Identification of microRNAs involved in cold adaptation of Litopenaeus vannamei by high-throughput sequencing

He, Pingping; Wei, Pinyuan; Zhang, Bin; Zhao, Yang; Li, Qiangyong; Chen, Xiuli; Zeng, Dingyuan; Peng, Min; Yang, Chunling; Peng, J.; Chen, Xiaohan

doi:10.1016/j.gene.2018.07.042

Cited by 30 publications

(15 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…And lipid was the main energy source of tilapia fish during long-time hypoxia stress (Li et al, 2018). In previous studies, the digestion and absorption of fat, and the protein pathways were significantly enhanced after cold adaptation by L. vannamei (He et al, 2018). In the current study, the results revealed that under low temperature stress, lipids (TG and TC, the major components of lipids) and proteins (TP) in the plasma significantly increased after acute cold-stress at 23 °C, while Glu did not change significantly.…”

Section: Discussionmentioning

confidence: 81%

Investigating the physiological responses of Pacific white shrimp Litopenaeus vannamei to acute cold-stress

Wang

Zhuo³

et al. 2019

PeerJ

View full text Add to dashboard Cite

Background Litopenaeus vannamei is one of the most important aquaculture shrimps in the world and low temperatures present a serious challenge to its survival, growth, and distribution. Methods To investigate their physiological responses during acute cold-stress, L. vannamei were treated under acute cooling conditions from 28 to 13 °C with a cooling rate of 2.5 °C/2 h and were maintained at 13 °C for 12 h. Plasma metabolite concentrations, histological changes, and relative gene expression related to the unfolded protein response (UPR) pathway and apoptosis in the hepatopancreas and the hemocytes of L. vannamei were investigated. Results The results revealed that the concentrations of triglycerides, total cholesterol, and total protein in plasma reached their peaks at 23 °C, and then decreased to their minimum values at 13 °C for 12 h. The activity of alkaline phosphatase in the plasma decreased to its lowest level while the activity of alanine aminotransferase increased to its highest level at 13 °C for 12 h. The hepatic tubules became necrotic and the basement membranes were ruptured at 13 °C for 12 h. The gene expression related to UPR and apoptosis in the hepatopancreas and hemocytes was significantly altered by the decrease in the temperature. Discussion The results revealed that acute cold-stress caused histological damage in the hepatopancreas of L. vannamei, reducing its immunity. The three UPR pathways were involved in the process of acute cold-stress and the response of activating transcription factor 6 to UPR may be faster and more directthan the IRE1 and PERK pathways.

show abstract

Section: Discussionmentioning

confidence: 81%

Investigating the physiological responses of Pacific white shrimp Litopenaeus vannamei to acute cold-stress

Wang

Zhuo³

et al. 2019

PeerJ

View full text Add to dashboard Cite

show abstract

“…miR-319 is a potential marker for selection of cold-tolerant sugarcane cultivars [36]. miR-210-3p modulates expression of genes related to metabolism, apoptosis and proliferation in rat cells under acute cold stress conditions [16], and miRNAs play key roles in cold adaptation of Litopenaeus vannamei [17]. Although mechanisms related to genome, transcriptome, DNA methylation, histone modification and so on have been reported in cold responses of fish [21,[37][38][39][40], the detailed mechanisms of miRNAs during cold acclimation in fish are still unclear.…”

Section: Discussionmentioning

confidence: 99%

“…Increasing reports have shown that specific protein-coding genes are differentially expressed under cold stress [9,10], and miRNAs play crucial roles in this process [11][12][13]. A number of studies have demonstrated that miRNAs have significant roles in response to cold stress in numerous species, such as arabidopsis [14], wheat [15], rat [16], Litopenaeus vannamei [17], and zebrafish [18]. However, most studies focus on plants and mammals under acute cold stress, the regulatory mechanisms of miRNA in long-term cold acclimation in fish are still obscure.…”

