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Zhang B, Zhang C, Zhang J, Lu S, Zhao H, Jiang Y, Ma W. Regulatory roles of long non-coding RNAs in short-term heat stress in adult worker bees. BMC Genomics 2024; 25:506. [PMID: 38778290 PMCID: PMC11110378 DOI: 10.1186/s12864-024-10399-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are crucial modulators of post-transcriptional gene expression regulation, cell fate determination, and disease development. However, lncRNA functions during short-term heat stress in adult worker bees are poorly understood. Here, we performed deep sequencing and bioinformatic analyses of honeybee lncRNAs. RNA interference was performed by using siRNA targeting the most highly expressed lncRNA. The silencing effect on lncRNA and the relative expression levels of seven heat shock protein (HSP) genes, were subsequently examined. Overall, 7,842 lncRNAs and 115 differentially expressed lncRNAs (DELs) were identified in adult worker bees following heat stress exposure. Structural analysis revealed that the overall expression abundance, length of transcripts, exon number, and open reading frames of lncRNAs were lower than those of mRNAs. GO analysis revealed that the target genes were mainly involved in "metabolism," "protein folding," "response to stress," and "signal transduction" pathways. KEGG analysis indicated that the "protein processing in endoplasmic reticulum" and "longevity regulating pathway-multiple species" pathways were most enriched. Quantitative real-time polymerase chain reaction (qRT-PCR) detection of the selected DELs confirmed the reliability of the sequencing data. Moreover, the siRNA experiment indicated that feeding siRNA yielded a silencing efficiency of 77.51% for lncRNA MSTRG.9645.5. Upon silencing this lncRNA, the expression levels of three HSP genes were significantly downregulated (p < 0.05), whereas those of three other HSP genes were significantly upregulated (p < 0.05). Our results provide a new perspective for understanding the regulatory mechanisms of lncRNAs in adult worker bees under short-term heat stress.
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Affiliation(s)
- Bing Zhang
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Chaoying Zhang
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Jiangchao Zhang
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Surong Lu
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Huiting Zhao
- College of Life Sciences, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Yusuo Jiang
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Weihua Ma
- College of Horticulture, Shanxi Agricultural University, Taiyuan, Shanxi, China.
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2
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Geens B, Goossens S, Li J, Van de Peer Y, Vanden Broeck J. Untangling the gordian knot: The intertwining interactions between developmental hormone signaling and epigenetic mechanisms in insects. Mol Cell Endocrinol 2024; 585:112178. [PMID: 38342134 DOI: 10.1016/j.mce.2024.112178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Hormones control developmental and physiological processes, often by regulating the expression of multiple genes simultaneously or sequentially. Crosstalk between hormones and epigenetics is pivotal to dynamically coordinate this process. Hormonal signals can guide the addition and removal of epigenetic marks, steering gene expression. Conversely, DNA methylation, histone modifications and non-coding RNAs can modulate regional chromatin structure and accessibility and regulate the expression of numerous (hormone-related) genes. Here, we provide a review of the interplay between the classical insect hormones, ecdysteroids and juvenile hormones, and epigenetics. We summarize the mode-of-action and roles of these hormones in post-embryonic development, and provide a general overview of epigenetic mechanisms. We then highlight recent advances on the interactions between these hormonal pathways and epigenetics, and their involvement in development. Furthermore, we give an overview of several 'omics techniques employed in the field. Finally, we discuss which questions remain unanswered and possible avenues for future research.
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Affiliation(s)
- Bart Geens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Stijn Goossens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Jia Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Jozef Vanden Broeck
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
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3
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Amwoma JG, Kituyi S, Wakoli DM, Ochora DO, Chemwor G, Maisiba R, Okore W, Opot B, Juma D, Muok EM, Garges EC, Egbo TE, Nyabuga FN, Andagalu B, Akala HM. Comparative analysis of peripheral whole blood transcriptome from asymptomatic carriers reveals upregulation of subsets of surface proteins implicated in Plasmodium falciparum phenotypic plasticity. Biochem Biophys Rep 2024; 37:101596. [PMID: 38146350 PMCID: PMC10749222 DOI: 10.1016/j.bbrep.2023.101596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023] Open
Abstract
The molecular mechanism underlying Plasmodium falciparum's persistence in the asymptomatic phase of infection remains largely unknown. However, large-scale shifts in the parasites' gene expression during asymptomatic infections may enhance phenotypic plasticity, maximizing their fitness and leading to the persistence of the asymptomatic infections. To uncover these mechanisms, we aimed to identify parasite genetic factors implicated in asymptomatic infections through whole transcriptome analysis. We analyzed publicly available transcriptome datasets containing asymptomatic malaria (ASM), uncomplicated malaria (SM), and malaria-naïve (NSM) samples from 35 subjects for differentially expressed genes (DEGs) and long noncoding RNAs. Our analysis identified 755 and 1773 DEGs in ASM vs SM and NSM, respectively. These DEGs revealed sets of genes coding for proteins of unknown functions (PUFs) upregulated in ASM vs SM and ASM, suggesting their role in underlying fundamental molecular mechanisms during asymptomatic infections. Upregulated genes in ASM vs SM revealed a subset of 24 clonal variant genes (CVGs) involved in host-parasite and symbiotic interactions and modulation of the symbiont of host erythrocyte aggregation pathways. Moreover, we identified 237 differentially expressed noncoding RNAs in ASM vs SM, of which 11 were found to interact with CVGs, suggesting their possible role in regulating the expression of CVGs. Our results suggest that P. falciparum utilizes phenotypic plasticity as an adaptive mechanism during asymptomatic infections by upregulating clonal variant genes, with long noncoding RNAs possibly playing a crucial role in their regulation. Thus, our study provides insights into the parasites' genetic factors that confer a fitness advantage during asymptomatic infections.
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Affiliation(s)
- Joseph G. Amwoma
- Department of Biological Sciences, University of Embu, Kenya
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Sarah Kituyi
- Department of Biological Sciences, University of Embu, Kenya
- Forgarty International Center of the National Institutes of Health, Bethesda, MD, USA
| | - Dancan M. Wakoli
- Department of Biochemistry and Molecular Biology, Egerton University, Kenya
| | - Douglas O. Ochora
- Department of Biological Sciences, School of Pure and Applied Sciences, Kisii University, Kenya
- DSI/NWU, Preclinical Drug Development Platform, Faculty of Health Sciences, North-West University, Potchefstroom, South Africa
| | - Gladys Chemwor
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Risper Maisiba
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Winnie Okore
- Department of Biomedical Sciences and Technology, Maseno University, Kenya
| | - Benjamin Opot
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Dennis Juma
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Eric M.O. Muok
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Eric C. Garges
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya
| | - Timothy E. Egbo
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya
| | | | - Ben Andagalu
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Hoseah M. Akala
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
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Maigoro AY, Lee JH, Kim H, Frunze O, Kwon HW. Gut Microbiota of Apis mellifera at Selected Ontogenetic Stages and Their Immunogenic Potential during Summer. Pathogens 2024; 13:122. [PMID: 38392860 PMCID: PMC10893431 DOI: 10.3390/pathogens13020122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Honeybees (Apis mellifera) are pollinating agents of economic importance. The role of the gut microbiome in honeybee health has become increasingly evident due to its relationship with immune function, growth, and development. Although their dynamics at various developmental stages have been documented, their dynamics during the era of colony collapse disorder and immunogenic potential, which are connected to the antagonistic immune response against pathogens, need to be elucidated. Using 16S rRNA gene Illumina sequencing, the results indicated changes in the gut microbiota with the developmental stage. The bacterial diversity of fifth stage larva was significantly different among the other age groups, in which Fructobacillus, Escherichia-Shigella, Bombella, and Tyzzerella were unique bacteria. In addition, the diversity of the worker bee microbiome was distinct from that of the younger microbiome. Lactobacillus and Gilliamella remained conserved throughout the developmental stages, while Bifidobacterium colonized only worker bees. Using an in silico approach, the production potential of lipopolysaccharide-endotoxin was predicted. Forager bees tend to have a higher abundance rate of Gram-negative bacteria. Our results revealed the evolutionary importance of some microbiome from the larval stage to the adult stage, providing insight into the potential dynamics of disease response and susceptibility. This finding provides a theoretical foundation for furthering the understanding of the function of the gut microbiota at various developmental stages related to probiotic development and immunogenic potential.
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Affiliation(s)
- Abdulkadir Yusif Maigoro
- Convergence Research Center for Insect Vectors, Incheon National University, Incheon 22012, Republic of Korea (H.K.)
| | - Jeong-Hyeon Lee
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea;
| | - Hyunjee Kim
- Convergence Research Center for Insect Vectors, Incheon National University, Incheon 22012, Republic of Korea (H.K.)
| | - Olga Frunze
- Convergence Research Center for Insect Vectors, Incheon National University, Incheon 22012, Republic of Korea (H.K.)
| | - Hyung-Wook Kwon
- Convergence Research Center for Insect Vectors, Incheon National University, Incheon 22012, Republic of Korea (H.K.)
