Systematic identification of circular RNAs and corresponding regulatory networks unveil their potential roles in the midguts of eastern honeybee workers

Dynamics and regulatory role of circRNAs in Asian honey bee larvae following fungal infection

Non-coding RNA (ncRNA) plays a vital part in the regulation of immune responses, growth, and development in plants and animals. Here, the identification, characteristic analysis, and molecular verification of circRNAs in Apis cerana cerana worker larval guts were conducted, followed by in-depth investigation of the expression pattern of larval circRNAs during Ascosphaera apis infection and exploration of the potential regulatory part of differentially expressed circRNAs (DEcircRNAs) in host immune responses. A total of 3178 circRNAs in the larval guts of A. c. cerana were identified, with a length distribution ranging from 15 to 96,007 nt. Additionally, 155, 95, and 86 DEcircRNAs were identified in the in the 4-, 5-, and 6-day-old larval guts following A. apis infection. These DEcircRNAs were predicted to target 29, 25, and 18 parental genes relevant to 12, 20, and 17 GO terms as well as 144, 114, and 61 KEGG pathways, including 5 cellular and 4 humoral immune pathways. Complex competing endogenous RNA (ceRNA) regulatory networks were detected as being formed among DEcircRNAs, DEmiRNAs, and DEmRNAs. The target DEmRNAs were engaged in 36, 47, and 47 GO terms as well as 331, 332, and 331 pathways, including 6 cellular and 6 humoral immune pathways. Further, 19 DEcircRNAs, 5 DEmiRNAs, and 3 mRNAs were included in the sub-networks relative to 3 antioxidant enzymes. Finally, back-splicing sites within 15 circRNAs and the difference in the 15 DEcircRNAs' expression between uninoculated and A. apis-inoculated larval guts were confirmed based on molecular methods. These findings not only enrich our understanding of bee host-fungal pathogen interactions but also lay a foundation for illuminating the mechanism underlying the DEcircRNA-mediated immune defense of A. c. cerana larvae against A. apis invasion. KEY POINTS: • The expression pattern of circRNAs was altered in the A. cerana worker larval guts following A. apis infection. • Back-splicing sites within 15 A. cerana circRNAs were verified using molecular approaches. DEcircRNAs potentially modulated immune responses and antioxidant enzymes in A. apis-challenged host guts.

Novel Insights into the circRNA-Modulated Developmental Mechanism of Western Honey Bee Larval Guts

Circular RNAs (circRNAs) are a class of novel non-coding RNAs (ncRNAs) that play essential roles in the development and growth of vertebrates through multiple manners. However, the mechanism by which circRNAs modulate the honey bee gut development is currently poorly understood. Utilizing the transcriptome data we obtained earlier, the highly expressed circRNAs in the Apis mellifera worker 4-, 5-, and 6-day-old larval guts were analyzed, which was followed by an in-depth investigation of the expression pattern of circRNAs during the process of larval guts development and the potential regulatory roles of differentially expressed circRNAs (DEcircRNAs). In total, 1728 expressed circRNAs were detected in the A. mellifera larval guts. Among the most highly expressed 10 circRNAs, seven (novel_circ_000069, novel_circ_000027, novel_circ_000438, etc.) were shared by the 4-, 5-, and 6-day-old larval guts. In addition, 21 (46) up-regulated and 22 (27) down-regulated circRNAs were, respectively, screened in the Am4 vs. Am5 (Am5 vs. Am6) comparison groups. Additionally, nine DEcircRNAs, such as novel_circ_000340, novel_circ_000758 and novel_circ_001116, were shared by these two comparison groups. These DEcircRNAs were predicted to be transcribed from 14 and 29 parental genes; these were respectively annotated to 15 and 22 GO terms such as biological regulation and catalytic activity as well as 16 and 21 KEGG pathways such as dorsoventral axis formation and apoptosis. Moreover, a complicated competing endogenous RNA (ceRNA) network was observed; novel_circ_000838 in the Am4 vs. Am5 comparison group potentially targeted ame-miR-6000a-3p, further targeting 518 mRNAs engaged in several developmental signaling pathways (e.g., TGF-beta, hedgehog, and wnt signaling pathway) and immune pathways (e.g., phagosome, lysosome, and MAPK signaling pathway). The results demonstrated that the novel_circ_000838-ame-miR-6000a-3p axis may plays a critical regulatory part in the larval gut development and immunity. Furthermore, back-splicing sites of six randomly selected DEcircRNAs were amplified and verified by PCR; an RT-qPCR assay of these six DEcircRNAs confirmed the reliability of the used high-throughput sequencing data. Our findings provide a novel insight into the honey bee gut development and pave a way for illustration of the circRNA-modulated developmental mechanisms underlying the A. mellifera worker larval guts.

