Molecular analysis of population and De Novo transcriptome sequencing of Thai medaka, Oryzias minutillus (Teleostei: Adrianichthyidae)

Abstract

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 (Dloop) 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.

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

“…The predominant gene functions and processes of O. mekongensis and O. songkhramensis are presented. In addition, the general gene functions of both fish species in this study were consistent with several reports of freshwater fish, such as Thai medaka, pond loach (Misgurnus anguillicaudatus), Yellow River scaleless carp (Gymnocypris eckloni) and goldfish (Carassius auratus) [12,[42][43][44]. These results suggested that the represented gene predictions of O. mekongensis and O. songkhramensis might conserve the main gene functions not only among Oryzias fish but also among other freshwater fish.…”

“…The cytb gene might converted to a molecular barcode and utilized in the further identification of freshwater ricefish in Thailand. Ngamniyom et al [12] reported a https://doi.org/10.1371/journal.pone.0242382.g003…”

“…In contrast, light yellow and thin black bands appear on the dorsal and ventral margins of the caudal fin of O. songkhramensis [8]. However, these characteristics are too obscure or insufficient to justify the differentiation of O. mekongensis from O. songkhramensis in the overlapping habitats of both species [12].…”

“…The cytb gene is also a potential molecular genetics tool to evaluate fish populations, including medaka [13][14][15][16]. In Thailand, only O. minutillus has been investigated at the population genetics level in association with geographic variation [12]. In contrast, the genetic diversity of O. mekongensis and O. songkhramensis in the northeast region of Thailand remains unclear [12].…”

“…In fish species of Oryzias, transcriptome sequencing data sets have been reported for O. javanicus, O. melastigma, O. latipes and O. woworae [3,[27][28][29][30]. Recently, Ngamniyom et al [12] provided transcriptome profiling data for male and female O. minutillus.…”