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea;
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Chen Y, Wang Z, Wu C, Li H, Qian H, Wang M, Wu P, Guo X, Zhang Z. Identification of long noncoding RNAs of silkworm at the early stage of Bombyx mori bidensovirus infection. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22082. [PMID: 38288492 DOI: 10.1002/arch.22082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 02/01/2024]
Abstract
Bombyx mori bidensovirus (BmBDV) is one of the most important pathogens of silkworm. It mainly infects midgut cells of silkworm and causes losses to the sericulture industry. Long noncoding RNAs (lncRNAs) have been reported to play an important role in the regulation of antiviral immune response in silkworm. To explore whether lncRNAs are involved in BmBDV infection and immune response of silkworm, we performed a comparative transcriptome analysis to identify the lncRNAs and mRNAs between the BmBDV infected and noninfected silkworm larvae at the early stage. A total of 16,069 genes and 974 candidate lncRNAs were identified, among which 142 messenger RNA (mRNAs) and four lncRNAs were differentially expressed (DE). Target gene prediction revealed that 142 DEmRNAs were coexpressed with four DElncRNAs, suggesting that the expression of mRNA is mainly affected through trans-regulation activities. A regulatory network of DElncRNAs and DEmRNAs was constructed, showing that many genes targeted by different DElncRNAs are involved in metabolism and immunity, which implies that these genes and lncRNAs play an important role in the replication of BmBDV. Our results will help us to improve our understanding of lncRNA-mediated regulatory roles in BmBDV infection, providing a new perspective for further exploring the interaction between host and BmBDV.
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Affiliation(s)
- Yeping Chen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Zihe Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Chengyue Wu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Hao Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Heying Qian
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Mengdong Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Ping Wu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Xijie Guo
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Zhendong Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
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Guo R, Wang S, Guo S, Fan X, Zang H, Gao X, Jing X, Liu Z, Na Z, Zou P, Chen D. Regulatory Roles of Long Non-Coding RNAs Relevant to Antioxidant Enzymes and Immune Responses of Apis cerana Larvae Following Ascosphaera apis Invasion. Int J Mol Sci 2023; 24:14175. [PMID: 37762477 PMCID: PMC10532054 DOI: 10.3390/ijms241814175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/06/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play an essential part in controlling gene expression and a variety of biological processes such as immune defense and stress-response. However, whether and how lncRNAs regulate responses of Apis cerana larvae to Ascosphaera apis invasion has remained unclear until now. Here, the identification and structural analysis of lncRNAs in the guts of A. cerana worker larvae were conducted, and the expression profile of larval lncRNAs during the A. apis infection process was then analyzed, followed by an investigation of the regulatory roles of differentially expressed lncRNAs (DElncRNAs) in the host response. In total, 76 sense lncRNAs, 836 antisense lncRNAs, 184 intron lncRNAs, 362 bidirectional lncRNAs, and 2181 intron lncRNAs were discovered in the larval guts. Additionally, 30 known and 9 novel lncRNAs were potential precursors for 36 and 11 miRNAs, respectively. In the three comparison groups, 386, 351, and 272 DElncRNAs were respectively identified, indicating the change in the overall expression pattern of host lncRNAs following the A. apis invasion. Analysis of cis-acting effect showed that DElncRNAs in the 4-, 5-, and 6-day-old comparison groups putatively regulated 55, 30, and 20 up- and down-stream genes, respectively, which were involved in a series of crucial functional terms and pathways, such as MAPK signaling pathway, and cell process. Analysis showed that 31, 8, and 11 DElncRNAs as potential antisense lncRNAs may interact with 26, 8, and 9 sense-strand mRNAs. Moreover, investigation of the competing endogenous RNA (ceRNA) network indicated that 148, 283, and 257 DElncRNAs were putatively regulated. The expression of target genes by targeting corresponding DEmiRNAs included those associated with antioxidant enzymes and immune responses. These results suggested that DElncRNAs played a potential part in the larval guts responding to the A. apis infection through a cis-acting manner and ceRNA mechanisms. Our findings deepen our understanding of interactions between A. cerana larvae and A. apis and offer a basis for clarifying the DElncRNA-mediated mechanisms underlying the host response to fungal invasion.
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Affiliation(s)
- Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
- Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siyi Wang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
| | - Sijia Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
| | - Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
| | - He Zang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
| | - Xuze Gao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
| | - Xin Jing
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
| | - Zhitan Liu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
| | - Zhihao Na
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
| | - Peiyuan Zou
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
- Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Shang Y, Feng Y, Ren L, Zhang X, Yang F, Zhang C, Guo Y. Genome-wide analysis of long noncoding RNAs and their association in regulating the metamorphosis of the Sarcophaga peregrina (Diptera: Sarcophagidae). PLoS Negl Trop Dis 2023; 17:e0011411. [PMID: 37363930 DOI: 10.1371/journal.pntd.0011411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND The flesh fly, Sarcophaga peregrina (Diptera: Sarcophagidae), is an important hygiene pest, that causes myiasis in humans and other mammals, typically livestock, and as a vector for various parasitic agents, including bacteria, viruses, and parasites. The role of long non-coding RNAs (lncRNAs) in regulating gene expression during metamorphosis of the flesh fly has not been well established. METHODOLOGY/PRINCIPAL FINDINGS In this study, we performed genome-wide identification and characterization of lncRNAs from the early pupal stage (1-days pupae), mid-term pupal stage (5-days pupae), and late pupal stage (9-days pupae) of S. peregrina by RNA-seq, and a total of 6921 lncRNAs transcripts were identified. RT-qPCR and enrichment analyses revealed the differentially expressed lncRNAs (DE lncRNAs) that might be associated with insect metamorphosis development. Furthermore, functional analysis revealed that the DE lncRNA (SP_lnc5000) could potentially be involved in regulating the metamorphosis of S. peregrina. RNA interference of SP_lnc5000 caused reduced expression of metamorphosis-related genes in 20-hydroxyecdysone (20E) signaling (Br-c, Ftz-F1), cuticle tanning pathway (TH, DOPA), and chitin related pathway (Cht5). Injection of dsSP_lnc5000 in 3rd instar larvae of S. peregrina resulted in deformed pupae, stagnation of pupal-adult metamorphosis, and a decrease in development time of pupal, pupariation rates and eclosion rates. Hematoxylin-eosin staining (H&E), scanning electron microscope (SEM) observation and cuticle hydrocarbons (CHCs) analysis indicated that SP_lnc5000 had crucial roles in the metamorphosis developmental by modulating pupal cuticular development. CONCLUSIONS/SIGNIFICANCE We established that the lncRNA SP_lnc5000 potentially regulates the metamorphosis of S. peregrina by putatively affecting the structure and composition of the pupal cuticle. This study enhances our understanding of lncRNAs as regulators of metamorphosis in S. peregrina, and provide valuable insights into the identification of potential targets for vector control and the development of effective strategies for controlling the spread of myiasis and parasitic diseases.
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Affiliation(s)
- Yanjie Shang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Yakai Feng
- Department of Forensic Science, School of Basic Medical Sciences, Xinjiang Medical University Ürümqi, China
| | - Lipin Ren
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Xiangyan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Fengqin Yang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Changquan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
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8
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Bresnahan ST, Lee E, Clark L, Ma R, Rangel J, Grozinger CM, Li-Byarlay H. Examining parent-of-origin effects on transcription and RNA methylation in mediating aggressive behavior in honey bees (Apis mellifera). BMC Genomics 2023; 24:315. [PMID: 37308882 DOI: 10.1186/s12864-023-09411-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/27/2023] [Indexed: 06/14/2023] Open
Abstract
Conflict between genes inherited from the mother (matrigenes) and the father (patrigenes) is predicted to arise during social interactions among offspring if these genes are not evenly distributed among offspring genotypes. This intragenomic conflict drives parent-specific transcription patterns in offspring resulting from parent-specific epigenetic modifications. Previous tests of the kinship theory of intragenomic conflict in honey bees (Apis mellifera) provided evidence in support of theoretical predictions for variation in worker reproduction, which is associated with extreme variation in morphology and behavior. However, more subtle behaviors - such as aggression - have not been extensively studied. Additionally, the canonical epigenetic mark (DNA methylation) associated with parent-specific transcription in plant and mammalian model species does not appear to play the same role as in honey bees, and thus the molecular mechanisms underlying intragenomic conflict in this species is an open area of investigation. Here, we examined the role of intragenomic conflict in shaping aggression in honey bee workers through a reciprocal cross design and Oxford Nanopore direct RNA sequencing. We attempted to probe the underlying regulatory basis of this conflict through analyses of parent-specific RNA m6A and alternative splicing patterns. We report evidence that intragenomic conflict occurs in the context of honey bee aggression, with increased paternal and maternal allele-biased transcription in aggressive compared to non-aggressive bees, and higher paternal allele-biased transcription overall. However, we found no evidence to suggest that RNA m6A or alternative splicing mediate intragenomic conflict in this species.
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Affiliation(s)
- Sean T Bresnahan
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, USA.
| | - Ellen Lee
- Agricultural Research and Development Program, Central State University, Wilberforce, USA
- Department of Biological Sciences, Wright State University, Dayton, USA
| | - Lindsay Clark
- HPCBio, University of Illinois at Urbana-Champaign, Champaign, USA
- Research Scientific Computing Group, Seattle Children's Research Institute, Seattle, USA
| | - Rong Ma
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, USA
| | - Juliana Rangel
- Department of Entomology, Texas A&M University, College Station, USA
| | - Christina M Grozinger
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, USA
| | - Hongmei Li-Byarlay
- Agricultural Research and Development Program, Central State University, Wilberforce, USA.