TMEM127 suppresses tumor development by promoting RET ubiquitination, positioning, and degradation

The TMEM127 gene encodes a transmembrane protein of poorly known function that is mutated in pheochromocytomas, neural crest-derived tumors of adrenomedullary cells. Here, we report that, at single-nucleus resolution, TMEM127-mutant tumors share precursor cells and transcription regulatory elements with pheochromocytomas carrying mutations of the tyrosine kinase receptor RET. Additionally, TMEM127-mutant pheochromocytomas, human cells, and mouse knockout models of TMEM127 accumulate RET and increase its signaling. TMEM127 contributes to RET cellular positioning, trafficking, and lysosome-mediated degradation. Mechanistically, TMEM127 binds to RET and recruits the NEDD4 E3 ubiquitin ligase for RET ubiquitination and degradation via TMEM127 C-terminal PxxY motifs. Lastly, increased cell proliferation and tumor burden after TMEM127 loss can be reversed by selective RET inhibitors in vitro and in vivo. Our results define TMEM127 as a component of the ubiquitin system and identify aberrant RET stabilization as a likely mechanism through which TMEM127 loss-of-function mutations cause pheochromocytoma.

Effect of fluvalinate on the expression profile of circular RNA in brain tissue of Apis mellifera ligustica workers

Fluvalinate is widely used in apiculture as an acaricide for removing Varroa mites, but there have been growing concerns about the negative effects of fluvalinate on honeybees in recent years. Previous research revealed changes in the miRNA and mRNA expression profiles of Apis mellifera ligustica brain tissues during fluvalinate exposure, as well as key genes and pathways. The role of circRNAs in this process, however, is unknown. The goal of this study was to discover the fluvalinate-induced changes in circular RNA (circRNA) expression profiles of brain tissue of A. mellifera ligustica workers. A total of 10,780 circRNAs were detected in A. mellifera ligustica brain tissue, of which eight were differentially expressed between at least two of the four time periods before and after fluvalinate administration, and six circRNAs were experimentally verified to be structurally correct, and their expression patterns were consistent with transcriptome sequencing results. Furthermore, ceRNA analysis revealed that five differentially expressed circRNAs (DECs) (novel_circ_012139, novel_circ_011690, novel_circ_002628, novel_circ_004765, and novel_circ_010008) were primarily involved in apoptosis-related functions by competitive binding with miRNAs. This study discovered changes in the circRNA expression profile of A. mellifera ligustica brain tissue caused by fluvalinate exposure, and it provides a useful reference for the biological function study of circRNAs in A. mellifera ligustica.

Whole-transcriptome profiling across different developmental stages of Aedes albopictus (Diptera: Culicidae) provides insights into chitin-related non-coding RNA and competing endogenous RNA networks

BACKGROUND

The Asian tiger mosquito, Aedes albopictus, is one of the most invasive species and a vector of numerous arboviruses. The deleterious effects of long-term and inappropriate use of chemical pesticides have stimulated the exploration of new, environmentally friendly control strategies. Non-coding RNAs (ncRNAs) have been proven to participate in almost all biological processes of insects.

METHODS

In this study, circular RNAs (circRNAs) and microRNAs (miRNAs) covering five developmental stages [egg, early larvae, late larvae, pupae, adult (female and male)] of A. albopictus were obtained using whole-transcriptome sequencing technology. Combined with long non-coding RNAs (lncRNAs) from previous research, circRNA/lncRNA‒miRNA‒mitochondrial RNA (mRNA) networks were constructed.

