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Cao L, Chen P, Hou X, Ma J, Yang N, Lu Y, Huang H. rDNA and mtDNA analysis for the identification of genetic characters in the hybrid grouper derived from hybridization of Cromileptes altivelis (female) × Epinephelus lanceolatus (male). BMC Genom Data 2024; 25:5. [PMID: 38216865 PMCID: PMC10787421 DOI: 10.1186/s12863-023-01188-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/20/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Hybridization is a useful strategy to produce offspring with more desirable phenotypic characteristics than those of parents. The hybrid grouper derived from the cross of Cromileptes altivelis (♀, 2n = 48) with Epinephelus lanceolatus (♂, 2n = 48) exhibits improved growth compared with its female parent, which makes it valuable to aquaculture. However, the genetic traits of the hybrid grouper are poorly understood. RESULTS The observations showed that the hybrid grouper was diploid (2n = 48) and displayed intermediate morphology with the parent's measurable characteristics. The ribosomal DNA (rDNA) and mitochondria DNA (mtDNA) were characterized at molecular and phylogenetic level. High similarity and low genetic distance of 5S rDNA and mtDNA sequences between the hybrid grouper and C. altivelis showed that the hybrid grouper had a closer genetic relationship with female parents. The reconstructed phylogenetic tree based on COI gene and D-loop region of mtDNA recovered that mtDNA was maternally inherited in the hybrid grouper. Additionally, the DNA methylation level of 5S rDNA intergenic spacers (IGS) sequence was tested in here. The results showed that the DNA methylation status of the hybrid grouper was significantly lower than that of C. altivelis. CONCLUSION Results of this study provide important data on the genetic characteristics of the hybrid derived from the cross of C. altivelis and E. lanceolatus, and contribute the knowledge of both evolution and marine fish breeding.
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Affiliation(s)
- Liu Cao
- Yazhou Bay Innovation Institute, Sanya, 572022, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, 572022, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, China
- Hainan Tropical Ocean University, Sanya, 572022, China
| | - Pan Chen
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, 572022, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, China
- Hainan Tropical Ocean University, Sanya, 572022, China
| | - Xingrong Hou
- Yazhou Bay Innovation Institute, Sanya, 572022, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, 572022, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, China
- Hainan Tropical Ocean University, Sanya, 572022, China
| | - Jun Ma
- Yazhou Bay Innovation Institute, Sanya, 572022, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, 572022, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, China
- Hainan Tropical Ocean University, Sanya, 572022, China
| | - Ning Yang
- Yazhou Bay Innovation Institute, Sanya, 572022, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, 572022, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, China
- Hainan Tropical Ocean University, Sanya, 572022, China
| | - Yan Lu
- Hainan Tropical Ocean University, Sanya, 572022, China
| | - Hai Huang
- Yazhou Bay Innovation Institute, Sanya, 572022, China.
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, 572022, China.
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, China.
- Hainan Tropical Ocean University, Sanya, 572022, China.
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Cao L, Chen P, Hou X, Ma J, Yang N, Xu Y, Zhang Y, Zhao A, Zhang J, Li X, Huang H. Genetic characteristics and growth patterns of the hybrid grouper derived from the hybridization of Epinephelus fuscoguttatus (female) × Epinephelus polyphekadion (male). JOURNAL OF FISH BIOLOGY 2023; 102:328-339. [PMID: 36317644 DOI: 10.1111/jfb.15263] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Hybridization is one of the primary methods used to cultivate farmed grouper species. The hybrid grouper derived from crossing Epinephelus fuscoguttatus (♀) and E. polyphekadion (♂) exhibits growth superiority over its parents. The genetic characteristics and growth patterns of the hybrid grouper have not yet been defined. This study confirms the ploidy level of the hybrid grouper (2n = 48) using chromosome count analysis and flow cytometry. The 5S rDNA family was used to evaluate genetic diversity. Only one 5S class (~400 bp) was detected in the hybrid grouper, which could be used to distinguish between two different types based on nucleotide sequences, likely representing homologous unit classes from the female and male parental species. Growth patterns of 5-8-month-old hybrid groupers were also monitored. In this phase, a positive allometric growth pattern in body mass with total length was found. Body height and body mass were significantly correlated based on correlation and path coefficient, suggesting that body height could serve as an excellent index to increase body mass. These results aid our understanding of the genetic evolution of the hybrid grouper and inform the development of improved rearing techniques.