- Department of Agricultural and Life Science, Central State University, Wilberforce, USA.
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9
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Lin S, Yin HT, Zhao ZM, Chen ZK, Zhou XMI, Zhang ZD, Guo XJ, Zhao WG, Wu P. LincRNA_XR209691.3 could promote Bombyx mori nucleopolyhedrovirus replication by interacting with BmHSP70. INSECT MOLECULAR BIOLOGY 2023; 32:160-172. [PMID: 36482511 DOI: 10.1111/imb.12821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Long non-coding RNAs (lncRNAs), a class of transcripts exceeding 200 nucleotides and lacking protein coding potential, have been proven to play important roles in viral infection and host immunity. Bombyx mori nucleopolyhedrovirus (BmNPV) is an important pathogen, which causes the silkworm disease and leads to a huge challenge to the sericultural industry. At present, research on the roles of insect lncRNAs in host-virus interaction are relatively few. In this study, we explored the function of lincRNA_XR209691.3 that was significantly up-regulated in the silkworm fat body upon BmNPV infection. Firstly, the subcellular localization experiment confirmed that lincRNA_XR209691.3 was present in both the nucleus and cytoplasm. Enhancing the expression of lincRNA_XR209691.3 in BmN cells could promote the proliferation of BmNPV, while inhibition of lincRNA_XR209691.3 by RNA interference suppresses the proliferation of BmNPV. Combining RNA pull-down and mass spectrometry, we identified the host and BmNPV proteins that could interact with lincRNA_XR209691.3. Next, by using truncation experiment and RNA immunoprecipitation (RIP) assay, it was found that lincRNA_XR209691.3 could bind to the Actin domain of BmHSP70. Subsequently, overexpression of lncRNA_XR209691.3 in BmN cells promoted the expression of BmHSP70, while knockdown of BmHsp70 suppressed the replication of BmNPV. Based on the above results, it is speculated that lincRNA_XR209691.3 could promote the proliferation of BmNPV through interaction with BmHSP70, possibly by improving the stability of BmHSP70 and thereby enhancing the expression of BmHSP70. Our results shed light on the lncRNA function in insect-pathogen interactions and provide a new clue to elucidate the molecular mechanism of BmNPV infection.
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Affiliation(s)
- Su Lin
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Hao Tong Yin
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhi Meng Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zi Kang Chen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Xue MIng Zhou
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zheng Dong Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Xi Jie Guo
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Wei Guo Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Ping Wu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
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10
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Wang Z, Wang S, Fan X, Zhang K, Zhang J, Zhao H, Gao X, Zhang Y, Guo S, Zhou D, Li Q, Na Z, Chen D, Guo R. Systematic Characterization and Regulatory Role of lncRNAs in Asian Honey Bees Responding to Microsporidian Infestation. Int J Mol Sci 2023; 24:ijms24065886. [PMID: 36982959 PMCID: PMC10058195 DOI: 10.3390/ijms24065886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are pivotal regulators in gene expression and diverse biological processes, such as immune defense and host-pathogen interactions. However, little is known about the roles of lncRNAs in the response of the Asian honey bee (Apis cerana) to microsporidian infestation. Based on our previously obtained high-quality transcriptome datasets from the midgut tissues of Apis cerana cerana workers at 7 days post inoculation (dpi) and 10 dpi with Nosema ceranae (AcT7 and AcT10 groups) and the corresponding un-inoculated midgut tissues (AcCK7 and AcCK10 groups), the transcriptome-wide identification and structural characterization of lncRNAs were conducted, and the differential expression pattern of lncRNAs was then analyzed, followed by investigation of the regulatory roles of differentially expressed lncRNAs (DElncRNAs) in host response. Here, 2365, 2322, 2487, and 1986 lncRNAs were, respectively, identified in the AcCK7, AcT7, AcCK7, and AcT10 groups. After removing redundant ones, a total of 3496 A. c. cerana lncRNAs were identified, which shared similar structural characteristics with those discovered in other animals and plants, such as shorter exons and introns than mRNAs. Additionally, 79 and 73 DElncRNAs were screened from the workers' midguts at 7 dpi and 10 dpi, respectively, indicating the alteration of the overall expression pattern of lncRNAs in host midguts after N. ceranae infestation. These DElncRNAs could, respectively, regulate 87 and 73 upstream and downstream genes, involving a suite of functional terms and pathways, such as metabolic process and Hippo signaling pathway. Additionally, 235 and 209 genes co-expressed with DElncRNAs were found to enrich in 29 and 27 terms, as well as 112 and 123 pathways, such as ABC transporters and the cAMP signaling pathway. Further, it was detected that 79 (73) DElncRNAs in the host midguts at 7 (10) dpi could target 321 (313) DEmiRNAs and further target 3631 (3130) DEmRNAs. TCONS_00024312 and XR_001765805.1 were potential precursors for ame-miR-315 and ame-miR-927, while TCONS_00006120 was the putative precursor for both ame-miR-87-1 and ame-miR-87-2. These results together suggested that DElncRNAs are likely to play regulatory roles in the host response to N. ceranae infestation through the regulation of neighboring genes via a cis-acting effect, modulation of co-expressed mRNAs via trans-acting effect, and control of downstream target genes' expression via competing endogenous RNA networks. Our findings provide a basis for disclosing the mechanism underlying DElncRNA-mediated host N. ceranae response and a new perspective into the interaction between A. c. cerana and N. ceranae.
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Affiliation(s)
- Zixin Wang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siyi Wang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kaiyao Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiaxin Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haodong Zhao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuze Gao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yiqiong Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sijia Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dingding Zhou
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qiming Li
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhihao Na
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
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11
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Robin S, Legeai F, Jouan V, Ogliastro M, Darboux I. Genome-wide identification of lncRNAs associated with viral infection in Spodoptera frugiperda. J Gen Virol 2023; 104. [PMID: 36757871 DOI: 10.1099/jgv.0.001827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
The role of lncRNAs in immune defence has been demonstrated in many multicellular and unicellular organisms. However, investigation of the identification and characterization of long non-coding RNAs (lncRNAs) involved in the insect immune response is still limited. In this study, we used RNA sequencing (RNA-seq) to investigate the expression profiles of lncRNAs and mRNAs in the fall armyworm Spodoptera frugiperda in response to virus infection. To assess the tissue- and virus-specificity of lncRNAs, we analysed and compared their expression profiles in haemocytes and fat body of larvae infected with two entomopathogenic viruses with different lifestyles, i.e. the polydnavirus HdIV (Hyposoter didymator IchnoVirus) and the densovirus JcDV (Junonia coenia densovirus). We identified 1883 candidate lncRNAs, of which 529 showed differential expression following viral infection. Expression profiles differed considerably between samples, indicating that many differentially expressed (DE) lncRNAs showed virus- and tissue-specific expression patterns. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and target prediction analyses indicated that DE-LncRNAs were mainly enriched in metabolic process, DNA replication and repair, immune response, metabolism of insect hormone and cell adhesion. In addition, we identified three DE-lncRNAs potentially acting as microRNA host genes, suggesting that they participate in gene regulation by producing miRNAs in response to virus infection. This study provides a catalogue of lncRNAs expressed in two important immune tissues and potential insight into their roles in the antiviral defence in S. frugiperda. The results may help future in-depth functional studies to better understand the biological function of lncRNAs in interaction between viruses and the fall armyworm.
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Affiliation(s)
- Stéphanie Robin
- BIPAA, IGEPP, INRAE, Institut Agro, University of Rennes, Rennes, France.,University of Rennes, INRIA, CNRS, IRISA, Rennes, France
| | - Fabrice Legeai
- BIPAA, IGEPP, INRAE, Institut Agro, University of Rennes, Rennes, France.,University of Rennes, INRIA, CNRS, IRISA, Rennes, France
| | - Véronique Jouan
- INRAE, University of Montpellier, UMR Diversité, Génomes & Interactions Microorganismes-Insectes (DGIMI), Montpellier, France
| | - Mylène Ogliastro
- INRAE, University of Montpellier, UMR Diversité, Génomes & Interactions Microorganismes-Insectes (DGIMI), Montpellier, France
| | - Isabelle Darboux
- INRAE, University of Montpellier, UMR Diversité, Génomes & Interactions Microorganismes-Insectes (DGIMI), Montpellier, France
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12
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Recent Advances and Future Potential of Long Non-Coding RNAs in Insects. Int J Mol Sci 2023; 24:ijms24032605. [PMID: 36768922 PMCID: PMC9917219 DOI: 10.3390/ijms24032605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
Over the last decade, long non-coding RNAs (lncRNAs) have witnessed a steep rise in interest amongst the scientific community. Because of their functional significance in several biological processes, i.e., alternative splicing, epigenetics, cell cycle, dosage compensation, and gene expression regulation, lncRNAs have transformed our understanding of RNA's regulatory potential. However, most knowledge concerning lncRNAs comes from mammals, and our understanding of the potential role of lncRNAs amongst insects remains unclear. Technological advances such as RNA-seq have enabled entomologists to profile several hundred lncRNAs in insect species, although few are functionally studied. This article will review experimentally validated lncRNAs from different insects and the lncRNAs identified via bioinformatic tools. Lastly, we will discuss the existing research challenges and the future of lncRNAs in insects.
