Deep sequencing of small RNAs from 11 tissues of grass carp Ctenopharyngodon idella and discovery of sex‐related microRNAs

Abstract

This research identified 169 known microRNAs (miRNAs), 380 novel miRNAs, and 30,538 targets in 11 tissues (blood, brain, derma, gill, heart, intestine, kidney, liver, muscle, pronephros, and spleen) from grass carp Ctenopharyngodon idella with high-throughput sequencing (HTS).Transcripts per million (TPM) expression analysis detected 41 brain-enriched miRNAs (accounting for 61.19% of all tissue-enriched miRNAs). Real-time quantitative PCR (RT-qPCR) confirmed that 21 of 24 randomly selected tissue-enriched miRNAs from the TPM analysis were indeed tissue-enriched (P < 0.05), suggesting the HTS and TPM analyses were reliable. Nine of the 41 brain-enriched miRNAs are complementary to members of the double-sex and mab-3 related transcription factor family (dmrt) involved in sex differentiation. RT-qPCR revealed that cid-miR-138 was more highly expressed in testis than in ovary (P < 0.01), while the reverse was true for target gene dmrt4a (P < 0.01). This opposite expression pattern suggested the direct participation of cid-miR-138-dmrt4a in neuroendocrine mechanisms related to brain-pituitary networks during sex development. The discovery of miRNAs from 11 C. idella tissues expands the available fish miRNA database, and enhances our understanding of the role of sex-related miRNAs in tissue differentiation and maintenance of specific tissue functions in fishes. K E Y W O R D Sdeep sequencing, dmrt, grass carp, microRNA, sex differentiation

Genome-Wide Identification, Phylogeny, and Expression Profile of the Dmrt (Doublesex and Mab-3 Related Transcription Factor) Gene Family in Channel Catfish (Ictalurus punctatus)

“…A total of seven Dmrt genes ( IpDmrt1 , IpDmrt2a , IpDmrt2b , IpDmrt3 , IpDmrt4 , IpDmrt5 , and IpDmrt6 ) were identified in the channel catfish genome, and were named based on the nomenclature of teleost Dmrt genes and the results of phylogenetic analyses. These gene numbers were relatively consistent compared to that previously reported in other fish species, such as large yellow croaker ( Wan et al, 2020 ), while it was less than that reported for grass carp ( Ctenopharyngodon idella ) ( Chen et al, 2019 ) and rainbow trout ( Oncorhynchus mykiss ) ( Wang et al, 2014 ), which experienced four rounds of whole genome duplication during evolution. The exon-intron structure analysis revealed that the IpDmrt gene family contained two to five exons; in particularly, IpDmrt1 had five exons; IpDmrt2a and IpDmrt6 had four; IpDmrt2b had three; and IpDmrt3 , IpDmrt4 , and IpDmrt5 had two.…”

Expression characteristics and interaction networks of microRNAs in spleen tissues of grass carp (Ctenopharyngodon idella)

“…For example, a total of 160 conserved miRNAs and 18 novel miRNAs were identified from grass carp in eight different tissues including the spleen [ 24 ] . There were 169 known miRNAs and 380 novel miRNAs obtained in 11 grass carp tissues including the spleen with high-throughput sequencing [ 25 ] . A total of 1208 miRNAs were identified from grass carp spleen at 0, 1, 3, 5, 7, and 9 days post-infection with a grass carp reovirus, of which 36 miRNAs exhibited differential expression [ 26 ] .…”

Modulation of hepatic miRNA expression in Atlantic salmon (Salmo salar) by family background and dietary fatty acid composition

“…Thus, miRNAs control the expression of a large number of genes and seem to be the major post‐transcriptional regulators of cellular gene networks in vertebrates (Friedman et al ., 2009). Studies in teleost fish have shown that miRNAs participate in the regulation of early development, apoptosis, the maintenance of tissue‐specific functions, reproduction and immune response (Andreassen & Hoyheim, 2017; Bizuayehu & Babiak, 2014; Chen et al ., 2019). Studies on miRNAs in commercially important fish species have indicated that they also participate in the regulation of economically interesting traits like growth or food conversion (Andreassen et al ., 2016; Mennigen, 2016).…”