Section: Introductionmentioning

confidence: 99%

Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells

Jiang

Luo

et al. 2020

PLoS ONE

View full text Add to dashboard Cite

MicroRNAs (miRNAs) play vital roles in various biological processes under multiple stress conditions by leading to mRNA cleavage or translational repression. However, the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study, highthroughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control (28˚C, 30 days) and cold-acclimation (18˚C, 30 days) conditions. A total of 414 miRNAs, 349 known and 65 novel, were identified. Among those miRNAs, 24 (19 known and 5 novel) were up-regulated, and 23 (9 known and 14 novel) were down-regulated in cold acclimated cells. The Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses indicated that the target genes of known differentially expressed miRNAs (DE-miRNA) are involved in cold acclimation by regulation of phosphorylation, cell junction, intracellular signal transduction, ECM-receptor interaction and so on. Moreover, both miR-100-3p inhibitor and miR-16b mimics could protect ZF4 cells under cold stress, indicating the involvement of miRNA in cold acclimation. Further study showed that miR-100-3p and miR-16b could regulate inversely the expression of their target gene (atad5a, cyp2ae1, lamp1, rilp, atxn7, tnika, btbd9), and that overexpression of miR-100-3p disturbed the early embryonic development of zebrafish. In summary, the present data show that miRNAs are closely involved in cold acclimation in zebrafish ZF4 cells and provide information for further understanding of the roles of miRNAs in cold acclimation in fish.

show abstract

“…Moreover, 24 nt siRNAs can induce transcriptional gene silencing by DNA and histone modi cations (Pontes et al 2009;Ye et al 2016). The relationship between miRNAs and cold response was reported in many plants (Yang et al 2018;He et al 2018;Shi et al 2018). In H. fulva, the genome-wide expression pro le of miRNAs in response to cold stress remains unreported.…”

Section: Discussionmentioning

confidence: 99%

Identification of cold stress responsive microRNAs in cold tolerant and susceptible Hemerocallis fulva by high throughput sequencing

Huang

Jiang

Jin

et al. 2020

Preprint

View full text Add to dashboard Cite

Background:Hemerocallis fulva is a perennial herb belonging to Hemerocallis of Hemerocallis. Because of the large and bright colors, it is often used as a garden ornamental plant. But most varieties of H. fulva on the market will wither in winter, which will affect their beauty. It is very important to study the effect of low temperature stress on the physiological indexes of H. fulva and understand the cold tolerance of different H. fulva. MiRNA is a kind of endogenous non coding small molecular RNA with length of 21-24nt. It mainly inhibits protein translation by cutting target genes, and plays an important role in the development of organisms, gene expression and biological stress. Low temperature is the main abiotic stress affecting the production of H. fulva in China, which hinders the growth and development of plants. A comprehensive understanding of the expression pattern of microRNA in H. fulva under low temperature stress can improve our understanding of microRNA mediated stress response. Although there are many studies on miRNAs of various plants under cold stress at home and abroad, there are few studies on miRNAs related to cold stress of H. fulva. It is of great significance to explore the cold stress resistant gene resources of H. fulva, especially the identification and functional research of miRNA closely related to cold stress, for the breeding of excellent H. fulva.Results A total of 5619 cold-responsive miRNAs, 315 putative novel and 5 304 conserved miRNAs, were identified from the leaves and roots of two different varieties ‘Jinyan’ (cold-tolerant) and ‘Lucretius ’ (cold-sensitive), which were stressed under -4 oC for 24 h. Twelve conserved and three novel miRNAs (novel-miR10, novel-miR19 and novel-miR48) were differentially expressed in leaves of ‘Jinyan’ under cold stress. Novel-miR19, novel-miR29 and novel-miR30 were up-regulated in roots of ‘Jinyan’ under cold stress. Thirteen and two conserved miRNAs were deferentially expressed in leaves and roots of ‘Lucretius’ after cold stress. The deferentially expressed miRNAs between two cultivars under cold stress include novel miRNAs and the members of the miR156, miR166 and miR319 families. A total of 6 598 target genes for 6 516 known miRNAs and 82 novel miRNAs were predicted by bioinformatic analysis, mainly involved in metabolic processes and stress responses. Ten differentially expressed miRNAs and predicted target genes were confirmed by quantitative reverse transcription PCR(q-PCR), and the expressional changes of target genes were negatively correlated to differentially expressed miRNAs. Our data indicated that some candidate miRNAs (e.g., miR156a-3-p, miR319a, and novel-miR19) may play important roles in plant response to cold stress.Conclusions Our study indicates that some putative target genes and miRNA mediated metabolic processes and stress responses are significant to cold tolerance in H. fulva.

show abstract

Identification of microRNAs involved in cold adaptation of Litopenaeus vannamei by high-throughput sequencing

Cited by 30 publications

References 41 publications

Investigating the physiological responses of Pacific white shrimp Litopenaeus vannamei to acute cold-stress

Investigating the physiological responses of Pacific white shrimp Litopenaeus vannamei to acute cold-stress

Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells

Identification of cold stress responsive microRNAs in cold tolerant and susceptible Hemerocallis fulva by high throughput sequencing

Contact Info

Product

Resources

About