Dataset Information

Molecular assessment and transcriptome profiling of wild fish populations of Oryzias mekongensis and O. songkhramensis (Adrianichthyidae: Beloniformes) from Thailand.

ABSTRACT: Among the fish of the genus Oryzias, two species are frequently used as model animals in biological research. In Thailand, Oryzias mekongensis is usually found in natural freshwater near the Mekong Basin in the northeast region, while O. songkhramensis inhabits the Songkhram Basin. For differential morphological identification, the coloured bands on the dorsal and ventral margins of the caudal fin are used to distinguish O. mekongensis from O. songkhramensis. However, these characteristics are insufficient to justify species differentiation, and little molecular evidence is available to supplement them. This study aimed to investigate the molecular population and transcriptome profiles of adult O. mekongensis and O. songkhramensis. In the molecular tree based on cytochrome b sequences, O. mekongensis exhibited four clades that were clearly distinguished from O. songkhramensis. Clade 1 of the O. mekongensis population was close to the Mekong River and lived in the eastern portion of the upper northeast region. Clade 2 was far from the Mekong River and inhabited the middle region of the Songkhram River. Clade 3 was positioned to the west of the Songkhram River, and clade 4 was to the south of the Songkhram River Basin. After RNA sequencing using an Illumina HiSeq 2500 platform, the gene category annotations hardly differentiated the species and were discussed in the text. Based on the present findings, population dispersal of these Oryzias species might be associated with geographic variations of the upper northeast region. Molecular genetics and transcriptome profiling might advance our understanding of the evolution of teleost fish.

SUBMITTER: Ngamniyom A

PROVIDER: S-EPMC7676673 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Molecular assessment and transcriptome profiling of wild fish populations of Oryzias mekongensis and O. songkhramensis (Adrianichthyidae: Beloniformes) from Thailand.

Ngamniyom Arin A

PloS one 20201119 11

Among the fish of the genus Oryzias, two species are frequently used as model animals in biological research. In Thailand, Oryzias mekongensis is usually found in natural freshwater near the Mekong Basin in the northeast region, while O. songkhramensis inhabits the Songkhram Basin. For differential morphological identification, the coloured bands on the dorsal and ventral margins of the caudal fin are used to distinguish O. mekongensis from O. songkhramensis. However, these characteristics are i ...[more]

PMID: 33211755

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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

Molecular assessment and transcriptome profiling of wild fish populations of Oryzias mekongensis and O. songkhramensis (Adrianichthyidae: Beloniformes) from Thailand.

Publications

Molecular assessment and transcriptome profiling of wild fish populations of Oryzias mekongensis and O. songkhramensis (Adrianichthyidae: Beloniformes) from Thailand.

Similar Datasets

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