Genetic diversity of the orange-spotted grouper (Epinephelus coioides) in Terengganu Malaysia based on mitochondrial cytochrome b sequence data

Orange-spotted grouper (Epinephelus coioides) is known to be one of the economically high values marine. However, its spawning condition is still not well understood by the aqua culturist in Terengganu, Malaysia. Fish farmers depend on natural supply by col-lecting eggs of orange-spotted grouper from the wild. A study was conducted to deter-mine the genetic diversity of farmed orange-spotted grouper population using partial Cytochrome b (Cyt-b) gene. A total of 20 farmed orange-spotted grouper were col-lected from a fish farm in Besut, Terengganu. A piece of dorsal fin area- (1 cm2) was individually clipped from the orange-spotted grouper and immediately preserved in 95% ethanol at ambient temperature upon sampling and kept on -80 ºC until DNA ex-traction was performed. DNA extraction was carried out using Qiagen Blood and Tis-sue kit. PCR amplification of partial Cyt-b was conducted using a universal Cyt-b pri-mer and amplicons of 491 bp was obtained. The amplicons were then purified, se-quenced and the genetic relationship among individuals was analyzed using MEGA6 software for their pairwise distance and phylogenetic tree. Phylogenetic analysis showed orange-spotted grouper is divided into two major groups. Genetic distance among individuals ranged between 0.000 – 0.014. These findings indicate that orange-spotted grouper has low genetic diversity and most of the individuals might be origi-nating from a small population

Genetic diversity of the orange-spotted grouper (Epinephelus coioides) in Terengganu Malaysia based on mitochondrial cytochrome b sequence data

Orange-spotted groupers (Epinephelus coioides) are marine fish which can be found in the state of Terengganu (in Malaysia) and are economically important. Overfishing and fish farmers’ dependency on wild orange-spotted grouper seed fish have caused a decline in their numbers. Hence, the aim of this study was to investigate the genetic diversity of wild orange-spotted grouper populations in Terengganu via partial cytochrome b (cyt-b) gene analysis. A total of 60 fish, which were reared from wild seed fish, were collected from farms in Besut and Setiu, Terengganu. Their DNA was extracted using the Qiagen Blood and Tissue kit. PCR amplification was conducted using cyt-b primers, and a sequence of 460 bp in length was obtained for each sample. Next, phylogenetic analysis was performed to study the relationships among the individuals. The haplotype and nucleotide diversities of the populations were investigated to measure genetic diversity. The haplotype diversity (Hd) of E. coioides was relatively low for both Besut (Hd = 0.4161) and Setiu (Hd = 0.8782) populations. The nucleotide diversity (π) for both Besut and Setiu populations was also low. Moreover, 15 haplotypes were identified among the 60 individuals, with 33 individuals sharing a single haplotype (Hap01). These findings similar with a previous study that reported that seed fish dependent can led to a decline in grouper numbers and in turn cause genetic deprivation in the populatio

Genetic diversity of the orange-spotted grouper (Epinephelus coioides) in Terengganu Malaysia based on mitochondrial cytochrome b sequence data

Orange-spotted groupers (Epinephelus coioides) are marine fish which can be found in the state of Terengganu (in Malaysia) and are economically important. Overfishing and fish farmers’ dependency on wild orange-spotted grouper seed fish have caused a decline in their numbers. Hence, the aim of this study was to investigate the genetic diversity of wild orange-spotted grouper populations in Terengganu via partial cytochrome b (cyt-b) gene analysis. A total of 60 fish, which were reared from wild seed fish, were collected from farms in Besut and Setiu, Terengganu. Their DNA was extracted using the Qiagen Blood and Tissue kit. PCR amplification was conducted using cyt-b primers, and a sequence of 460 bp in length was obtained for each sample. Next, phylogenetic analysis was performed to study the relationships among the individuals. The haplotype and nucleotide diversities of the populations were investigated to measure genetic diversity. The haplotype diversity (Hd) of E. coioides was relatively low for both Besut (Hd = 0.4161) and Setiu (Hd = 0.8782) populations. The nucleotide diversity (π) for both Besut and Setiu populations was also low. Moreover, 15 haplotypes were identified among the 60 individuals, with 33 individuals sharing a single haplotype (Hap01). These findings similar with a previous study that reported that seed fish dependent can led to a decline in grouper numbers and in turn cause genetic deprivation in the population

Morphological and 18s rRNA sequencing of Euplotes sp.: a potential live feed for marine finfish larvae

Euplotes is a ciliated protozoan that is highly diverse in size and species and has poten-tial to be used as live feed for marine feed larvae. This study was conducted to identify the suitable Euplotes candidate through molecular and morphological methods. Euplotes sp. was characterized by its morphological and 18S rRNA gene sequence. The selected Euplotes sp. was identified morphologically based on its unique present of infracillia-ture, dorsal-ventrally flattened, dorsally ridged and oval in shaped. For molecular identi-fication, samples of Euplotes sp. were collected and starved overnight before pelleted through centrifugation to provide closely packed Euplotes species. The extraction and amplification of genomic DNA of Euplotes sp. were done using REDExtract-N-AmpTM Tissue PCR Kit (Sigma). The phylogenetic analyses of the SSU RNA gene was ana-lyzed with evolutionary distance calculated using Kimura-two-parameter and further analyzed by using Maximum Likelihood (ML) and Neighbor-joining (NJ) with Coris julis (accession number HM049942.1) as an out group. The result showed Euplotes sp. is 96% related to Euplotes encysticus (accession number LN864512.1) and Euplotes no-vemcarinatus (accession number HM140407.1)