Comparative Transcriptome Analysis Revealed Genes Involved in Sexual and Polyploid Growth Dimorphisms in Loach (Misgurnus anguillicaudatus)

Characterization of sexual size dimorphism in mandarin fish and association with igfbp-5a/b regulation

Mandarin fish (Siniperca chuatsi) is an important cultured fish in East Asia that shows sexual size dimorphism (SSD), with females growing faster than males when reaching marketable size. However, the regulatory mechanism of SSD is not clear. To characterize SSD of mandarin fish and its association with gh/igf1/igfbp-5 expression, gonadal developmental atlas of the females and the males were described, and growth parameters and serum levels of E2 and T, as well as the relative expression levels of gh, igf1, and igfbp-5a/b mRNAs, were determined. The results showed that the logistic growth equation of body mass and total length of female and male were W(♀) = 667.57/(1 + e^(4.19 - 1.24*t)), W(♂) = 582.71/(1 + e^(4.07 - 1.27*t)), L(♀) = 31.47/(1 + e^1.95 - 1.08*t)), L(♂) = 26.20/(1 + e^(2.56 - 1.5*t)). The month of inflection points for body mass for females and males were 3.37 mph and 3.20 mph, respectively, when the body mass were 333.79 g and 291.36 g. The month of inflection points for total length growth were 1.80 mph and 1.70 mph, respectively, when the total length were 18.52 cm and 16.28 cm. At 1.5-2.0 mph, SSD was not clearly demonstrated. At 3.0 mph, the body mass of the females was significantly higher than that of the males (P < 0.05), Serum E2, brain gh, and liver igf1 expression of the females was significantly higher than that of the males (P < 0.05); T content of the males was significantly higher than that of the females (P < 0.05). At 4.0 months of age, the body mass of the females was highly significantly higher than that of the males (P < 0.01), Serum E2, brain gh, and liver igf1 expression of the females was highly significantly higher than that of the males (P < 0.05); T content of the males was significantly higher than that of the females (P < 0.05). With the continuous development of gonads, muscle and liver igfbp-5a and -5b expression generally tend to increase in females and males, while igfbp-5a showed a gradual increasing trend, and igfbp-5b expression showed a trend of decreasing and then increasing. Male igfbp-5a/b expression was significantly higher than female at the age of 3.0-4.0 months (P < 0.05). This work verified that the females had faster growth rate since 3.0 mph compared to the males, which may be related to higher E2 levels in females leading to higher igf1 level, through inhibition of igfbp-5a/b expression.

Chromosome-scale and haplotype-resolved genome assembly of the autotetraploid Misgurnus anguillicaudatus

In nature, diploids and tetraploids are two common types of polyploid evolution. Misgurnus anguillicaudatus (mud loach) is a remarkable fish species that exhibits both diploid and tetraploid forms. However, reconstructing the four haplotypes of its autotetraploid genome remains unresolved. Here, we generated the first haplotype-resolved, chromosome-level genome of autotetraploid M. anguillicaudatus with a size of 4.76 Gb, contig N50 of 6.78 Mb, and scaffold N50 of 44.11 Mb. We identified approximately 2.9 Gb (61.03% of genome) of repetitive sequences and predicted 91,485 protein-coding genes. Moreover, allelic gene expression levels indicated the absence of significant dominant haplotypes within the autotetraploid loach genome. This genome will provide a valuable biological model for unraveling the mechanisms of polyploid formation and evolution, adaptation to environmental changes, and benefit for aquaculture applications and biodiversity conservation.

Comparative transcriptome analysis revealed genes involved in the sexual size dimorphisms and expressed sequence tag-Simple Sequence Repeat loci validation in Odorrana graminea

Sexual size dimorphism (SSD) is widespread among animals and is characterized by differences in body size between sexes. Previous studies suggested SSD might reflect the adaptations of particular sexes to their specific reproductive or ecological roles. The large green cascade frogs (Odorrana graminea) exhibit obvious SSD that females are nearly twice the body size of males. However, the molecular mechanisms underlying SSD of O. graminea are still unknown. In the present study, we first obtained nearly 5 Gb of the transcriptome data through Illumina sequencing, and the de novo transcriptome assembly produced 189,868 unigenes of O. graminea. A total of 774 significantly sex-differentially expressed genes (DEGs) were identified. Of which, 436 DEGs showed significantly higher expression levels in females than those in males, whereas 338 DEGs showed significantly lower expression in females than those in males. We also found 10 sex-differentially expressed genes related to energy metabolism between sexes of O. graminea, and these DEGs were related to the estrogen signaling pathway, oxidative phosphorylation, fatty acid biosynthesis, gastric acid secretion, and nitrogen metabolism. We found that the differences in energy metabolism and steroid hormone synthesis might be the main driving force leading to the sexual growth dimorphism of O. graminea. In addition, a total of 63,269 potential EST-SSR loci and 4,669 EST-SSR loci were detected and validated in different populations of O. graminea and other species within Odorrana. The assembled transcriptome will facilitate functional genomic studies of O. graminea and the developed EST-SSR markers will contribute to the population genetics of the species within Odorrana. The sex-differentially expressed genes involved in energy metabolism might provide insights into the genetic mechanisms underlying the SSD of O. graminea.

Transcriptome analysis of the muscle of fast- and slow-growing phoenix barb (Spinibarbus denticulatus denticulatus)

Growth rate is a commercial trait in aquaculture that is influenced by multiple factors, among which genetic composition plays a fundamental role in the growth rate of species. The phoenix barb (Spinibarbus denticulatus denticulatus) is a widely distributed freshwater fish species in South China. Although S. d. denticulatus is reared in South China, the molecular mechanisms underlying the growth rate of the species remain unclear. Here, the authors performed transcriptome analysis of muscle tissues from fast-growing (FG) and slow-growing (SG) S. d. denticulatus at 90, 150, and 300 days after hatch (DAH) to elucidate its growth mechanism. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that differentially expressed genes (DEGs) between the two groups were enriched in pathways related to muscle growth, glycolysis, and energy and lipid metabolism. Nonetheless, a higher number of DEGs were identified in the FG vs. SG groups at 90 and 300 DAH compared with 150 DAH. DEGs identified at 90 DAH were mainly enriched in the GH/IGF axis, PI3K-Akt signalling pathway, AMPK signalling pathway and lipid metabolism highly expressed in FG individuals. DEGs identified at 300 DAH were mainly enriched in PI3K-Akt signalling pathway, glycolysis/gluconeogenesis, gene translation and lipid metabolism. In addition, some genes were expressed during the early growth stage in FG individuals but expressed during the late stage in SG individuals, indicating considerable variations in the expression profiles of growth-related genes at different developmental stages. Overall, these findings contribute to the understanding of the growth mechanism of S. d. denticulatus, which would be useful for the propagation of fast-growing breeds.