This study is the first report to characterize the Rhodus uyekii genome and study the development of microsatellite markers and their markers applied to the genetic structure of the wild population. Genome assembly was based on PacBio HiFi and Illumina HiSeq paired-end sequencing, resulting in a draft genome assembly of R. uyekii. The draft genome was assembled into 2652 contigs. The integrity assessment of the assemblies indicates that the quality of the draft assemblies is high, with 3259 complete BUSCOs (97.2%) in the database of Verbrata. A total of 31,166 predicted protein-coding genes were annotated in the protein database. The phylogenetic tree showed that R. uyekii is a close but distinct relative of Onychostoma macrolepis. Among the 10 fish genomes, there were significant gene family expansions (8-2387) and contractions (16-2886). The average number of alleles amplified by the 21 polymorphic markers ranged from 6 to 23, and the average PIC value was 0.753, which will be useful for evolutionary and genetic analysis. Using population genetic analysis, we analyzed genetic diversity and the genetic structures of 120 individuals from 6 populations. The average number of alleles per population ranged from 7.6 to 9.9, observed heterozygosity ranged from 0.496 to 0.642, and expected heterozygosity ranged from 0.587 to 0.783. Discriminant analysis of principal components According to the analysis method, the population was divided into three populations (BS vs. DC vs. GG, GC, MS, DC). In conclusion, our study provides a useful resource for comparative genomics, phylogeny, and future population studies of R. uyekii.

The tripartite motif-containing (TRIM) proteins are involved in a wide range of cellular processes, and the role of TRIM1 in immunity has been explored. However, fundamental studies on fish TRIM1 are lacking. In this study, we cloned and characterized TRIM1 cDNA from the Korean rose bitterling, Rhodeus uyekii (RuTRIM1). Two RuTRIM1 isoforms (RuTRIM1-X1 and RuTRIM1-X2) were identified. The coding sequence (CDS) of RuTRIM1-X1 comprised 2157 bp encoding a 718-aa protein, and the CDS of RuTRIM1-X2 comprised 1929 bp encoding a 642-aa protein. Both RuTRIM1 isoforms contained a RING finger domain, B-box 1, B-box 2, coiled-coil domain, COS box, FN3 motif, and PRY/SPRY domain. The deduced RuTRIM1-X1 and RuTRIM1-X2 proteins had high amino acid identity (76.27-98.89%) with orthologs from various other species, and a phylogenetic tree was constructed. RuTRIM1-X1 and RuTRIM1-X2 mRNA were expressed in all tissues examined, with the highest expression levels detected in the hepatopancreas. During early development, RuTRIM1-X1 and RuTRIM1-X2 mRNA levels changed differently from the gastrula period to the first feeding stage. An in vivo ubiquitination assay showed that RuTRIM1 exhibited RING-dependent E3 ubiquitin ligase activity, mainly by comparing RuTRIM1-X2 to RuTRIM1-X1. The subcellular localization of the two RuTRIM1 protein isoforms was characterized, revealing that they formed aggregates in cytoplasmic bodies in Raw264.7 cells. Interferon-γ/lipopolysaccharide-induced nuclear factor-κB signaling was negatively regulated by RuTRIM1-X1 and RuTRIM1-X2, and the negative effect was reversed in RING deletion mutants. To our knowledge, this is the first study to characterize fish TRIM1, which may play a role in the inflammatory response.

The purpose of this study is to investigate the early life history of the Rhodeus fish, Rhodeus uyekii and R. ocellatus, in the Nakdong River to use as the preliminary data for the systematic study. The embryos used in the study were fertilized eggs (embryo) and larvae after artificial fertilization. The long diameter of the eggs of the R. uyekii was 3.39-3.97 mm (average 3.68±0.41 mm, n=30) and the short diameter was 1.36-1.55 mm (average 1.45±0.13 mm, n=30). The long diameter of the eggs of the R. ocellatus was 2.53-2.71 mm (average 2.62±0.12 mm, n=30) and the short diameter was 1.47-1.60 mm (average 1.53±0.09 mm, n=30). Hatching time was 48 hours for the R. uyekii and 50 hours for the R. ocellatus given that the average water temperature was 21.5°C. The hatched larvae were 4.95-5.00 mm (average 4.98±0.04 mm, n=5) for the R. uyekii and the total length was 3.66-3.69 mm (average 3.67±0.02 mm, n=5) for the R. ocellatus. R. uyekii was found to be 15.5-15.8 mm at total length (average 15.6±0.21 mm, n=5) on the 56 days after hatching with the number of dorsal fins being iii-9, anal fins iii-10, ventral fins iii-5. The R. ocellatus was found to be 15.8-16.0 mm (average 15.9±0.14 mm, n=5) at total length on the 58 days with the number of dorsal fins being iii-11, anal fins iii-12 and ventral fins iii-5 where the number of all fin stalks reached maximum.

