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Balogh RE, Csorbai B, Guti C, Keszte S, Urbányi B, Orbán L, Kovács B. Validation of a male-specific DNA marker confirms XX/XY-type sex determination in several Hungarian strains of African catfish (Clarias gariepinus). Theriogenology 2023; 205:106-113. [PMID: 37116410 DOI: 10.1016/j.theriogenology.2023.04.017] [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: 12/19/2022] [Revised: 03/24/2023] [Accepted: 04/15/2023] [Indexed: 04/30/2023]
Abstract
African catfish (Clarias gariepinus) is a promising food fish species with significant potential and growing mass of production in freshwater aquaculture. Male African catfish possess improved production characteristics over females, therefore the use of monosex populations could be advantageous for aquaculture production. However, our knowledge about the sex determination mechanism of this species is still limited and controversial. A previously isolated male-specific DNA marker (CgaY1) was validated using offspring groups from targeted crosses (n = 630) and it was found to predict the sex of 608 individuals correctly (96.43% accuracy). Using the proportion of recombinants, we estimated the average genetic distance between the potential sex determination locus and the sex-specific marker to be 3.57 cM. As an earlier study suggested that both XX/XY and ZZ/ZW systems coexist in this species, we tested the applicability of their putative 'moderately sex-linked loci' and found that no sex-specific amplification could be detected for any of them. In addition, temperature-induced masculinization suggested by others was also tested, but no such effect was detected in our stocks when the published parameters were used for heat treatment. Altogether, our results support an exclusive XX/XY sex determination system in our African catfish stock and indicate a good potential for the future use of this male-specific DNA marker in research and commercial production.
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Affiliation(s)
- Réka Enikő Balogh
- Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Balázs Csorbai
- Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Csaba Guti
- The Hungarian National Fishing Association, Budapest, Hungary
| | - Szilvia Keszte
- Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Béla Urbányi
- Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - László Orbán
- Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, Keszthely, Hungary.
| | - Balázs Kovács
- Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary.
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Zhao X, Liu Y, Du X, Ma S, Song N, Zhao L. Whole-Genome Survey Analyses Provide a New Perspective for the Evolutionary Biology of Shimofuri Goby, Tridentiger bifasciatus. Animals (Basel) 2022; 12:ani12151914. [PMID: 35953903 PMCID: PMC9367431 DOI: 10.3390/ani12151914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/12/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
The shimofuri goby (Tridentiger bifasciatus) is a small and highly adaptable goby, distributed along the coasts of China, the Sea of Japan, and the west coastal and estuarine areas of the Northwest Pacific. Next-generation sequencing was used to generate genome-wide survey data to provide essential characterization of the shimofuri goby genome and for the further mining of genomic information. The genome size of the shimofuri goby was estimated to be approximately 887.60 Mb through K-mer analysis, with a heterozygosity ratio and repeat sequence ratio of 0.47% and 32.60%, respectively. The assembled genome was used to identify microsatellite motifs (Simple Sequence Repeats, SSRs), extract single-copy homologous genes and assemble the mitochondrial genome. A total of 288,730 SSRs were identified. The most frequent SSRs were dinucleotide repeats (with a frequency of 61.15%), followed by trinucleotide (29.87%), tetranucleotide (6.19%), pentanucleotide (1.13%), and hexanucleotide repeats (1.66%). The results of the phylogenetic analysis based on single-copy homologous genes showed that the shimofuri goby and Rhinogobius similis can be clustered into one branch. The shimofuri goby was originally thought to be the same as the chameleon goby (Tridentiger trigonocephalus) due to their close morphological resemblance. However, a complete mitochondrial genome was assembled and the results of the phylogenetic analysis support the inclusion of the shimofuri goby as a separate species. PSMC analysis indicated that the shimofuri goby experienced a bottleneck event during the Pleistocene Glacial Epoch, in which its population size decreased massively, and then it began to recover gradually after the Last Glacial Maximum. This study provides a reference for the further assembly of the complete genome map of the shimofuri goby, and is a valuable genomic resource for the study of its evolutionary biology.
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Affiliation(s)
- Xiang Zhao
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao 266003, China; (X.Z.); (X.D.); (S.M.); (N.S.)
| | - Yaxian Liu
- Yantai Laishan Marine Fisheries Supervision and Monitoring Brigade, Yantai 264000, China;
| | - Xueqing Du
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao 266003, China; (X.Z.); (X.D.); (S.M.); (N.S.)
| | - Siyu Ma
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao 266003, China; (X.Z.); (X.D.); (S.M.); (N.S.)
| | - Na Song
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao 266003, China; (X.Z.); (X.D.); (S.M.); (N.S.)
| | - Linlin Zhao
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
- Marine Ecology and Environmental Science Laboratory, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Correspondence:
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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 Draft Genome Analyses of Three Rockfishes (Scorpaeniformes, Sebastiscus) via Genome Survey Sequencing. Curr Issues Mol Biol 2021; 43:2048-2058. [PMID: 34889891 PMCID: PMC8929126 DOI: 10.3390/cimb43030141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 01/03/2023] Open
Abstract
Sebastiscus species, marine rockfishes, are of essential economic value. However, the genomic data of this genus is lacking and incomplete. Here, whole genome sequencing of all species of Sebastiscus was conducted to provide fundamental genomic information. The genome sizes were estimated to be 802.49 Mb (S. albofasciatus), 786.79 Mb (S. tertius), and 776.00 Mb (S. marmoratus) by using k-mer analyses. The draft genome sequences were initially assembled, and genome-wide microsatellite motifs were identified. The heterozygosity, repeat ratios, and numbers of microsatellite motifs all suggested possibly that S. tertius is more closely related to S. albofasciatus than S. marmoratus at the genetic level. Moreover, the complete mitochondrial genome sequences were assembled from the whole genome data and the phylogenetic analyses genetically supported the validation of Sebastiscus species. This study provides an important genome resource for further studies of Sebastiscus species.
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Zhao R, Lu Z, Cai S, Gao T, Xu S. Whole genome survey and genetic markers development of crocodile flathead Cociella crocodilus. Anim Genet 2021; 52:891-895. [PMID: 34486145 DOI: 10.1111/age.13136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 11/30/2022]
Abstract
Flatheads in family Platycephalidae are ecologically and commercially important marine fish species in the Indo-West Pacific. Due to similar morphological characters, the taxonomy and phylogenetics of flatheads are in confusion. Studies on phylogenetics and molecular marker development are required to discriminate congeners of flatheads. In the present study, we performed whole genome survey sequencing of crocodile flathead Cociella crocodilus to provide genomic information and genetic markers of this species. In total, 54.03 Gb of clean genomic data were generated. The genome size was estimated to be 732.99 Mb with the heterozygosity ratio of 0.73% and the repeat sequence ratio of 33.48%. The preliminary assembled genome sequences were 794.07 Mb with contig N50 of 1504 bp. We detected 2 624 875 genome-wide SNPs with transition/transversion ratio of 1.422. A total of 313 842 microsatellite motifs were identified, most of which were dinucleotide motifs with a frequency of 74.89%. In addition, we assembled the complete mitogenome of C. crocodilus and subsequent phylogenetic analysis were performed. Phylogenetic analyses revealed numbers of polyphyletic groups in family Platycephalidae. The reported genomic data and genetic markers in our study should be useful in further phylogeny and phylogenomics studies of flathead species.
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Affiliation(s)
- R Zhao
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Z Lu
- Dalian Key Laboratory of Conservation Biology for Endangered Marine Mammals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - S Cai
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, China
| | - T Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, China
| | - S Xu
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, China
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