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13
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Ye Y, Fan X, Long Q, Wang J, Zhang W, Cai Z, Sun M, Gu X, Zou P, Chen D, Guo R. Comprehensive investigation and regulatory function of lncRNAs engaged in western honey bee larval immune response to Ascosphaera apis invasion. Front Physiol 2022; 13:1082522. [PMID: 36589426 PMCID: PMC9800914 DOI: 10.3389/fphys.2022.1082522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Ascosphaera apis is a fungal pathogen that exclusively infects bee larvae, causing chalkbrood disease, which results in severe damage for beekeeping industry. Long non-coding RNAs (lncRNAs) are versatile regulators in various biological processes such as immune defense and host-pathogen interaction. However, expression pattern and regulatory role of lncRNAs involved in immune response of bee host to A. apis invasion is still very limited. Here, the gut tissues of Apis mellifera ligustica 4-, 5-, and 6-day-old larvae inoculated by A. apis spores (AmT1, AmT2, and AmT3 groups) and corresponding un-inoculated larval guts (AmCK1, AmCK2, and AmCK3 groups) were prepared and subjected to deep sequencing, followed by identification of lncRNAs, analysis of differentially expressed lncRNAs (DElncRNAs), and investigation of competing endogenous RNA (ceRNA) network. In total, 3,746 A. m. ligustica lncRNAs were identified, including 78 sense lncRNAs, 891 antisense lncRNAs, 1,893 intergenic lncRNAs, 346 bidirectional lncRNAs, and 210 intronic lncRNAs. In the 4-, 5-, and 6- comparison groups, 357, 236, and 505 DElncRNAs were discovered. Additionally, 217, 129, and 272 DElncRNAs were respectively predicted to regulate neighboring genes via cis-acting manner, and these targets were associated with a series of GO terms and KEGG pathways of great importance, such as response to stimulus and Jak-STAT signaling pathway. Moreover, 197, 95, and 356 DElncRNAs were observed to target 10, eight, and 21 DEmiRNAs and further target 147, 79, and 315 DEmRNAs, forming complex regulatory networks. Further investigation suggested that these targets were engaged in several key cellular and humoral immune pathways, such as phagosome and MAPK signaling pathway. Ultimately, the expression trends of nine randomly selected DElncRNAs were verified by RT-qPCR, confirming the authenticity and reliability of our transcriptome data. Findings in this current work not only provide candidate DElncRNAs for functional study, but also lay a foundation for unclosing the mechanism underlying DElncRNA-regulated larval immune responses to A. apis invasion.
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Affiliation(s)
- Yaping Ye
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Qi Long
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jie Wang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Wende Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zongbing Cai
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Minghui Sun
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaoyu Gu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Peiyuan Zou
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China,Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China,Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China,*Correspondence: Rui Guo,
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14
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Zafar J, Huang J, Xu X, Jin F. Analysis of Long Non-Coding RNA-Mediated Regulatory Networks of Plutella xylostella in Response to Metarhizium anisopliae Infection. INSECTS 2022; 13:916. [PMID: 36292864 PMCID: PMC9604237 DOI: 10.3390/insects13100916] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Long non-coding RNAs (lncRNAs) represent a diverse class of RNAs that are structurally similar to messenger RNAs (mRNAs) but do not encode proteins. Growing evidence suggests that in response to biotic and abiotic stresses, the lncRNAs play crucial regulatory roles in plants and animals. However, the potential role of lncRNAs during fungal infection has yet to be characterized in Plutella xylostella, a devastating pest of cruciferous crops. In the current study, we performed a strand-specific RNA sequencing of Metarhizium anisopliae-infected (Px36hT, Px72hT) and uninfected (Px36hCK, Px72hCK) P. xylostella fat body tissues. Comprehensive bioinformatic analysis revealed a total of 5665 and 4941 lncRNAs at 36 and 72-h post-infection (hpi), including 563 (Px36hT), 532 (Px72hT) known and 5102 (Px36hT), 4409 (Px72hT) novel lncRNA transcripts. These lncRNAs shared structural similarities with their counterparts in other species, including shorter exon and intron length, fewer exon numbers, and a lower expression profile than mRNAs. LncRNAs regulate the expression of neighboring protein-coding genes by acting in a cis and trans manner. Functional annotation and pathway analysis of cis-acting lncRNAs revealed their role in several immune-related genes, including Toll, serpin, transferrin, βGRP etc. Furthermore, we identified multiple lncRNAs acting as microRNA (miRNA) precursors. These miRNAs can potentially regulate the expression of mRNAs involved in immunity and development, suggesting a crucial lncRNA-miRNA-mRNA complex. Our findings will provide a genetic resource for future functional studies of lncRNAs involved in P. xylostella immune responses to M. anisopliae infection and shed light on understanding insect host-pathogen interactions.
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Affiliation(s)
| | | | - Xiaoxia Xu
- Correspondence: (X.X.); (F.J.); Tel.: +86-135-6047-8369 (F.J.)
| | - Fengliang Jin
- Correspondence: (X.X.); (F.J.); Tel.: +86-135-6047-8369 (F.J.)
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15
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Wu JL, Hu RY, Li NN, Tan J, Zhou CX, Han B, Xu SF. Integrative Analysis of lncRNA-mRNA Co-expression Provides Novel Insights Into the Regulation of Developmental Transitions in Female Varroa destructor. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.842704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Varroa destructor is a major pathogenic driver of the Western honeybee colony losses globally. Understanding the developmental regulation of V. destructor is critical to develop effective control measures. Development is a complex biological process regulated by numerous genes and long non-coding RNAs (lncRNAs); however, the underlying regulation of lncRNAs in the development of V. destructor remains unknown. In this study, we analyzed the RNA sequencing (RNA-Seq) data derived from the four stages of female V. destructor in the reproductive phase (i.e., egg, protonymph, deutonymph, and adult). The identified differentially expressed mRNAs and lncRNAs exhibited a stage-specific pattern during developmental transitions. Further functional enrichment established that fat digestion and absorption, ATP-binding cassette (ABC) transporters, mitogen-activated protein kinase (MAPK) signaling pathway, and ubiquitin-proteasome pathway play key roles in the maturation of female V. destructor. Moreover, the lncRNAs and mRNAs of some pivotal genes were significantly upregulated at the deutonymph stage, such as cuticle protein 65/6.4/63/38 and mucin 5AC, suggesting that deutonymph is the key stage of metamorphosis development and pathogen resistance acquisition for female V. destructor. Our study provides novel insights into a foundational understanding of V. destructor biology.
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16
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Abd El Halim HM, Ali A. Long noncoding RNAs: Emerging players regulating innate immune memory in the red flour beetle. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 127:104304. [PMID: 34756931 DOI: 10.1016/j.dci.2021.104304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/03/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
A variety of strategies have been evolved to eradicate invading microbes. Phagocytes have developed in vertebrates and invertebrates to confer a non-specific immune response to pathogens. Besides, vertebrates have evolved lymphocytes to develop memory cells that can quickly respond upon the next exposure to the same pathogen. Although lymphocytes are absent in invertebrates, historical evidence, dating back to the 1920s, indicated the presence of immune memory in invertebrates. However, the concept of long-lasting non-specific defense predominated until recent evidence has been introduced in the first decade of the 21st century. Although more evidence has been introduced later, the molecular mechanism underlying the innate immune memory is largely undefined in invertebrates. Long noncoding RNAs (lncRNAs) have demonstrated a role in regulating various biological processes, including immune response. In this review, we will explore the potential role of lncRNAs in developing innate immune memory in the red flour beetle (Tribolium castaneum).
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Affiliation(s)
| | - Ali Ali
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742-231, USA; Department of Zoology, Faculty of Science, Benha University, Benha, 13518, Egypt.
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17
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Shang F, Ding BY, Zhang YT, Wu JJ, Pan ST, Wang JJ. Genome-wide analysis of long non-coding RNAs and their association with wing development in Aphis citricidus (Hemiptera: Aphididae). INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 139:103666. [PMID: 34619323 DOI: 10.1016/j.ibmb.2021.103666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Long non-coding RNAs (lncRNAs) play critical roles in the various physiological processes of insects. The wing is a successful adaptation allowing insects to escape from unfavorable environments, while information on lncRNAs related to wing development is limited. In this study, we constructed 12 libraries from two RNA-seq comparisons: 4th instar winged nymphs versus winged adults and 4th instar wingless nymphs versus wingless adults in the brown citrus aphid Aphis citricidus, to identify the wing development-associated lncRNAs. A total of 2914 lncRNAs were identified and 50 lncRNAs were differentially expressed during the 4th instar winged nymphs to winged adults transition, and 28 lncRNAs changed during the 4th instar wingless nymphs to wingless adults transition. The differentially expressed lncRNAs were grouped into six clusters according to the expression patterns in the combined two-winged morphs. lncRNA Ac_lnc54106.1 was up-regulated during 4th instar winged nymphs to winged adults transition, but a lack of change during the 4th instar wingless nymphs to wingless adults transition implied a critical role in the specific regulation of wing development. RNA interference of Ac_lnc54106.1 resulted in malformed wings. Targets prediction, expression patterns, and RNAi assay results showed that Ac_lnc54106.1 may target the PiggyBac transposable element-derived protein 4 (PGBD4) gene, decrease expression of the canonical wing development-related genes, and finally regulate wing development. The systematic identification of lncRNAs in an aphid increases our understanding of how non-coding RNA mediates the wing plasticity of insects.