RESULTS

A total of 1434 circRNAs and 208 miRNAs were identified. More differentially expressed circRNAs (DE circRNAs) and miRNAs (DE miRNAs) were found in the egg versus early larvae comparison group. Functional enrichment analysis demonstrated that most of the circRNA/lncRNA‒miRNA‒mRNA networks were involved in chitin metabolism. Hub genes of each circRNA/lncRNA‒miRNA‒mRNA network were screened out, which can be used as novel targets to disturb the molting process of A. albopictus.

CONCLUSIONS

Regulatory relationships obtained from competing endogenous RNA (ceRNA) networks provide more information to manipulate the metamorphosis process and are helpful for developing effective and sustainable methods to control mosquitoes.

Effect of Ascosphaera apis Infestation on the Activities of Four Antioxidant Enzymes in Asian Honey Bee Larval Guts

Ascosphaera apis infects exclusively bee larvae and causes chalkbrood, a lethal fungal disease that results in a sharp reduction in adult bees and colony productivity. However, little is known about the effect of A. apis infestation on the activities of antioxidant enzymes in bee larvae. Here, A. apis spores were purified and used to inoculate Asian honey bee (Apis cerana) larvae, followed by the detection of the host survival rate and an evaluation of the activities of four major antioxidant enzymes. At 6 days after inoculation (dpi) with A. apis spores, obvious symptoms of chalkbrood disease similar to what occurs in Apis mellifera larvae were observed. PCR identification verified the A. apis infection of A. cerana larvae. Additionally, the survival rate of larvae inoculated with A. apis was high at 1−2 dpi, which sharply decreased to 4.16% at 4 dpi and which reached 0% at 5 dpi, whereas that of uninoculated larvae was always high at 1~8 dpi, with an average survival rate of 95.37%, indicating the negative impact of A. apis infection on larval survival. As compared with those in the corresponding uninoculated groups, the superoxide dismutase (SOD) and catalase (CAT) activities in the 5- and 6-day-old larval guts in the A. apis−inoculated groups were significantly decreased (p < 0.05) and the glutathione S-transferase (GST) activity in the 4- and 5-day-old larval guts was significantly increased (p < 0.05), which suggests that the inhibition of SOD and CAT activities and the activation of GST activity in the larval guts was caused by A. apis infestation. In comparison with that in the corresponding uninoculated groups, the polyphenol oxidase (PPO) activity was significantly increased (p < 0.05) in the 5-day-old larval gut but significantly reduced (p < 0.01) in the 6-day-old larval gut, indicating that the PPO activity in the larval guts was first enhanced and then suppressed. Our findings not only unravel the response of A. cerana larvae to A. apis infestation from a biochemical perspective but also offer a valuable insight into the interaction between Asian honey bee larvae and A. apis.

Unveiling the circRNA-Mediated Immune Responses of Western Honey Bee Larvae to Ascosphaera apis Invasion

