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Liu Y, Hou L, Liu L, Sulaman A, Muhammad F. Mitochondrial DNA reveals two recent diverged lineages in Amphioctopusaegina (Gray, 1849) (Cephalopoda, Octopodidae) across the Leizhou Peninsula: a marine ecoregion barrier. Zookeys 2023; 1179:299-311. [PMID: 37745623 PMCID: PMC10514695 DOI: 10.3897/zookeys.1179.96015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 08/07/2023] [Indexed: 09/26/2023] Open
Abstract
Amphioctopusaegina is an economically important species that has been intensively exploited in the marine areas along the Chinese coast. However, the genetic variation and population genetic structure, which would provide valuable information for their fisheries management, have rarely been investigated. In this study, the genetic variation within and among four A.aegina populations throughout its full distribution range were estimated based on mitochondrial cytochrome b DNA sequences. Our results indicated low (Qinzhou) to high (Dongshan) genetic diversities among the four populations. Analysis of molecular variance (AMOVA), ΦST statistics, phylogenetic tree and haplotype networks revealed two significant (p < 0.01) divergent lineages with a ΦST value of 0.7116 between them, one from a population in Qinzhou and the other from the remaining three populations of Dongshan, Huizhou and Zhanjiang. However, the low genetic distance (0.0032) and only two fixed substitutions between them suggest their recent divergence is possibly due to the last glacial period barriers to gene flow produced by the Leizhou Peninsula. The observed lineage divergence suggests that populations of A.aegina in China are genetically subdivided and may represent evolutionary lineages that should be managed individually.
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Affiliation(s)
- Yantao Liu
- National Engineering Research Centre of Marine Facilities Aquaculture, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
| | - Long Hou
- National Engineering Research Centre of Marine Facilities Aquaculture, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
| | - Liqin Liu
- National Engineering Research Centre of Marine Facilities Aquaculture, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
| | - Amna Sulaman
- Center of Excellence in Marine Biology, University of Karachi, Karachi, PakistanUniversity of KarachiKarachiPakistan
| | - Faiz Muhammad
- Center of Excellence in Marine Biology, University of Karachi, Karachi, PakistanUniversity of KarachiKarachiPakistan
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Xu R, Zheng X. Hemocytes transcriptomes reveal metabolism changes and detoxification mechanisms in response to ammonia stress in Octopus minor. ECOTOXICOLOGY (LONDON, ENGLAND) 2020; 29:1441-1452. [PMID: 32945976 DOI: 10.1007/s10646-020-02279-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/04/2020] [Indexed: 06/11/2023]
Abstract
Ammonia is one of the major aquatic environmental pollutants that can bring detrimental effects to the growth and survival of aquatic organisms. However, the molecular mechanisms of ammonia toxicity and ammonia excretion in marine invertebrates especially mollusks are still poorly understood. Cephalopods are exclusively ammonotelic with high protein metabolism and ammonia excretion rate, making this taxonomic group an ideal specimen to explore the ammonia detoxification mechanism. In this study, comparative transcriptomes were employed to investigate the transcriptional changes of O. minor in responses to acute ammonia exposure. A total of 63,237 unigenes with an average length of 811 bp were discovered and 25,708 unigenes were successfully annotated. The transcription of 1845 genes were significantly changed after ammonia stress, including 315 up-regulated genes and 1530 down-regulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis based on differentially expressed genes (DEGs) revealed that 44 GO terms and 55 KEGG pathways were over-represented. Notably, a large number of genes involved in immune defense, citric acid (TCA) cycle, oxidative phosphorylation and amino acid metabolisms were significantly down-regulated, indicating the decelerated energy production and amino acid rate in response to acute ammonia stress. These results provide new insights into the potential molecular mechanism of ammonia detoxification on transcriptomic level and will facilitate further mechanism studies on mollusks.
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Affiliation(s)
- Ran Xu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Yushan Road 5, 266003, Qingdao, China
- Key Laboratory of Mariculture, Ocean University of China, Yushan Road 5, 266003, Qingdao, China
| | - Xiaodong Zheng
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Yushan Road 5, 266003, Qingdao, China.