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Affiliation(s)
- Liu Cao
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Tropical Ocean University, Sanya, China
| | - Pan Chen
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Tropical Ocean University, Sanya, China
| | - Xingrong Hou
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Tropical Ocean University, Sanya, China
| | - Jun Ma
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Tropical Ocean University, Sanya, China
| | - Ning Yang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Tropical Ocean University, Sanya, China
| | - Yanping Xu
- Hainan Tropical Ocean University, Sanya, China
| | | | - Anqi Zhao
- Hainan Tropical Ocean University, Sanya, China
| | | | - Xinyu Li
- Hainan Tropical Ocean University, Sanya, China
| | - Hai Huang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Tropical Ocean University, Sanya, China
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Meng L, Gao Y, Gong L. Recombination and incomplete concerted evolution of the ribosomal 18S (partial) -ITS1-5.8S-ITS2-28S (partial) rDNA in Cynoglossus trigrammus genome. BIOCHEM SYST ECOL 2022. [DOI: 10.1016/j.bse.2022.104513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Moraes JN, Viana PF, Favarato RM, Pinheiro-Figliuolo VS, Feldberg E. Karyotype variability in six Amazonian species of the family Curimatidae (Characiformes) revealed by repetitive sequence mapping. Genet Mol Biol 2022; 45:e20210125. [PMID: 35766400 PMCID: PMC9240918 DOI: 10.1590/1678-4685-gmb-2021-0125] [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: 04/27/2021] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
Fishes of the Curimatidae family represent one of the most important freshwater
ichthyofauna groups of Central and South America, with 117 recognized species
distributed in eight genera. In this study, six species - Curimata
inornata, Curimatella dorsalis, and
Psectrogaster falcata collected from the Lower Araguaia
River, Pará, Brazil; Curimata vittata, Curimatella
meyeri, and Psectrogaster rutiloides collected
from the Catalão Lake, Amazonas, Brazil - were cytogenetically analyzed,
investigate the occurrence and distribution of repetitive DNA classes in the
karyotypes. All species had 2n=54 metacentric/submetacentric chromosomes.
Despite the conservative diploid number, we observed variations in the
karyotypic structure among species. Ribosomal DNA (rDNA) 18S and 5S were found
in single or multiple sites, with the first report of synteny in
Curimatella dorsalis, and the occurrence of several
interstitial telomeric sequences (ITSs) in species of the genera
Curimatella and Psectrogaster.
Interspecific karyotypic diversity both concerning structure and
location/position of the nucleolar organizer regions (NOR) and ribosomal DNA,
suggesting the occurrence of several non-Robertsonian rearrangements driving the
evolution of this family.
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Affiliation(s)
- Juliana Nascimento Moraes
- Instituto Nacional de Pesquisas da Amazônia (INPA), Coordenação de Biodiversidade, Laboratório de Genética Animal, Manaus, AM, Brazil
| | - Patrik Ferreira Viana
- Instituto Nacional de Pesquisas da Amazônia (INPA), Coordenação de Biodiversidade, Laboratório de Genética Animal, Manaus, AM, Brazil
| | - Ramon Marin Favarato
- Instituto Nacional de Pesquisas da Amazônia (INPA), Coordenação de Biodiversidade, Laboratório de Genética Animal, Manaus, AM, Brazil
| | - Vanessa Susan Pinheiro-Figliuolo
- Instituto Nacional de Pesquisas da Amazônia (INPA), Coordenação de Biodiversidade, Laboratório de Genética Animal, Manaus, AM, Brazil
| | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia (INPA), Coordenação de Biodiversidade, Laboratório de Genética Animal, Manaus, AM, Brazil
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Sun X, Cheng J. Phylogenetic Signal Dissection of Heterogeneous 28S and 16S rRNA Genes in Spinicaudata (Branchiopoda, Diplostraca). Genes (Basel) 2021; 12:1705. [PMID: 34828311 PMCID: PMC8625258 DOI: 10.3390/genes12111705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 12/05/2022] Open
Abstract
It is still a challenge to reconstruct the deep phylogenetic relationships within spinicaudatans, and there are several different competing hypotheses regarding the interrelationships among Eocyzicidae, Cyzicidae s. s., Leptestheriidae, and Limnadiidae of the Suborder Spinicaudata. In order to explore the source of the inconsistencies, we focus on the sequence variation and the structure model of two rRNA genes based on extensive taxa sampling. The comparative sequence analysis revealed heterogeneity across species and the existence of conserved motifs in all spinicaudatan species. The level of intraspecific heterogeneity differed among species, which suggested that some species might have undergone a relaxed concerted evolution with respect to the 28S rRNA gene. The Bayesian analyses were performed on nuclear (28S rRNA, EF1α) and mitochondrial (16S rRNA, COI) genes. Further, we investigated compositional heterogeneity between lineages and assessed the potential for phylogenetic noise compared to signal in the combined data set. Reducing the non-phylogenetic signals and application of optimal rRNA model recovered a topology congruent with inference from the transcriptome data, whereby Limnadiidae was placed as a sister group to Leptestheriidae + Eocyzicidae with high support (topology I). Tests of alternative hypotheses provided implicit support for four competing topologies, and topology I was the best.
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Affiliation(s)
| | - Jinhui Cheng
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, No. 39, Beijing Eastroad, Nanjing 210008, China;
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