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Affiliation(s)
- Feng Shang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China.
| | - Bi-Yue Ding
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China.
| | - Yong-Te Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Jin-Jin Wu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Si-Tong Pan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China.
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18
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Li WJ, Wei D, Han HL, Song YJ, Wang Y, Xu HQ, Smagghe G, Wang JJ. lnc94638 is a testis-specific long non-coding RNA involved in spermatozoa formation in Zeugodacus cucurbitae (Coquillett). INSECT MOLECULAR BIOLOGY 2021; 30:605-614. [PMID: 34318563 DOI: 10.1111/imb.12729] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/24/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Long non-coding RNAs (lncRNAs) generally display tissue-specific distributions, and testis-specific lncRNAs form the highest proportion of lncRNAs in many species. Here, we presented a detailed analysis of testis-specific lncRNAs in the melon fly, Zeugodacus cucurbitae, a highly destructive insect pest of cucurbitaceous and other related crops. Most testis-specific lncRNAs were found to be long intergenic non-coding RNAs (lincRNA). The size distribution of these lncRNAs ranged between 600 and 1000 nucleotides. Testis-specific lncRNAs that harboured one isoform number and two exons were the most abundant. Compared to other male tissues, the testis had more highly expressed lncRNAs. The quantitative real-time polymerase chain reaction results of 10 randomly selected testis-specific lncRNAs showed expression patterns consistent with RNA-seq data. Further analysis of the most highly expressed testis-specific lncRNA, lnc94638, was undertaken. Fluorescent in situ hybridization assays localized lnc94638 to the apical region of the testis that contains mature spermatozoa. RNA interference-mediated knockdown of lnc94638 expression reduced spermatozoa numbers and impaired the fertility of Z. cucurbitae male. This study provides a catalogue of testis-specific lncRNAs, shows that the testis-specific lnc94638 is involved in spermatogenesis and has the potential to be used for treating male sterility.
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Affiliation(s)
- W-J Li
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - D Wei
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - H-L Han
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Y-J Song
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Y Wang
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - H-Q Xu
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - G Smagghe
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - J-J Wang
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
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19
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Identification and comparative analysis of long non-coding RNAs in the brain of fire ant queens in two different reproductive states. BMC Genomics 2021; 22:917. [PMID: 35418014 PMCID: PMC9006410 DOI: 10.1186/s12864-022-08539-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/07/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Many long non-coding RNAs (lncRNAs) have been extensively identified in higher eukaryotic species. The function of lncRNAs has been reported to play important roles in diverse biological processes, including developmental regulation and behavioral plasticity. However, there are no reports of systematic characterization of long non-coding RNAs in the fire ant Solenopsis invicta.
Results
In this study, we performed a genome-wide analysis of lncRNAs in the brains of S. invicta from RNA-seq. In total, 1,393 novel lncRNA transcripts were identified in the fire ant. In contrast to the annotated lncRNA transcripts having at least two exons, novel lncRNAs are monoexonic transcripts with a shorter length. Besides, the transcriptome from virgin alate and dealate mated queens were analyzed and compared. The results showed 295 differentially expressed mRNA genes (DEGs) and 65 differentially expressed lncRNA genes (DELs) between virgin and mated queens, of which 17 lncRNAs were highly expressed in the virgin alates and 47 lncRNAs were highly expressed in the mated dealates. By identifying the DEL:DEG pairs with a high association in their expression (Spearman’s |rho|> 0.8 and p-value < 0.01), many DELs were co-regulated with DEGs after mating. Furthermore, several remarkable lncRNAs (MSTRG.6523, MSTRG.588, and nc909) that were found to associate with particular coding genes may play important roles in the regulation of brain gene expression in reproductive transition in fire ants.
Conclusion
This study provides the first genome-wide identification of S. invicta lncRNAs in the brains in different reproductive states. It will contribute to a fuller understanding of the transcriptional regulation underpinning reproductive changes.
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20
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Yang L, Wang YW, Lu YY, Li B, Chen KP, Li CJ. Genome-wide identification and characterization of long non-coding RNAs in Tribolium castaneum. INSECT SCIENCE 2021; 28:1262-1276. [PMID: 32978885 DOI: 10.1111/1744-7917.12867] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/19/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
Long non-coding RNAs (lncRNAs) are poorly understood in insects. In this study, we performed genome-wide analysis of lncRNAs in Tribolium castaneum by RNA-seq. In total, 4516 lncRNA transcripts corresponding to 3917 genes were identified from late embryos, early larvae, late larvae, early pupae, late pupae and early adults of T. castaneum, including 3152 novel lncRNAs and 1364 known lncRNAs. These lncRNAs have few exons and transcripts, and are short in length. During development, they exhibited nine different expression patterns. Functionally, they can act either by targeting messenger RNAs (1813 lncRNAs) and lncRNAs (45 lncRNAs) or as micro RNA (miRNA) precursors (46 lncRNAs). LncRNAs were observed to target the metabolic enzymes of glycolysis, TCA cycle and amino acids, demonstrating that lncRNAs control metabolism by regulating metabolic enzymes. Moreover, lncRNAs were shown to participate in cell differentiation and development via their targets. As miRNA precursors, lncRNAs could participate in the ecdysone signaling pathway. This study provides comprehensive information for lncRNAs of T. castaneum, and will promote functional analysis and target identification of lncRNAs in the insect.
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Affiliation(s)
- Liu Yang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, 212013, China
| | - You-Wei Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, 212013, China
| | - Yao-Yao Lu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Bin Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ke-Ping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, 212013, China
| | - Cheng-Jun Li
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, 212013, China
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21
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Huang M, Dong J, Guo H, Xiao M, Wang D. Identification of long noncoding RNAs reveals the effects of dinotefuran on the brain in Apis mellifera (Hymenopptera: Apidae). BMC Genomics 2021; 22:502. [PMID: 34217210 PMCID: PMC8254963 DOI: 10.1186/s12864-021-07811-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/14/2021] [Indexed: 12/19/2022] Open
Abstract
Background Dinotefuran (CAS No. 165252–70-0), a neonicotinoid insecticide, has been used to protect various crops against invertebrate pests and has been associated with numerous negative sublethal effects on honey bees. Long noncoding RNAs (lncRNAs) play important roles in mediating various biological and pathological processes, involving transcriptional and gene regulation. The effects of dinotefuran on lncRNA expression and lncRNA function in the honey bee brain are still obscure. Results Through RNA sequencing, a comprehensive analysis of lncRNAs and mRNAs was performed following exposure to 0.01 mg/L dinotefuran for 1, 5, and 10 d. In total, 312 lncRNAs and 1341 mRNAs, 347 lncRNAs and 1458 mRNAs, and 345 lncRNAs and 1155 mRNAs were found to be differentially expressed (DE) on days 1, 5 and 10, respectively. Gene set enrichment analysis (GSEA) indicated that the dinotefuran-treated group showed enrichment in carbohydrate and protein metabolism and immune-inflammatory responses such as glycine, serine and threonine metabolism, pentose and glucuronate interconversion, and Hippo and transforming growth factor-β (TGF-β) signaling pathways. Moreover, the DE lncRNA TCONS_00086519 was shown by fluorescence in situ hybridization (FISH) to be distributed mainly in the cytoplasm, suggesting that it may serve as a competing endogenous RNA and a regulatory factor in the immune response to dinotefuran. Conclusion This study characterized the expression profile of lncRNAs upon exposure to neonicotinoid insecticides in young adult honey bees and provided a framework for further study of the role of lncRNAs in honey bee growth and the immune response. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07811-y.
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Affiliation(s)
- Minjie Huang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jie Dong
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Haikun Guo
- Institute of Quality and Standard for Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Minghui Xiao
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.,State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Deqian Wang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
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22
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Li G, Liu X, Smagghe G, Niu J, Wang J. Genome-Wide Characterization and Identification of Long Non-Coding RNAs during the Molting Process of a Spider Mite, Panonychus citri. Int J Mol Sci 2021; 22:6909. [PMID: 34199120 PMCID: PMC8269015 DOI: 10.3390/ijms22136909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/23/2021] [Accepted: 06/23/2021] [Indexed: 01/26/2023] Open
Abstract
Molting is essential for arthropods to grow. As one of the important arthropod pests in agriculture, key spider mite species (Tetranychus and Panonychus) can normally molt three times from the larva to adult stage within a week. This physiological strategy results in the short lifecycle of spider mites and difficulties in their control in the field. Long non-coding RNAs (lncRNAs) regulate transcriptional editing, cellular function, and biological processes. Thus, analysis of the lncRNAs in the spider mite molting process may provide new insights into their roles in the molting mechanism. For this purpose, we used high-throughput RNA-seq to examine the expression dynamics of lncRNAs and mRNAs in the molting process of different development stages in Panonychus citri. We identified 9199 lncRNAs from 18 transcriptomes. Analysis of the lncRNAs suggested that they were shorter and had fewer exons and transcripts than mRNAs. Among these, 356 lncRNAs were differentially expressed during three molting processes: late larva to early protonymph, late protonymph to early deutonymph, and late deutonymph to early adult. A time series profile analysis of differentially expressed lncRNAs showed that 77 lncRNAs were clustered into two dynamic expression profiles (Pattern a and Pattern c), implying that lncRNAs were involved in the molting process of spider mites. Furthermore, the lncRNA-mRNA co-expression networks showed that several differentially expressed hub lncRNAs were predicted to be functionally associated with typical molting-related proteins, such as cuticle protein and chitin biosynthesis. These data reveal the potential regulatory function of lncRNAs in the molting process and provide datasets for further analysis of lncRNAs and mRNAs in spider mites.