Western honey bee (Apis mellifera), a eusocial insect with a superior economic and ecological value, is widely used in the beekeeping industry throughout the world. As a new class of non-coding RNAs (ncRNAs), circular RNAs (circRNAs) participate in the modulation of considerable biological processes, such as the immune response via diverse manners. Here, the identification, characteristic investigation, and molecular verification of circRNAs in the Apis mellifera ligustica larval guts were conducted, and the expression pattern of larval circRNAs during the Ascosphaera apis infection was analyzed, followed by the exploration of the potential regulatory part of differentially expressed circRNAs (DEcircRNAs) in host immune responses. A total of 2083 circRNAs in the larval guts of A. m. ligustcia were identified, with a length distribution ranging from 106 nt to 92,798 nt. Among these, exonic circRNAs were the most abundant type and LG1 was the most distributed chromosome. Additionally, 25, 14, and 30 up-regulated circRNAs as well as 26, 25, and 62 down-regulated ones were identified in the A. apis-inoculated 4-, 5-, and 6-day-old larval guts in comparison with the corresponding un-inoculated larval guts. These DEcircRNAs were predicted to target 35, 70, and 129 source genes, which were relative to 12, 23, and 20 GO terms as well as 11, 10, and 27 KEGG pathways, including 5 cellular and humoral immune pathways containing apoptosis, autophagy, endocytosis, MAPK, Toll, and Imd signaling pathways. Furthermore, complex competing endogenous RNA (ceRNA) regulatory networks were detected to be formed among DEcircRNAs, DEmiRNAs, and DEmRNAs. The Target DEmRNAs were engaged in 24, 20, and 25 functional terms as well as 62, 80, and 159 pathways, including several vital immune defense-associated pathways, namely the lysosome, endocytosis, phagosome, autophagy, apoptosis, MAPK, Jak-STAT, Toll, and Imd signaling pathways. Finally, back-splicing sites within 15 circRNAs and the difference in the 9 DEcircRNAs' expression between un-inoculated and A. apis-inoculated larval guts were confirmed utilizing molecular methods. These findings not only enrich our understanding of bee host-fungal pathogen interactions, but also lay a foundation for illuminating the mechanism underlying the DEcircRNA-mediated immune defense of A. m. ligustica larvae against A. apis invasion.

CircRNA-regulated immune responses of asian honey bee workers to microsporidian infection

Nosema ceranae is a widespread fungal parasite for honey bees, causing bee nosemosis. Based on deep sequencing and bioinformatics, identification of circular RNAs (circRNAs) in Apis cerana workers’ midguts and circRNA-regulated immune response of host to N. ceranae invasion were conducted in this current work, followed by molecular verification of back-splicing sites and expression trends of circRNAs. Here, 10185 and 7405 circRNAs were identified in the midguts of workers at 7 days (AcT1) and 10 days (AcT2) post inoculation days post-inoculation with N. ceranae. PCR amplification result verified the back-splicing sites within three specific circRNAs (novel_circ_005123, novel_circ_007177, and novel_circ_015140) expressed in N. ceranae-inoculated midgut. In combination with transcriptome data from corresponding un-inoculated midguts (AcCK1 and AcCK2), 2266 circRNAs were found to be shared by the aforementioned four groups, whereas the numbers of specific ones were 2618, 1917, 5691, and 3723 respectively. Further, 83 52) differentially expressed circRNAs (DEcircRNAs) were identified in AcCK1 vs. AcT1 (AcCK2 vs. AcT2) comparison group. Source genes of DEcircRNAs in workers’ midgut at seven dpi were involved in two cellular immune-related pathways such as endocytosis and ubiquitin mediated proteolysis. Additionally, competing endogenous RNA (ceRNA) network analysis showed that 23 13) DEcircRNAs in AcCK1 vs. AcT1 (AcCK2 vs. AcT2) comparison group could target 18 14) miRNAs and further link to 1111 (1093) mRNAs. These target mRNAs were annotated to six cellular immunity pathways including endocytosis, lysosome, phagosome, ubiquitin mediated proteolysis, metabolism of xenobiotics by cytochrome P450, and insect hormone biosynthesis. Moreover, 284 164) internal ribosome entry site and 54 26) ORFs were identified from DEcircRNAs in AcCK1 vs. AcT1 (AcCK2 vs. AcT2) comparison group; additionally, ORFs in DEcircRNAs in midgut at seven dpi with N. ceranae were associated with several cellular immune pathways including endocytosis and ubiquitin-mediated proteolysis. Ultimately, RT-qPCR results showed that the expression trends of six DEcircRNAs were consistent with those in transcriptome data. These results demonstrated that N. ceranae altered the expression pattern of circRNAs in A. c. cerana workers’ midguts, and DEcircRNAs were likely to regulate host cellular and humoral immune response to microsporidian infection. Our findings lay a foundation for clarifying the mechanism underlying host immune response to N. ceranae infection and provide a new insight into interaction between Asian honey bee and microsporidian.

