Identification of Potential Blind-Side Hypermelanosis-Related lncRNA–miRNA–mRNA Regulatory Network in a Flatfish Species, Chinese Tongue Sole (Cynoglossus semilaevis)

TCONS_00025035-miR-101-UROS is potentially involved in the regulation of heme synthesis pathway and influences mantle melanin deposition by targeting porphyrin in Manila clam (Ruditapes philippinarum)

Shell color is an important economic trait and one of the target traits in breeding and production. Non-coding RNA (ncRNA) refers to RNA molecules transcribed from the genome and do not encoding proteins, which can regulate the expression of target genes after transcription and participate in the regulation of many important traits, such as the formation of shell color and body color. In this study, we detected the porphyrins in the shells of three Manila clams with different shell colors, explored the expression pattern and function of Uroporphyrinogen III synthetase (UROS) in the shell color pigmentation of Ruditapes philippinarum, and found that it might be involved in the synthesis of porphyrins and potentially in the synthesis of melanin. The results showed that the expression levels of heme synthesis-related genes such as UROS, Uroporphyrinogen decarboxylase (UROD), Ferrochelatase (FECH), Hephaestin (HEPH), and pigment synthesis-related genes (Peroxidasin PXDN) in the positive group were significantly reduced compared with the control group after injection of UROS dsRNA, indicating that UROS plays a crucial role in the porphyrin synthesis pathway. Additionally, transmission electron microscopy and melanin extraction experiments also proved that it might participate in the synthesis of melanin. We further explored and verified the relationship between TCONS_00025035-miR-101-UROS and identified the changes in the expression level of UROS through RNA interference and injection of miR-101 antagomir, respectively. Our results imply that miR-101 antagonists affect the expression of UROS. Furthermore, dual-luciferase reporter gene experiments confirmed the relationship between TCON_00025035, miR-101, and UROS. The regulatory relationship between TCONS_00025035 and miR-101 is negative, and the regulatory relationship between miR-101 and UROS is also negative. In summary, we verified the function of UROS through RNA interference, qPCR, in situ hybridization, and melanin content detection. We speculated that there was a negative relationship between miR-101 and UROS, and there was also a negative relationship between TCONS_00025035 and miR-101. TCONS_00025035 might regulate UROS through the regulation of miR-101, and UROS might also regulate other pigmentation-related genes and affect the formation of pigments, thereby influencing porphyrin and melanin formation in Manila clam.

Decoding the fish genome opens a new era in important trait research and molecular breeding in China

Aquaculture represents the fastest-growing global food production sector, as it has become an essential component of the global food supply. China has the world's largest aquaculture industry in terms of production volume. However, the sustainable development of fish culture is hindered by several concerns, including germplasm degradation and disease outbreaks. The practice of genomic breeding, which relies heavily on genome information and genotypephenotype relationships, has significant potential for increasing the efficiency of aquaculture production. In 2014, the completion of the genome sequencing and annotation of the Chinese tongue sole signified the beginning of the fish genomics era in China. Since then, domestic researchers have made dramatic progress in functional genomic studies. To date, the genomes of more than 60 species of fish in China have been assembled and annotated. Based on these reference genomes, evolutionary, comparative, and functional genomic studies have revolutionized our understanding of a wide range of biologically and economically important traits of fishes, including growth and development, sex determination, disease resistance, metamorphosis, and pigmentation. Furthermore, genomic tools and breeding techniques such as SNP arrays, genomic selection, and genome editing have greatly accelerated genetic improvement through the incorporation of functional genomic information into breeding activities. This review aims to summarize the current status, advances, and perspectives of the genome resources, genomic study of important traits, and genomic breeding techniques of fish in China. The review will provide aquaculture researchers, fish breeders, and farmers with updated information concerning fish genomic research and breeding technology. The summary will help to promote the genetic improvement of production traits and thus will support the sustainable development of fish aquaculture.

Small RNA and degradome sequencing reveal the role of blackberry miRNAs in flavonoid and anthocyanin synthesis during fruit ripening

Blackberry shrubs are economically important for their production of small, pulped fruits. This species has attracted much attention because of the unique flavor of its fruits and their rich nutritional and medicinal value. In this study, microRNAs (miRNAs) and their target genes related to flavonoids and anthocyanins in blackberry fruits during ripening were analyzed and identified by small RNA and degradome sequencing technology, and the expression levels of key miRNAs in unripe and ripe blackberry fruits were verified via the RT-qPCR. A total of 258 known miRNAs were identified. Eighty differentially expressed miRNAs (DEMs) were detected in the fruits of the ripe group compared with those of the unripe group. Differentially expressed miR828-x/miR828-z and unigene0086056 (unknown function) were coexpressed. Moreover, miR858 had the most target genes for the synthesis of flavonoids and anthocyanins. Taken together, these results provide important value for improving the quality of blackberry fruits and breeding blackberry plants that produce high-flavonoid fruits for the pharmaceutical industry.