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Affiliation(s)
- Gang Li
- Provincial Key Laboratory of Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang 550025, China;
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China; (X.L.); (G.S.); (J.N.)
| | - Xunyan Liu
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China; (X.L.); (G.S.); (J.N.)
| | - Guy Smagghe
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China; (X.L.); (G.S.); (J.N.)
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Jinzhi Niu
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China; (X.L.); (G.S.); (J.N.)
| | - Jinjun Wang
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China; (X.L.); (G.S.); (J.N.)
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23
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Tang Y, Song G, Liu H, Yang S, Yu X, Shi L. Silencing of Long Non-Coding RNA HOTAIR Alleviates Epithelial-Mesenchymal Transition in Pancreatic Cancer via the Wnt/β-Catenin Signaling Pathway. Cancer Manag Res 2021; 13:3247-3257. [PMID: 33883938 PMCID: PMC8053715 DOI: 10.2147/cmar.s265578] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 12/18/2020] [Indexed: 12/20/2022] Open
Abstract
Purpose Pancreatic cancer (PC) is a malignancy with poor prognosis and controversial treatment options. Long non-coding RNA (lncRNA) is a significant factor in the development of PC. In the current study, the possible effects of HOTAIR on the epithelial-mesenchymal transition (EMT) of PC and the related mechanisms were investigated. Methods The PC models were induced by 10 mg/100 g dimethylbenzoanthracene (DMBA) in pancreas. Mice were injected with the HOTAIR mimic and HOTAIR shRNA to determine the role of HOTAIR in PC. Subsequently, the expression of HOTAIR in PC cells was assayed. To determine the mechanism of HOTAIR in PC, human PC cell line PANC-1, Miapaca-2 and human normal pancreatic ductal epithelial cell line HPDE6-C7 were transfected with the HOTAIR mimic, the shRNA against HOTAIR, the Wnt/b-catenin activator (LiCl), and the Wnt/b-catenin inhibitor (XAV939), respectively. Moreover, the expressions of the Wnt/β-catenin signaling pathway-related genes (β-catenin, cyclinD1, c-myc, LEF-1 and c-Jun) and the levels of the EMT markers (E-cadherin, N-cadherin and Vimentin) were determined. Finally, the cell biological processes were evaluated by functional experiments. Results HOTAIR was found to be highly expressed in the PC cells in mice. The expression of β-catenin, cyclinD1, c-myc, LEF-1 and c-Jun, N-cadherin and Vimentin was found to be decreased, while the expression of E-cadherin was found to be increased subsequent to the silencing of HOTAIR in human PC cell lines PANC-1 and Miapaca-2. Additionally, it was observed that the silencing of HOTAIR could inhibit the Wnt/β-catenin signaling pathway to alleviate EMT of tumor cells and inhibit the capacities of cell proliferation, migration, and invasion. Conclusion The key finding of the present study is that the silencing of HOTAIR could potentially inhibit EMT and growth of PC through the Wnt/β-catenin signaling pathway, providing a novel therapy for PC.
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Affiliation(s)
- Yinhua Tang
- Department of Gastroenterology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - Guang Song
- Department of Gastroenterology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - Hongcheng Liu
- Department of Gastroenterology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - Shuang Yang
- Department of Gastroenterology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - Xiaoyi Yu
- Department of Gastroenterology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - Lijun Shi
- Department of Gastroenterology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
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24
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Choudhary C, Sharma S, Meghwanshi KK, Patel S, Mehta P, Shukla N, Do DN, Rajpurohit S, Suravajhala P, Shukla JN. Long Non-Coding RNAs in Insects. Animals (Basel) 2021; 11:1118. [PMID: 33919662 PMCID: PMC8069800 DOI: 10.3390/ani11041118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 12/27/2022] Open
Abstract
Only a small subset of all the transcribed RNAs are used as a template for protein translation, whereas RNA molecules that are not translated play a very important role as regulatory non-coding RNAs (ncRNAs). Besides traditionally known RNAs (ribosomal and transfer RNAs), ncRNAs also include small non-coding RNAs (sncRNAs) and long non-coding RNAs (lncRNAs). The lncRNAs, which were initially thought to be junk, have gained a great deal attention because of their regulatory roles in diverse biological processes in animals and plants. Insects are the most abundant and diverse group of animals on this planet. Recent studies have demonstrated the role of lncRNAs in almost all aspects of insect development, reproduction, and genetic plasticity. In this review, we describe the function and molecular mechanisms of the mode of action of different insect lncRNAs discovered up to date.
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Affiliation(s)
- Chhavi Choudhary
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindari, Ajmer 305801, India; (C.C.); (K.K.M.)
| | - Shivasmi Sharma
- Department of Biotechnology, Amity University Jaipur, Jaipur 303002, India; (S.S.); (S.P.)
| | - Keshav Kumar Meghwanshi
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindari, Ajmer 305801, India; (C.C.); (K.K.M.)
| | - Smit Patel
- Department of Biotechnology, Amity University Jaipur, Jaipur 303002, India; (S.S.); (S.P.)
| | - Prachi Mehta
- Division of Biological & Life Sciences, School of Arts and Sciences, Ahmedabad University, Gujarat 380009, India; (P.M.); (S.R.)
| | - Nidhi Shukla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur 302001, India;
| | - Duy Ngoc Do
- Institute of Research and Development, Duy Tan University, Danang 550000, Vietnam;
| | - Subhash Rajpurohit
- Division of Biological & Life Sciences, School of Arts and Sciences, Ahmedabad University, Gujarat 380009, India; (P.M.); (S.R.)
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur 302001, India;
- Bioclues.org, Vivekananda Nagar, Kukatpally, Hyderabad, Telangana 500072, India
| | - Jayendra Nath Shukla
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindari, Ajmer 305801, India; (C.C.); (K.K.M.)
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25
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Xing L, Xi Y, Qiao X, Huang C, Wu Q, Yang N, Guo J, Liu W, Fan W, Wan F, Qian W. The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation. BMC Genomics 2021; 22:4. [PMID: 33402093 PMCID: PMC7786964 DOI: 10.1186/s12864-020-07313-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) have emerged as an important class of transcriptional regulators in cellular processes. The past decades have witnessed great progress in lncRNA studies in a variety of organisms. The codling moth (Cydia pomonella L.) is an important invasive insect in China. However, the functional impact of lncRNAs in this insect remains unclear. In this study, an atlas of codling moth lncRNAs was constructed based on publicly available RNA-seq datasets. Results In total, 9875 lncRNA transcripts encoded by 9161 loci were identified in the codling moth. As expected, the lncRNAs exhibited shorter transcript lengths, lower GC contents, and lower expression levels than protein-coding genes (PCGs). Additionally, the lncRNAs were more likely to show tissue-specific expression patterns than PCGs. Interestingly, a substantial fraction of the lncRNAs showed a testis-biased expression pattern. Additionally, conservation analysis indicated that lncRNA sequences were weakly conserved across insect species, though additional lncRNAs with homologous relationships could be identified based on synteny, suggesting that synteny could be a more reliable approach for the cross-species comparison of lncRNAs. Furthermore, the correlation analysis of lncRNAs with neighbouring PCGs indicated a stronger correlation between them, suggesting potential cis-acting roles of these lncRNAs in the regulation of gene expression. Conclusions Taken together, our work provides a valuable resource for the comparative and functional study of lncRNAs, which will facilitate the understanding of their mechanistic roles in transcriptional regulation.
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Affiliation(s)
- Longsheng Xing
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yu Xi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xi Qiao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Cong Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Qiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Nianwan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jianyang Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wanxue Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wei Fan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Fanghao Wan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China. .,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Wanqiang Qian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
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26
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Kang SH, Pandey RP, Lee CM, Sim JS, Jeong JT, Choi BS, Jung M, Ginzburg D, Zhao K, Won SY, Oh TJ, Yu Y, Kim NH, Lee OR, Lee TH, Bashyal P, Kim TS, Lee WH, Hawkins C, Kim CK, Kim JS, Ahn BO, Rhee SY, Sohng JK. Genome-enabled discovery of anthraquinone biosynthesis in Senna tora. Nat Commun 2020; 11:5875. [PMID: 33208749 PMCID: PMC7674472 DOI: 10.1038/s41467-020-19681-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023] Open
Abstract
Senna tora is a widely used medicinal plant. Its health benefits have been attributed to the large quantity of anthraquinones, but how they are made in plants remains a mystery. To identify the genes responsible for plant anthraquinone biosynthesis, we reveal the genome sequence of S. tora at the chromosome level with 526 Mb (96%) assembled into 13 chromosomes. Comparison among related plant species shows that a chalcone synthase-like (CHS-L) gene family has lineage-specifically and rapidly expanded in S. tora. Combining genomics, transcriptomics, metabolomics, and biochemistry, we identify a CHS-L gene contributing to the biosynthesis of anthraquinones. The S. tora reference genome will accelerate the discovery of biologically active anthraquinone biosynthesis pathways in medicinal plants.