- Key Laboratory of Mariculture, Ocean University of China, Yushan Road 5, 266003, Qingdao, China.
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Tang Y, Zheng X, Liu H, Sunxie F. Population genetics and comparative mitogenomic analyses reveal cryptic diversity of Amphioctopus neglectus (Cephalopoda: Octopodidae). Genomics 2020; 112:3893-3902. [PMID: 32603760 DOI: 10.1016/j.ygeno.2020.06.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/14/2020] [Accepted: 06/22/2020] [Indexed: 12/28/2022]
Abstract
This study presented 96 cox1 and 76 cox3 genes of Amphioctopus neglectus populations. Three distinct lineages were formed from phylogenetic trees and networks constructed using haplotypes. Mitogenomes of A. neglectus-a and A. neglectus-b as the representatives of two lineages separated from population genetics were sequenced to compare with A. neglectus at the genome-level. Amphioctopus neglectus-a showed significant differences with A. neglectus, mainly reflected in gene length, intergenic regions and the secondary structure of tandem repeat motifs. Notably, two sequence deletions in mitogenomes of the two representative species were detected in different positions of major non-coding regions, which were the most distinct differences with A. neglectus. Pairwise genetic distances and the phylogenetic analysis supported the relationship of (A. neglectus-a + (A. neglectus + A. neglectus-b)). This study suggested that A. neglectus-a should be considered as a potential cryptic species of this complex, while A. neglectus-b needed further verification to be defined.
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Affiliation(s)
- Yan Tang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture, Ocean University of China, Qingdao 266003, China
| | - Xiaodong Zheng
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture, Ocean University of China, Qingdao 266003, China.
| | - Haijuan Liu
- Guangxi Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai 536000, China
| | - Feige Sunxie
- Dongshan Boguangtianxing Foods Co., Ltd., Zhangzhou 363000, China
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Identification and characterization of 23 microsatellite loci for Chlorostoma rustica based on RAD-seq. J Genet 2018. [DOI: 10.1007/s12041-018-0935-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Wang L, Yu H, Li Q. Development of microsatellite markers and analysis of genetic diversity of Barbatia virescens in the southern coasts of China. Genes Genomics 2018; 41:407-416. [PMID: 30478704 DOI: 10.1007/s13258-018-0769-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 11/19/2018] [Indexed: 11/28/2022]
Abstract
BACKGROUND The blood clam Barbatia virescens is an ecologically and economically important species in the southern coast of China. Understanding of the genetic structure of B. virescens populations is vital to breeding strategies and conservation programs. OBJECTIVE To develop and characterize a set of microsatellites loci primers for B. virescens, and provide helpful information for reasonable utilization and protection of B. virescens natural resources. METHODS The microsatellites of B. virescens were detected using a RAD-seq approach based on an Illumina sequencing platform. For the test of microsatellite development, we calculated the number of alleles (Na), observed heterozygosities (Ho), expected heterozygosities (He) and exact tests for deviations from Hardy-Weinberg equilibrium (HWE). Twelve polymorphic loci were used to access the genetic diversity and population structure of four B. virescens populations. RESULTS In this study, 50,729 microsatellites of B. virescens were detected. Twenty-two polymorphic microsatellite loci were developed for B. virescens. The number of alleles per locus ranged from 6 to 15, and expected heterozygosities varied from 0. 567 to 0.911. All the PIC values of the 22 loci were greater than 0.5, indicating that these markers were highly informative for further genetic analysis. Twelve loci were selected to analyze genetic diversity and population structure of four B. virescens populations collected from different geographical regions along the southern coast of China. The results showed moderate to high levels of genetic diversity in the four populations (mean Ar = 7.756-8.133; mean Ho = 0.575-0.639; mean He = 0.754-0.775). Pairwise FST estimates indicated that there was significant divergence among the four populations. CONCLUSION This study not only provides a large scale of sequence information of microsatellites which are valuable for future genetic mapping, trait association and kinship among B. virescens, but also offers useful information for the sustainable management of natural stocks and the development of breeding industry of B. virescens.
