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Wang J, He W, Huang H, Ou D, Wang L, Li J, Li W, Luo S. A Comprehensive Analysis of the Fowleria variegata (Valenciennes, 1832) Mitochondrial Genome and Its Phylogenetic Implications within the Family Apogonidae. Genes (Basel) 2023; 14:1612. [PMID: 37628663 PMCID: PMC10454648 DOI: 10.3390/genes14081612] [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: 07/07/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Controversies surrounding the phylogenetic relationships within the family Apogonidae have persisted due to the limited molecular data, obscuring the evolution of these diverse tropical marine fishes. This study presents the first complete mitochondrial genome of Fowleria variegata, a previously unrepresented genus, using high-throughput Illumina sequencing. Through a comparative mitogenomic analysis, F. variegate was shown to exhibit a typical genome architecture and composition, including 13 protein-coding, 22 tRNA and 2 rRNA genes and a control region, consistent with studies of other Apogonidae species. Nearly all protein-coding genes started with ATG, while stop codons TAA/TAG/T were observed, along with evidence of strong functional constraints imposed via purifying selection. Phylogenetic reconstruction based on maximum likelihood and Bayesian approaches provided robust evidence that F. variegata forms a basal lineage closely related to P. trimaculatus within Apogonidae, offering novel perspectives into the molecular evolution of this family. By generating new mitogenomic resources and evolutionary insights, this study makes important headway in elucidating the phylogenetic relationships and mitogenomic characteristics of Apogonidae fishes. The findings provide critical groundwork for future investigations into the drivers of diversification, speciation patterns, and adaptive radiation underlying the extensive ecological diversity and biological success of these marine fishes using phylogenomics and population genomics approaches.
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Affiliation(s)
- Jiaqiao Wang
- Fisheries College of Ji Mei University, Xiamen 361000, China
- Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Xiamen 361000, China
| | - Weiyi He
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Hao Huang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Danyun Ou
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Lei Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Jun Li
- Fisheries College of Ji Mei University, Xiamen 361000, China
- Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Xiamen 361000, China
| | - Weiwen Li
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Site Luo
- School of Life Sciences, Xiamen University, Xiamen 361102, China
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Huang G, Cao J, Chen C, Wang M, Liu Z, Gao F, Yi M, Chen G, Lu M. Genome survey of Misgurnus anguillicaudatus to identify genomic information, simple sequence repeat (SSR) markers, and mitochondrial genome. Mol Biol Rep 2022; 49:2185-2196. [PMID: 35064399 DOI: 10.1007/s11033-021-07037-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/29/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND The dojo loach Misgurnus anguillicaudatus is an important economic species in Asia because of its nutritional value and broad environmental adaptability. Despite its economic importance, genomic data for M. anguillicaudatus is currently unavailable. METHODS AND RESULTS In the present study, we conducted a genome survey of M. anguillicaudatus using next-generation sequencing technology. Its genome size was estimated to be 1105.97 Mb by using K-mer analysis, and its heterozygosity ratio, repeat sequence content, GC content were 1.45%, 58.98%, and 38.03%, respectively. A total of 376,357 microsatellite motifs were identified, and mononucleotides, with a frequency of 42.57%, were the most frequently repeated motifs, followed by 40.83% dinucleotide, 7.49% trinucleotide, 8.09% tetranucleotide, and 0.91% pentanucleotide motifs. The AC/GT, AAT/ATT, and ACAG/CTGT repeats were the most abundant motifs among dinucleotide, trinucleotide, and tetranucleotide motifs, respectively. Besides, the complete mitochondrial genome was sequenced. Based on the Maximum Likelihood and Bayesian inference analyses, M. anguillicaudatus yingde in this study was the "introgressed" mitochondrial type. Seventy microsatellite loci were randomly selected from detected SSR loci to test polymorphic, of which, 20 microsatellite loci were assessed in 30 individuals from a wild population. The number of alleles (Na), observed heterozygosity (Ho), and expected heterozygosity (He) per locus ranged from 7 to 19, 0.400 to 0.933, and 0.752 to 0.938, respectively. All 20 loci were highly informative (PIC > 0.700). Eight loci deviated from Hardy-Weinberg equilibrium after Bonferroni correction (P < 0.05). CONCLUSIONS This is the first report of genome survey sequencing in M. anguillicaudatus, genome information, mitochondrial genome, and microsatellite markers will be valuable for further studies on population genetic analysis, natural resource conservation, and molecular marker-assisted selective breeding.
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Affiliation(s)
- Guiyun Huang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524025, China.,Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute of CAFS, Xingyu Road No. 1, Guangzhou, 510380, China
| | - Jianmeng Cao
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute of CAFS, Xingyu Road No. 1, Guangzhou, 510380, China
| | - Chen Chen
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture and Rural Affairs, Aquatic Germplasm Resources and Genetic Breeding Library, Pearl River Fisheries Research Institute of CAFS, Xingyu Road No. 1, Guangzhou, 510380, China
| | - Miao Wang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute of CAFS, Xingyu Road No. 1, Guangzhou, 510380, China
| | - Zhigang Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute of CAFS, Xingyu Road No. 1, Guangzhou, 510380, China
| | - Fengying Gao
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute of CAFS, Xingyu Road No. 1, Guangzhou, 510380, China
| | - Mengmeng Yi
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute of CAFS, Xingyu Road No. 1, Guangzhou, 510380, China
| | - Gang Chen
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524025, China.
| | - Maixin Lu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute of CAFS, Xingyu Road No. 1, Guangzhou, 510380, China.
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Comprehensive whole genome survey analyses of male and female brown-spotted flathead fish Platycephalus sp.1. Genomics 2020; 112:4742-4748. [PMID: 32871221 DOI: 10.1016/j.ygeno.2020.08.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/14/2020] [Accepted: 08/25/2020] [Indexed: 01/20/2023]
Abstract
The flathead fish Platycephalus sp.1 is an ecologically and commercially important marine fish in the northwestern Pacific with notable sexual differences in growth and development. Yet the genomic data of this species is lacking. In the present study, whole genome sequencing of two individuals (one male and one female) of Platycephalus sp.1 were conducted to provide fundamental genomic information. The genome sizes were estimated to be 674.96 Mb (male) and 684.15 Mb (female) by using k-mer analyses. The heterozygosity and repeat ratios suggested possible male heterogamety of this species. The draft genome sequences were initially assembled and genome-wide microsatellite motifs were identified. Besides, the complete mitochondrial genome sequences were assembled and the phylogenetic analyses genetically supported the validation of Platycephalus sp.1. The reported genomic data and genetic markers in this study could be useful in future comparative genomics and evolutionary biology studies.
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