Deciphering the CircRNA-Regulated Response of Western Honey Bee (Apis mellifera) Workers to Microsporidian Invasion

Vairimorpha ceranae is a widespread fungal parasite of adult honey bees that leads to a serious disease called nosemosis. Circular RNAs (circRNAs) are newly discovered non-coding RNAs (ncRNAs) that regulate biological processes such as immune defense and development. Here, 8199 and 8711 circRNAs were predicted from the midguts of Apis mellifera ligustica workers at 7 d (Am7T) and 10 d (Am10T) after inoculation (dpi) with V. ceranae spores. In combination with transcriptome data from corresponding uninoculated midguts (Am7CK and Am10CK), 4464 circRNAs were found to be shared by these four groups. Additionally, 16 circRNAs were highly conserved among A. m. ligustica, Apis cerana cerana, and Homo sapiens. In the Am7CK vs. Am7T (Am10CK vs. Am10T) comparison group, 168 (306) differentially expressed circRNAs (DEcircRNAs) were identified. RT-qPCR results showed that the expression trend of eight DEcircRNAs was consistent with that in the transcriptome datasets. The source genes of DEcircRNAs in Am7CK vs. Am7T (Am10CK vs. Am10T) were engaged in 27 (35) GO functional terms, including 1 (1) immunity-associated terms. Moreover, the aforementioned source genes were involved in three cellular immune-related pathways. Moreover, 86 (178) DEcircRNAs in workers' midguts at 7 (10) dpi could interact with 75 (103) miRNAs, further targeting 215 (305) mRNAs. These targets were associated with cellular renewal, cellular structure, carbohydrate and energy metabolism, and cellular and humoral immunity. Findings in the present study unraveled the mechanism underlying circRNA-mediated immune responses of western honey bee workers to V. ceranae invasion, but also provided new insights into host-microsporidian interaction during nosemosis.

CircRNA expression profiles in deltamethrin-susceptible and -resistant Culex pipiens pallens (Diptera: Culicidae)

The excessive and improper application of insecticides has caused the evolution of resistance in many mosquito populations, including Culex pipiens pallens (L.). Deltamethrin, a representative pyrethroid insecticide, is the most widely used synthetic insecticide in mosquito-borne control field. Comprehensively identifying genes and regulators associated with deltamethrin resistance and elucidating the manner in which they regulate this process is critical for effective control of mosquitoes. CircRNAs are the upstream regulatory factors of miRNAs and mRNAs, which play a role via the competitive endogenous RNA mechanism. In this study, we used high-throughput circRNA sequencing to identify circRNAs that were expressed differently in deltamethrin-susceptible strain (DS strain) and -resistant strain (DR strain) mosquitoes [NCBI Sequence Read Archive (SRA) database accession number: PRJNA714543]. We detected a total of 12,816 significantly differentially expressed circRNAs (DE-circRNAs). Among them, 6769 circRNAs were up-regulated and 6047 circRNAs were down-regulated in the DR strain compared to DS strain. Among the DE-circRNAs, we further screened that supercont3.352:252102|253283 was significantly over-expressed in the DR strain through qPCR multiple verification (P < 0.05).We used the divergent primer to amplify the rolling circle product and obtained the full-length sequence of supercont3.352:252102|253283 (GeneBank accession number: MW729338). Through software comparison and bioinformatics analysis, we predicted that supercont3.352:252102|253283 might participate in deltamethrin resistance by sponging cpp-miR-1671 and blocking its inhibition on CYP4G15.We further found that the expression of cpp-miR-1671 was significantly lower in DR strain (P < 0.01), while the expression of CYP4G15 was significantly higher in DR strain (P < 0.05).Taken together, the present study provided the most comprehensive circRNA expression profile of mosquitoes, and suggested that supercont3.352:252102|253283 might participate in deltamethrin resistance through the supercont3.352:252102|253283/cpp-miR-1671/CYP4G15 pathway.