In this study, we induced tetraploidy in Korean rose bitterling, Rhodeus uyekii, by applying various hydrostatic pressure shock conditions. Tetraploidy was not induced under 4500 psi pressure treatment in any experimental group. Instead, the induction rate of tetraploidy was highest under 7500 psi hydrostatic pressure treatment. As a result, when the processing method was similar and as the process time increased, the induction rate of each experimental group increased; however, there was no significant difference (P > 0.05). The production rate was 3.1 %, which was highest in all experimental groups exposed to 6000 psi for 10 min after being fertilized for 100 min. The production rate was highest in the experimental groups treated with hydrostatic pressure alone, whereas the production rate was lowest in groups treated under hydrostatic pressure with chemical treatment. The abnormal rate of all experimental groups treated with 7500 psi for 20 min was very high, at about 5 %. Based on these studies, only hydrostatic pressure shock was considered effective at inducing tetraploidy based on the calculated hatching, abnormal, and induction rates. The most effective condition for inducing tetraploidy was 6000 psi of hydrostatic pressure shock for 10 min after being fertilized for 100 min. The chromosome number of the induced tetraploid Korean rose bitterling was 4n = 96, while that of the diploid was 2n = 48. In the diploid, there were 1 or 2 nucleoli in the cells, whereas the induced tetraploids contained 1, 2, 3, or 4. The DNA content of tetraploids and diploids were 3.68 ± 0.009 pg/nucleus and 1.84 ± 0.019 pg/nucleus, respectively, according to flow cytometric analysis. The DNA content and chromosome number of the tetraploids were twice that of the diploids.

Heat shock protein (HSP) 70, the highly conserved stress protein families, plays important roles in protecting cells against heat and other stresses in most animal species. In the present study, we identified and characterized four Hsp70 (RuHSP4, RuHSC70, RuHSP12A, RuGRP78) family proteins based on the expressed sequence tag (EST) analysis of the Korean rose bitterling R. uyekii cDNA library. The deduced RuHSP70 family has high amino acid identities of 72-99% with those of other species. Phylogenetic analysis revealed that RuHsp70 family clustered with fish groups (HSP4, HSC70, HSP12A, GRP78) proteins. Quantitative RT-PCR analysis showed the specific expression patterns of RuHsp70 family members in the early developmental stages and several tissues in Korean rose bitterling. The expression of 4 groups of Hsp70 family was detected in all tested tissue. Particularly, Hsp70 family of Korean rose bitterling is highly expressed in hepatopancreas and sexual gonad (testis and ovary). The expression of Hsp70 family was differentially regulated in accordance with early development stage of Rhodeus uyekii.

Serine-arginine-rich nuclear protein LUC7L plays an important role in the regulation of myogenesis in mice. In the present study, we isolated and characterized the Korean rose bitterling Rhodeus uyekii Luc7l cDNA, designated RuLuc7l. The RuLuc7l cDNA is 1,688 bp long and encodes a 364-amino-acid polypeptide containing serine/arginine-rich region at the C-terminus. The deduced RuLuc7l protein has high amino acid identity (71-97%) with those of other species including human. Phylogenetic analysis revealed that RuLUC7L clustered with fish LUC7L proteins. The expression of RuLuc7l mRNA was high in the brain, kidney, and stomach of Korean rose bitterling. Expression of the RuLuc7l mRNA was detected from 1 day post-fertilization (dpf) and moderately increased until 21 dpf during the early development. Further investigations are required to elucidate the functional role of RuLUC7L in myogenesis in R. uyekii.

We investigated the process of yolk absorption in Korean rose bitterling, Rhodeus uyekii, and determined the changes in its morphometric characteristics. The R. uyekii from 1 days post hatching (DPH) to 21 DPH, the eye diameter (ED) was 5.4 at 5 DPH. Thereafter, the ED/total length (TL) ratio increased to 10.7 at 21 DPH (p<0.05). The yolk length (YL) decreased from 95.4 to 1.1 by 21 DPH, and this rate of decrease was greater than that for any other dimension (p<0.05). 12 morphometric dimensions/TL for the R. uyekii were measured at each sampling day from 21 DPH to 170 DPH. At just hatching, the average TL and BW were 6.1±0.09 mm and 4.9±0.07 mg, respectively. At 53 DPH, the average TL was 12.9±0.28 mm and the average BW was 14.7±0.72 mg; the total length growth equation was TL=5.507e(0.038t) (R (2)=0.916). Further, the body weight growth equation was BW=3.3647e(0.0296t) (R (2)=0.9354). The dimensions with regard to body depth showed the greatest growth rates in the external characteristics of the fish (p<0.05). The patterns of the morphometric characteristics measured in this study can be classified in three ways. The patterns were shown to be increased (y=0.0992x+ 12.07, R (2)=0.8333), decreased (y=-0.0569x+42.029, R (2)=0.8395) or maintained (y=0.005x+18.263, R (2)=0.3678) from 21 DPH to 170. These results will provide useful indices for the successful rearing of the R. uyekii.