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Affiliation(s)
- Ling Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Muhammad F, Lü ZM, Liu L, Gong L, Du X, Muhammad Shafi, Kaleri HA. Genetic structure of Octopus minor around Chinese waters as indicated by nuclear DNA variations (Mollusca, Cephalopoda). Zookeys 2018; 775:1-14. [PMID: 30057468 PMCID: PMC6058003 DOI: 10.3897/zookeys.775.24258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/29/2018] [Indexed: 11/12/2022] Open
Abstract
Octopus minor is an economically important resource commonly found in Chinese coastal waters. The nuclear gene (RD and ODH) approach of investigation has not reported in this species. Rhodopsin (RD) and octopine dehydrogenase (ODH) genes were used to elaborate the genetic structure collected from eight localities ranging from the northern to the southern coast of China. In total, 118 individuals for the RD gene and 108 for the ODH were sequenced. Overall (RD and ODH) genes resulted in high (0.741±0.032; 0.805±0.038) haplotype and low nucleotide (0.01261±0.00165; 0.00747±0.00086) diversity. Molecular variance displayed higher values among the populations and lower values within the population where the fixation index FST denoted 0.880 and 0.584 in RD and ODH genes respectively. The Dongshan population clustered separately in a phylogenetic tree as in the haplotype networking assessment. The current data suggests that the Dongshan population needs separate management.
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Affiliation(s)
- Faiz Muhammad
- National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Sciences and Technology, Zhejiang Ocean University
- Center of Excellence in Marine Biology, University of Karachi
| | - Zhen-ming Lü
- National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Sciences and Technology, Zhejiang Ocean University
| | - Liqin Liu
- National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Sciences and Technology, Zhejiang Ocean University
| | - Li Gong
- National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Sciences and Technology, Zhejiang Ocean University
| | - Xun Du
- National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Sciences and Technology, Zhejiang Ocean University
| | - Muhammad Shafi
- Lasbella University of Agriculture, Water and Marine Sciences
| | - Hubdar Ali Kaleri
- Department of Animal Science and Aquaculture, Dalhousie University, Canada
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Wang JH, Zheng XD. Comparison of the genetic relationship between nine Cephalopod species based on cluster analysis of karyotype evolutionary distance. COMPARATIVE CYTOGENETICS 2017; 11:477-494. [PMID: 29093799 PMCID: PMC5646656 DOI: 10.3897/compcytogen.v11i3.12752] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/28/2017] [Indexed: 05/20/2023]
Abstract
Karyotype analysis was carried out on gill cells of three species of octopods using a conventional air-drying method. The karyotype results showed that all the three species have the same diploid chromosome number, 2n=60, but with different karyograms as 2n=38M+6SM+8ST+8T, FN (fundamental number)=104 (Cistopus chinensis Zheng et al., 2012), 2n=42M+6SM+4ST+8T, FN=108 (Octopus minor (Sasaki, 1920)) and 2n=32M+16SM+12T, FN=108 (Amphioctopus fangsiao (d'Orbigny, 1839-1841)). These findings were combined with data from earlier studies to infer the genetic relationships between nine species via cluster analysis using the karyotype evolutionary distance (De ) and resemblance-near coefficient (λ). The resulting tree revealed a clear distinction between different families and orders which was substantially consistent with molecular phylogenies. The smallest intraspecific evolutionary distance (De =0.2013, 0.2399) and largest resemblance-near coefficient (λ=0.8184, 0.7871) appeared between O. minor and C. chinensis, and Sepia esculenta Hoyle, 1885 and S. lycidas Gray, 1849, respectively, indicating that these species have the closest relationship. The largest evolutionary gap appeared between species with complicated karyotypes and species with simple karyotypes. Cluster analysis of De and λ provides information to supplement traditional taxonomy and molecular systematics, and it would serve as an important auxiliary for routine phylogenetic study.
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Affiliation(s)
- Jin-hai Wang
- Laboratory of Shellfish Genetics and Breeding, Fisheries College, Ocean University of China, Qingdao 266003, China
| | - Xiao-dong Zheng
- Laboratory of Shellfish Genetics and Breeding, Fisheries College, Ocean University of China, Qingdao 266003, China
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