Identification of circular RNAs and corresponding regulatory networks reveals potential roles in the brains of honey bee workers exposed to dinotefuran

Honey bees are important and highly efficient pollinators of agricultural crops and have been negatively affected by insecticides in recent years. Circular RNA (circRNA) plays an important role in the regulation of multiple biological and pathological processes; however, its role in the honey bee brain after exposure to dinotefuran is not well understood. Here, the expression profiles and potential modulation networks of circRNAs in the brains of workers (Apis mellifera) were comprehensively investigated using RNA sequencing and bioinformatics. In total, 33, 144, and 211 differentially expressed (DE) circRNAs were identified on the 1st, 5th and 10th days after exposure to dinotefuran, respectively. Enrichment analyses revealed that the host genes of DE circRNAs were enriched in the Hippo signaling pathway-fly, Wnt signaling pathway, and neuroactive ligand-receptor interaction. circ_0002266, circ_0005080, circ_0010239 and circ_0005415 were found to have translational potential due to the presence of an internal ribosome entry site (IRES). An integrated analysis of the DE circRNA-miRNA-mRNA networks suggest that circ_0008898 and circ_0001829 may participate in the immune response to dinotefuran exposure by acting as miRNA sponges. Our results provide invaluable basic data on A. mellifera brain circRNA patterns and a molecular basis for further study of the biological function of circRNAs in the development and immune response of honey bees.

Age and Behavior-Dependent Differential miRNAs Expression in the Hypopharyngeal Glands of Honeybees (Apis mellifera L.)

This study aims to investigate the expression differences of miRNAs in the hypopharyngeal glands (HPGs) of honeybees at three developmental stages and to explore their regulation functions in the HPGs development. Small RNA sequencing was employed to analyze the miRNA profiles of HPGs in newly-emerged bees (NEB), nurse bees (NB), and forager bees (FB). Results showed that a total of 153 known miRNAs were found in the three stages, and ame-miR-276-3p, ame-miR-375-3p, ame-miR-14-3p, ame-miR-275-3p, and ame-miR-3477-5p were the top five most abundant ones. Furthermore, the expression of 11 miRNAs, 17 miRNAs, and 18 miRNAs were significantly different in NB vs. FB comparison, NB vs. NEB comparison, and in FB vs. NEB comparison, respectively, of which ame-miR-184-3p and ame-miR-252a-5p were downregulated in NB compared with that in both the FB and NEB, while ame-miR-11-3p, ame-miR-281-3p, and ame-miR-31a-5p had lower expression levels in FB compared with that in both the NB and NEB. Bioinformatic analysis showed that the potential target genes of the differentially expressed miRNAs (DEMs) were mainly enriched in several key signaling pathways, including mTOR signaling pathway, MAPK signaling pathway-fly, FoxO signaling pathway, Hippo signaling pathway-fly. Overall, our study characterized the miRNA profiles in the HPGs of honeybees at three different developmental stages and provided a basis for further study of the roles of miRNAs in HPGs development.

Integrative analysis of circRNA/miRNA/mRNA regulatory network reveals the potential immune function of circRNAs in the Bombyx mori fat body

Bombyx mori nucleopolyhedrosis virus (BmNPV) is one of the greatest threats to sustainable development of the sericulture industry. Circular RNA (circRNA), a type of non-coding RNA, has been shown to play important roles in gene expression regulation, immune response, and diseases. The fat body is a tissue with both metabolic and immune functions. To explore the potential immune function of circRNAs, we analyzed differentially expressed (DE)circRNAs, microRNAs(miRNAs), and mRNAs in the B. mori fat body in response to BmNPV infection using high-throughput RNA sequencing. A total of 77 DEcircRNAs, 32 DEmiRNAs, and 730 DEmRNAs that are associated with BmNPV infection were identified. We constructed a DEcircRNA/DEmiRNA/DEmRNA and DEcircRNA/DEmiRNA/BmNPV gene regulatory network and validated the differential expression of circ_0001432 and its corresponding miRNA (miR-2774c and miR-3406-5p) and mRNA (778467 and 101745232) in the network. Tissue-specific expression of circ_0001432 and its expression at different time points were also examined. KEGG pathway analysis of DEmRNAs, target genes of DEmiRNAs, and host genes of DEcircRNAs in the network showed that these genes were enriched in several metabolic pathways and signaling pathways, which could play important roles in insect immune responses. Our results suggest that circRNA could be involved in immune responses of the B. mori fat body and help in understanding the molecular mechanisms underlying silkworm-pathogen interactions.

