Dataset Information

Complete mitogenome of Hainan medaka Oryzias curvinotus (Teleostei: Beloniformes) and transcriptional differences between male and female liver.

ABSTRACT: In this study, combining the liver transcripts from both sexes by RNA-Seq with DNA sequences by conventional PCRs, we have determined the complete mitogenome of Hainan medaka Oryzias curvinotus collected from the mangrove seawater of the Leizhou Peninsula in tropical South China (Accession no.: KY364884). The mitochondrial genome is 16,676?bp, and its content and structure are highly homologous to those of other teleostean fishes, including 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNA and 1 control region. Among the PCGs, ATG is used as the initiation codon, except for GTG in COI gene. There are 7 overlapping genes with overlap lengths ranging from 1 to 10 nucleotides (nt), while ten intergenic regions with a total of 66?nt and a maximum interval of 37?nt between tRNA^Asn and tRNA^Cys. Moreover, the data from RNA-Seq shows that the significant differences exist in the expression patterns of mitogenomes between male and female.

SUBMITTER: Wang Z

PROVIDER: S-EPMC7800997 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature

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Complete mitogenome of Hainan medaka <i>Oryzias curvinotus</i> (Teleostei: Beloniformes) and transcriptional differences between male and female liver.

Wang Zhongduo Z Long Shuisheng S Liao Jian J Huang Chengqin C Zhang Hairui H Huang Shunkai S Zhang Yanping Y Liu Li L Guo Yusong Y

Mitochondrial DNA. Part B, Resources 20170321 1

In this study, combining the liver transcripts from both sexes by RNA-Seq with DNA sequences by conventional PCRs, we have determined the complete mitogenome of Hainan medaka <i>Oryzias curvinotus</i> collected from the mangrove seawater of the Leizhou Peninsula in tropical South China (Accession no.: KY364884). The mitochondrial genome is 16,676 bp, and its content and structure are highly homologous to those of other teleostean fishes, including 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNA ...[more]

PMID: 33490443

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Project description:Thai medaka (Oryzias minutillus) are alternatively known as Thai rice-fish or dwarf medaka, and they widely inhabit natural freshwater environments in all regions of Thailand. In this study, we aimed to investigate the molecular genetics of the Thai medaka population in Thailand inferred from the mitochondrial control region (D-loop) and the cytochrome c oxidase subunit 1 (coxI) sequences. Furthermore, we examined RNA sequencing (RNA-seq) of adult males and females was performed with next-generation sequencing. Together, the combination of the D-loop and coxI sequences clearly distinguished the Thai medaka populations into 2 groups, such as group 1, which generally included samples from the central, northern, western, and eastern regions of the northeastern region. In this group, the fish populations seem to be a little monophyly in which the first subpopulation comprised the main samples from the northern and central regions. The second subpopulation commonly contained fish from the eastern region and specimens from the southern part of the central region near the Gulf of Thailand. Although these subgroups related to geographical distribution, bootstrap values were low in branch considered significant for both subgroups. Group 2 consisted of almost all samples from the southern population and those from the central and southern part of the northeastern region. Group 2 was found that it was made of samples from the northeastern region and samples from the southern population. A total of 73551 unigenes were identified after gene annotation. Signal transduction was the predominant protein classification among the Thai medaka orthologous groups. A differentially expressed gene (DEG) analysis identified 6 subclusters between both sexes that were composed of 257, 131, 364, 386, 114 and 108 genes. Phototransduction was the most enriched pathway and was highly expressed in males, while viral carcinogenesis, oocyte genesis, and the complement and coagulation cascades were highly expressed in females. Further details of these DEGs are discussed below. These results suggest that Thai medaka may genetically exhibit independent populations in the geographic habitats of Thailand. Moreover, these fish also reveal the genes that are conserved in other organisms and those that may be specific to this species.

Dataset Information

Complete mitogenome of Hainan medaka Oryzias curvinotus (Teleostei: Beloniformes) and transcriptional differences between male and female liver.

Publications

Complete mitogenome of Hainan medaka <i>Oryzias curvinotus</i> (Teleostei: Beloniformes) and transcriptional differences between male and female liver.

Similar Datasets

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