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Affiliation(s)
- Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea.
| | - Ramesh Prasad Pandey
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Chang-Muk Lee
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Joon-Soo Sim
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Jin-Tae Jeong
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, RDA, Eumseong, 55365, Republic of Korea
| | - Beom-Soon Choi
- Phyzen Genomics Institute, Seongnam, 13488, Republic of Korea
| | - Myunghee Jung
- Department of Forest Science, College of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Daniel Ginzburg
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Kangmei Zhao
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - So Youn Won
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Tae-Jin Oh
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Yeisoo Yu
- Phyzen Genomics Institute, Seongnam, 13488, Republic of Korea
- DNACARE Co. Ltd, Seoul, 06730, Republic of Korea
| | - Nam-Hoon Kim
- Phyzen Genomics Institute, Seongnam, 13488, Republic of Korea
| | - Ok Ran Lee
- Department of Applied Plant Science, College of Agriculture and Life Science, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Tae-Ho Lee
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Puspalata Bashyal
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Tae-Su Kim
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Woo-Haeng Lee
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Charles Hawkins
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Jung Sun Kim
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Byoung Ohg Ahn
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Seung Yon Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
| | - Jae Kyung Sohng
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea.
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27
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Kang SH, Pandey RP, Lee CM, Sim JS, Jeong JT, Choi BS, Jung M, Ginzburg D, Zhao K, Won SY, Oh TJ, Yu Y, Kim NH, Lee OR, Lee TH, Bashyal P, Kim TS, Lee WH, Hawkins C, Kim CK, Kim JS, Ahn BO, Rhee SY, Sohng JK. Genome-enabled discovery of anthraquinone biosynthesis in Senna tora. Nat Commun 2020. [PMID: 33208749 DOI: 10.1101/2020.04.27.063495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Senna tora is a widely used medicinal plant. Its health benefits have been attributed to the large quantity of anthraquinones, but how they are made in plants remains a mystery. To identify the genes responsible for plant anthraquinone biosynthesis, we reveal the genome sequence of S. tora at the chromosome level with 526 Mb (96%) assembled into 13 chromosomes. Comparison among related plant species shows that a chalcone synthase-like (CHS-L) gene family has lineage-specifically and rapidly expanded in S. tora. Combining genomics, transcriptomics, metabolomics, and biochemistry, we identify a CHS-L gene contributing to the biosynthesis of anthraquinones. The S. tora reference genome will accelerate the discovery of biologically active anthraquinone biosynthesis pathways in medicinal plants.
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Affiliation(s)
- Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea.
| | - Ramesh Prasad Pandey
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Chang-Muk Lee
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Joon-Soo Sim
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Jin-Tae Jeong
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, RDA, Eumseong, 55365, Republic of Korea
| | - Beom-Soon Choi
- Phyzen Genomics Institute, Seongnam, 13488, Republic of Korea
| | - Myunghee Jung
- Department of Forest Science, College of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Daniel Ginzburg
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Kangmei Zhao
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - So Youn Won
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Tae-Jin Oh
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Yeisoo Yu
- Phyzen Genomics Institute, Seongnam, 13488, Republic of Korea
- DNACARE Co. Ltd, Seoul, 06730, Republic of Korea
| | - Nam-Hoon Kim
- Phyzen Genomics Institute, Seongnam, 13488, Republic of Korea
| | - Ok Ran Lee
- Department of Applied Plant Science, College of Agriculture and Life Science, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Tae-Ho Lee
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Puspalata Bashyal
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Tae-Su Kim
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Woo-Haeng Lee
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Charles Hawkins
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Jung Sun Kim
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Byoung Ohg Ahn
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Seung Yon Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
| | - Jae Kyung Sohng
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea.
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Lin Z, Liu Y, Chen X, Han C, Wang W, Ke Y, Su X, Li Y, Chen H, Xu H, Chen G, Ji T. Genome-Wide Identification of Long Non-coding RNAs in the Gravid Ectoparasite Varroa destructor. Front Genet 2020; 11:575680. [PMID: 33193688 PMCID: PMC7596327 DOI: 10.3389/fgene.2020.575680] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/24/2020] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) emerge as critical regulators across a wide variety of biological functions in living organisms. However, to date, no systematic characterization of lncRNAs has been investigated in the ectoparasitic mite Varroa destructor, the most severe biotic threat to honey bees worldwide. Here, we performed an initial genome-wide identification of lncRNAs in V. destructor via high-throughput sequencing technology and reported, for the first time, the transcriptomic landscape of lncRNAs in the devastating parasite. By means of a lncRNA identification pipeline, 6,645 novel lncRNA transcripts, encoded by 3,897 gene loci, were identified, including 2,066 sense lncRNAs, 2,772 lincRNAs, and 1,807 lncNATs. Compared with protein-coding mRNAs, V. destructor lncRNAs are shorter in terms of full length, as well as of the ORF length, contain less exons, and express at lower level. GO term and KEGG pathway enrichment analyses of the lncRNA target genes demonstrated that these predicted lncRNAs may be potentially responsible for the regulatory functions of cellular and biological progresses in the reproductive phase of V. destructor. To our knowledge, this is the first catalog of lncRNA profile in the parasitiformes species, providing a valuable resource for genetic and genomic studies. Understanding the characteristics and features of lncRNAs in V. destructor would promote sustainable parasite control.
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Affiliation(s)
- Zheguang Lin
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yibing Liu
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiaomei Chen
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Cong Han
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Wei Wang
- Wuzhong Animal Health Supervision Institute, Suzhou, China
| | - Yalu Ke
- Wuzhong Animal Health Supervision Institute, Suzhou, China
| | - Xiaoling Su
- Jinhua Academy of Agricultural Sciences, Jinhua, China
| | - Yujiao Li
- Shandong Apiculture Breeding of Improved Varieties and Extension Center, Tai’an, China
| | - Heng Chen
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Hao Xu
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guohong Chen
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ting Ji
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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29
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Chang ZX, Ajayi OE, Guo DY, Wu QF. Genome-wide characterization and developmental expression profiling of long non-coding RNAs in Sogatella furcifera. INSECT SCIENCE 2020; 27:987-997. [PMID: 31264303 DOI: 10.1111/1744-7917.12707] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/16/2019] [Accepted: 06/13/2019] [Indexed: 06/09/2023]
Abstract
The genome-wide characterization of long non-coding RNA (lncRNA) in insects demonstrates their importance in fundamental biological processes. Essentially, an in-depth understanding of the functional repertoire of lncRNA in insects is pivotal to insect resources utilization and sustainable pest control. Using a custom bioinformatics pipeline, we identified 1861 lncRNAs encoded by 1852 loci in the Sogatella furcifera genome. We profiled lncRNA expression in different developmental stages and observed that the expression of lncRNAs is more highly temporally restricted compared to protein-coding genes. More up-regulated Sogatella furcifera lncRNA expressed in the embryo, 4th and 5th instars, suggesting that increased lncRNA levels may play a role in these developmental stages. We compared the relationship between the expression of Sogatella furcifera lncRNA and its nearest protein gene and found that lncRNAs were more correlated to their downstream coding neighbors on the opposite strand. Our genome-wide profiling of lncRNAs in Sogatella furcifera identifies exciting candidates for characterization of lncRNAs, and also provides information on lncRNA regulation during insect development.
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Affiliation(s)
- Zhao-Xia Chang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Olugbenga Emmanuel Ajayi
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Dong-Yang Guo
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Qing-Fa Wu
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei, China
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30
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Villagra C, Frías-Lasserre D. Epigenetic Molecular Mechanisms in Insects. NEOTROPICAL ENTOMOLOGY 2020; 49:615-642. [PMID: 32514997 DOI: 10.1007/s13744-020-00777-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
Insects are the largest animal group on Earth both in biomass and diversity. Their outstanding success has inspired genetics and developmental research, allowing the discovery of dynamic process explaining extreme phenotypic plasticity and canalization. Epigenetic molecular mechanisms (EMMs) are vital for several housekeeping functions in multicellular organisms, regulating developmental, ontogenetic trajectories and environmental adaptations. In Insecta, EMMs are involved in the development of extreme phenotypic divergences such as polyphenisms and eusocial castes. Here, we review the history of this research field and how the main EMMs found in insects help to understand their biological processes and diversity. EMMs in insects confer them rapid response capacity allowing insect either to change with plastic divergence or to keep constant when facing different stressors or stimuli. EMMs function both at intra as well as transgenerational scales, playing important roles in insect ecology and evolution. We discuss on how EMMs pervasive influences in Insecta require not only the control of gene expression but also the dynamic interplay of EMMs with further regulatory levels, including genetic, physiological, behavioral, and environmental among others, as was earlier proposed by the Probabilistic Epigenesis model and Developmental System Theory.