Investigation of circular RNAs in an ectoparasitic mite Varroa destructor (Acarina: Varroidae) of the honey bee

Circular RNAs (circRNAs) are a large class of non-protein-coding transcripts that are involved in a diverse spectrum of regulatory mechanisms across a broad range of biological processes. To date, however, few studies on circRNAs have investigated their role in the biology of invertebrate parasites. The ectoparasitic mite Varroa destructor is perceived as the principal biotic threat towards global honey bee health. This parasite cannot be sustainably controlled partially due to the lack of knowledge about its basic molecular biology. In this paper, we unveil the circRNA profile of V. destructor for the first time and report the sources, distribution, and features of the identified circRNAs. Exonic, intronic, exon-intron, and intergenic circRNAs were discovered and exon-intron circRNAs were the most abundant within the largest spliced length. Three hundred and eighty-six (8.3%) circRNAs were predicted to possess translational potential. Eleven circRNAs, derived from six parental genes, exhibited strong bonds with miRNAs as sponges, suggesting an efficient post-transcriptional regulation. GO term and KEGG pathway enrichment analyses of the parental genes of the identified circRNAs showed that these non-coding RNAs were mainly engaged in protein processing, signal transduction, and various metabolism processes. To our knowledge, this is the first catalog of a circRNA profile of parasitiformes species, which reveals the prevalence of circRNAs in the parasite and provides biological insights for future genetic studies on this ubiquitous parasitic mite.

The whole-transcriptome landscape of muscle and adipose tissues reveals the ceRNA regulation network related to intramuscular fat deposition in yak

Background

The Intramuscular fat (IMF) content in meat products, which is positively correlated with meat quality, is an important trait considered by consumers. The regulation of IMF deposition is species specific. However, the IMF-deposition-related mRNA and non-coding RNA and their regulatory network in yak (Bos grunniens) remain unknown. High-throughput sequencing technology provides a powerful approach for analyzing the association between transcriptome-related differences and specific traits in animals. Thus, the whole transcriptomes of yak muscle and adipose tissues were screened and analyzed to elucidate the IMF deposition-related genes. The muscle tissues were used for IMF content measurements.

Results

Significant differences were observed between the 0.5- and 2.5-year-old yaks. Several mRNAs, miRNAs, lncRNAs and circRNAs were generally expressed in both muscle and adipose tissues. Between the 0.5- and 2.5-year-old yaks, 149 mRNAs, 62 miRNAs, 4 lncRNAs, and 223 circRNAs were differentially expressed in muscle tissue, and 72 mRNAs, 15 miRNAs, 9 lncRNAs, and 211 circRNAs were differentially expressed in adipose tissue. KEGG annotation revelved that these differentially expressed genes were related to pathways that maintain normal biological functions of muscle and adipose tissues. Moreover, 16 mRNAs, 5 miRNAs, 3 lncRNAs, and 5 circRNAs were co-differentially expressed in both types of tissue. We suspected that these co-differentially expressed genes were involved in IMF-deposition in the yak. Additionally, LPL, ACADL, SCD, and FASN, which were previously shown to be associated with the IMF content, were identified in the competing endogenous RNA (ceRNA) regulatory network that was constructed on the basis of the IMF deposition-related genes. Three ceRNA subnetworks also revealed that TCONS-00016416 and its target SIRT1 “talk” to each other through the same miR-381-y and miR-208 response elements, whereas TCONS-00061798 and its target PRKCA, and TCONS-00084092 and its target LPL “talk” to each other through miR-122-x and miR-499-y response elements, respectively.

Conclusion

Taken together, our results reveal the potential mRNA and noncoding RNAs involved in IMF deposition in the yak, providing a useful resource for further research on IMF deposition in this animal species.