Hao J. Comparative mitogenomic analysis reveals cryptic species: A case study in Mactridae (Mollusca: Bivalvia). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2014; 12:1-9. [PMID: 25247670 DOI: 10.1016/j.cbd.2014.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 11/17/2022]
Abstract
The Chinese surf clam Mactra chinensis Philippi, 1846 is a commercially important marine bivalve belonging to the family Mactridae (Mollusca: Bivalvia). In this study, the M. chinensis mitochondrial genomic features are analyzed. The genome has 34 genes on the same strand, lacking atp8 and both trnS (trnS1 and trnS2) as compared with the typical gene content of metazoan mitochondrial genomes. The A+T content of M. chinensis mitochondrial genome is 63.72%, which is slightly lower than that of M. veneriformis (67.59%) and Coelomactra antiquata (64.33% and 64.14% for the samples from Ri Zhao, Shandong Province, and Zhang Zhou, Fujian Province, China, respectively) in the same family. There are 22 NCRs in the M. chinensis mitochondrial genome, accounting for 12.91% of the genome length. The longest NCR (1,075bp in length) is located between trnT and trnQ. A TRS (127bp×8.15) accounts for 96.3% (1,035/1,075) of this NCR. The occurrence of TRS in NCR is shared by the two Mactra mitochondrial genomes, but is not found in the two Coelomactra mitochondrial genomes. A phylogenetic tree constructed based on 12 PCGs of 25 bivalve mitochondrial genomes shows that all seven genera (Mactra, Coelomactra, Paphia, Meretrix, Solen, Mytilus, and Crassostrea) constitute monophyletic groups with very high support values. Pairwise genetic distance analyses indicate that the genetic distance of C. antiquata from the two localities is 0.084, which is greater than values between congeneric species, such as those in Mactra, Mytilus, Meretrix, and Crassostrea. The results show that the C. antiquata from the two localities represent cryptic species.
Collapse
Affiliation(s)
- Xin Shen
- Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China; Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Xue Ping Meng
- Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China.
| | - Ka Hou Chu
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Na Na Zhao
- Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China; Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Mei Tian
- Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China
| | - Meng Liang
- Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China
| | - Jue Hao
- Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China
| |
Collapse
|
6
|
Affiliation(s)
- Brahim Aissani
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| |
Collapse
|