ABSTRACT
A species-specific quantitative PCR (qPCR) assay using environmental DNA (eDNA) is a promising tool for both qualitative and quantitative analyses of target species directly from water samples. Despite its reliability, an eDNA-based qPCR assay pipeline has not yet developed to monitor salmon species inhabiting Korean waters, which have been rapidly decreasing. We designed species-specific primers for four Oncorhynchus species inhabiting the eastern coastal waters along the Korean Peninsula. These include primers for two native species (Oncorhynchus keta and O. masou) and two that were introduced (O. mykiss and O. kisutch). The limit of detection and limit of quantification for the four qPCR assays ranged from 4.11 to 10.38 copies and from 30 to 81 copies, respectively, indicating a high sensitivity and specificity across all four species. Following optimization, the qPCR assays were used for the quantitative analyses of the four Oncorhynchus species in the Yangyangnamdae River during the spawning and non-spawning seasons in the year 2019-2020, one of the main rivers where salmon migrate during the spawning season in Korea. The raw copy numbers in all of the examined samples were normalized by PCR inhibition rates to standardize and compare with other studies. Among the four Oncorhynchus species examined, the eDNA concentration of O. keta increased significantly (63.60-fold, p < 0.0001) during the spawning season (November) compared with that in the non-spawning season (March), suggesting that O. keta is the main salmon species migrating through the Yangyangnamdae River. In contrast, we did not detect any differences in eDNA concentration for the other three Oncorhynchus species between the spawning and non-spawning seasons, indicating that their presence does not alter during the year. Their eDNA concentration is also relatively low compared to O. keta, which suggests that small numbers of these three species are present in the river. Overall, these newly developed qPCR assays represent useful monitoring tools for the management of four salmon species in Korean waters.
ABSTRACT
The complete mitochondrial DNA information of Pseudotolithus typus Bleeker, 1863, collected from Sierra Leone was determined using next-generation sequencing (NGS) and bioinfromatic analysis. Its mitogenome (16,504 bp) encoded the typical 13 protein-coding genes (PCGs), 2 ribosomal RNAs (12S & 16S), and 22 tRNAs. All 13 PCGs showed a standard start codon (ATG) but an unusual stop codon (AGA) was identified in COX1 gene. Except for ND6, all 12 PCGs were encoded on the light strand. Except for tRNASer-GCT, 21 tRNAs formed the typical clover-leaf structures. Phylogenetic analysis showed three mitochondrial genomes in the genus Pseudotolithus formed a clade distinct from the other species in the same family. The mitogenome of P. typus identified in this study exhibited 96.27% and 88.86% identity to T. typus in the Guinean water and P. elongatus, respectively. Additional mitogenome sequences of Pseudotolithus species will provide useful information for their scientific management in western African countries.
ABSTRACT
The first mitochondrial genome of Ophiocara porocephala was determined by the combination of next-generation sequencing (NGS) and Sanger sequencing methods. A complete circular mitogenome of O. porocephala (16,529 bp) consisted of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and two non-coding regions, including a control region (D-loop) and a light strand origin of replication (OL). Two start codons (ATG and GTG) and four stop codons (TAG, TAA, TA-, and T-) were used in all the PCGs. Except for ND6 and eight transfer RNAs (tRNAs), all the other genes were encoded in the heavy strand. Based on phylogenetic analysis, O. porocephala formed a clade with three other species in the subfamily Butinae, while the other 10 made a subfamily Eleotrinae clade.
ABSTRACT
We applied next-generation sequencing (NGS) method to construct the complete mitochondrial genome of Glossogobius aureus. The obtained mitogenome of G. aureus (16,590 bp) exhibited a typical structure harboring 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control regions (D-loop). Most of mitochondrial genes are encoded on the heavy (H) strand, except for eight tRNAs and ND6. Unusual start codons were identified in COX1 (GTG) and ATP6 (TTG). Six genes (ND2, COX2, COX3, ND3, ND4, and CytB) were terminated by an incomplete stop codon (TA-/T-). A phylogenetic study showed that Glossogobius formed a clade distinct from other species in the subfamily Gobiinae. G. aureus was most closely related to G. giuris with 87.04% sequence identity among the four species in the genus Glossogobius.