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Affiliation(s)
- C Villagra
- Instituto de Entomología, Univ Metropolitana de Ciencias de la Educación, Santiago, Chile.
| | - D Frías-Lasserre
- Instituto de Entomología, Univ Metropolitana de Ciencias de la Educación, Santiago, Chile
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31
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Zhang S, Yin H, Shen M, Huang H, Hou Q, Zhang Z, Zhao W, Guo X, Wu P. Analysis of lncRNA-mediated gene regulatory network of Bombyx mori in response to BmNPV infection. J Invertebr Pathol 2020; 170:107323. [DOI: 10.1016/j.jip.2020.107323] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/02/2020] [Accepted: 01/03/2020] [Indexed: 01/20/2023]
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32
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Guan R, Li H, Zhang H, An S. Comparative analysis of dsRNA-induced lncRNAs in three kinds of insect species. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2020; 103:e21640. [PMID: 31667893 DOI: 10.1002/arch.21640] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/24/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Long noncoding RNAs (lncRNAs) that have immune responses to various stimuli have been identified in some insects. One type of pathogen-associated molecular pattern, double-stranded RNA (dsRNA), can trigger the RNA interference (RNAi) pathway and immune response. Interestingly, there has been no research into characterizing the relationship between lncRNA and dsRNA-induced RNAi pathways. In this study, dsRNA-induced lncRNAs were investigated in two species of lepidopteran insects, Helicoverpa armigera and Plutella xylostella, and one species of coleopteran insects, Tribolium castaneum. Between untreated group and dsRNA-induced group; 3,463 H. armigera, 6,245 P. xylostella, and 3,067 T. castaneum differentially expressed lncRNAs were identified while 156 H. armigera, 247 P. xylostella, 415 T. castaneum lncRNAs and their putative target genes showed consistent changes in gene expression. In T. castaneum, most target genes of the differentially expressed lncRNAs are enriched in the cyclic adenosine monophosphate signaling pathway, ABC transporters, and Janus kinase-signal transducers and activators of the transcription signaling pathway. Conversely, in H. armigera and P. xylostella, the differentially expressed lncRNAs were mainly enriched in the metabolic, digestive, and synthetic signaling pathways. This result indicates that dsRNA-induced lncRNA is species-dependent. We also found that both Dicer-2 and the lncRNA that targets Dicer-2 were significantly upregulated after dsRNA treatment in P. xylostella, indicating that some lncRNAs may be involved in the regulation of the core RNAi pathway in insects. Our results are the first to identify a relationship between lncRNAs and dsRNA in various insect species with different RNAi efficiencies. These results provide a reference for future study of the dsRNA-induced RNAi pathway and different RNAi efficiencies among insect species.
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Affiliation(s)
- Ruobing Guan
- State Key Laboratory of Wheat and Maize Crop Science, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Haichao Li
- State Key Laboratory of Wheat and Maize Crop Science, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Hao Zhang
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Shiheng An
- State Key Laboratory of Wheat and Maize Crop Science, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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High-Quality Genome Assemblies Reveal Long Non-coding RNAs Expressed in Ant Brains. Cell Rep 2019; 23:3078-3090. [PMID: 29874592 PMCID: PMC6023404 DOI: 10.1016/j.celrep.2018.05.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 04/04/2018] [Accepted: 05/03/2018] [Indexed: 12/31/2022] Open
Abstract
Ants are an emerging model system for neuroepigenetics, as embryos with virtually identical genomes develop into different adult castes that display diverse physiology, morphology, and behavior. Although a number of ant genomes have been sequenced to date, their draft quality is an obstacle to sophisticated analyses of epigenetic gene regulation. We reassembled de novo high-quality genomes for two ant species, Camponotus floridanus and Harpegnathos saltator. Using long reads enabled us to span large repetitive regions and improve genome contiguity, leading to comprehensive and accurate protein-coding annotations that facilitated the identification of a Gp-9-like gene as differentially expressed in Harpegnathos castes. The new assemblies also enabled us to annotate long non-coding RNAs in ants, revealing caste-, brain-, and developmental-stage-specific long non-coding RNAs (lncRNAs) in Harpegnathos. These upgraded genomes, along with the new gene annotations, will aid future efforts to identify epigenetic mechanisms of phenotypic and behavioral plasticity in ants.
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Zhang J, Guan W, Huang C, Hu Y, Chen Y, Guo J, Zhou C, Chen R, Du B, Zhu L, Huanhan D, He G. Combining next-generation sequencing and single-molecule sequencing to explore brown plant hopper responses to contrasting genotypes of japonica rice. BMC Genomics 2019; 20:682. [PMID: 31464583 PMCID: PMC6716848 DOI: 10.1186/s12864-019-6049-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/20/2019] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The brown plant hopper (BPH), Nilaparvata lugens, is one of the major pest of rice (Oryza sativa). Plant defenses against insect herbivores have been extensively studied, but our understanding of insect responses to host plants' resistance mechanisms is still limited. The purpose of this study is to characterize transcripts of BPH and reveal the responses of BPH insects to resistant rice at transcription level by using the advanced molecular techniques, the next-generation sequencing (NGS) and the single-molecule, real-time (SMRT) sequencing. RESULTS The current study obtained 24,891 collapsed isoforms of full-length transcripts, and 20,662 were mapped to known annotated genes, including 17,175 novel transcripts. The current study also identified 915 fusion genes, 1794 novel genes, 2435 long non-coding RNAs (lncRNAs), and 20,356 alternative splicing events. Moreover, analysis of differentially expressed genes (DEGs) revealed that genes involved in metabolic and cell proliferation processes were significantly enriched in up-regulated and down-regulated sets, respectively, in BPH fed on resistant rice relative to BPH fed on susceptible wild type rice. Furthermore, the FoxO signaling pathway was involved and genes related to BPH starvation response (Nlbmm), apoptosis and autophagy (caspase 8, ATG13, BNIP3 and IAP), active oxygen elimination (catalase, MSR, ferritin) and detoxification (GST, CarE) were up-regulated in BPH responses to resistant rice. CONCLUSIONS The current study provides the first demonstrations of the full diversity and complexity of the BPH transcriptome, and indicates that BPH responses to rice resistance, might be related to starvation stress responses, nutrient transformation, oxidative decomposition, and detoxification. The current result findings will facilitate further exploration of molecular mechanisms of interaction between BPH insects and host rice.
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Affiliation(s)
- Jing Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wei Guan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Chaomei Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yinxia Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yu Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jianping Guo
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Cong Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Rongzhi Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Bo Du
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lili Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Danax Huanhan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Guangcun He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
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Ali A, Abd El Halim HM. Re-thinking adaptive immunity in the beetles: Evolutionary and functional trajectories of lncRNAs. Genomics 2019; 112:1425-1436. [PMID: 31442561 DOI: 10.1016/j.ygeno.2019.08.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/04/2019] [Accepted: 08/16/2019] [Indexed: 12/24/2022]
Abstract
Unlike vertebrate animals, invertebrates lack lymphocytes and therefore have historically been believed not to develop immune memory. A few studies have reported evidence of immune priming in insects; however, these studies lack the molecular mechanism and proposed it might be different among taxa. Since lncRNAs are known to regulate the immune response, we identified 10,120 lncRNAs in Tribolium castaneum genome-wide followed by transcriptome analysis of primed and unprimed larvae of different infectious status. A shift in lncRNA expression between Btt primed larvae and other treatment groups provides evidence of immune memory response. A few "priming" lncRNAs (n = 9) were uniquely regulated in Btt primed larvae. Evidence suggests these lncRNAs are likely controlling immune priming in Tribolium by regulating expression of genes involved in proteasomal machinery, Notch system, zinc metabolism, and methyltransferase activity, which are necessary to modulate phagocytosis. Our results support a conserved immune priming mechanism in a macrophage-dependent manner.
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Affiliation(s)
- Ali Ali
- Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN 37132, United States of America; Department of Zoology, Faculty of Science, Benha University, Benha, Egypt.
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36
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Chen D, Chen H, Du Y, Zhou D, Geng S, Wang H, Wan J, Xiong C, Zheng Y, Guo R. Genome-Wide Identification of Long Non-Coding RNAs and Their Regulatory Networks Involved in Apis mellifera ligustica Response to Nosema ceranae Infection. INSECTS 2019; 10:insects10080245. [PMID: 31405016 PMCID: PMC6723323 DOI: 10.3390/insects10080245] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 12/23/2022]
Abstract
Long non-coding RNAs (lncRNAs) are a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins, and lncRNAs have been proven to play pivotal roles in a wide range of biological processes in animals and plants. However, knowledge of expression patterns and potential roles of honeybee lncRNA response to Nosema ceranae infection is completely unknown. Here, we performed whole transcriptome strand-specific RNA sequencing of normal midguts of Apis mellifera ligustica workers (Am7CK, Am10CK) and N. ceranae-inoculated midguts (Am7T, Am10T), followed by comprehensive analyses using bioinformatic and molecular approaches. A total of 6353 A. m. ligustica lncRNAs were identified, including 4749 conserved lncRNAs and 1604 novel lncRNAs. These lncRNAs had minimal sequence similarities with other known lncRNAs in other species; however, their structural features were similar to counterparts in mammals and plants, including shorter exon and intron length, lower exon number, and lower expression level, compared with protein-coding transcripts. Further, 111 and 146 N. ceranae-responsive lncRNAs were identified from midguts at 7-days post-inoculation (dpi) and 10 dpi compared with control midguts. Twelve differentially expressed lncRNAs (DElncRNAs) were shared by Am7CK vs. Am7T and Am10CK vs. Am10T comparison groups, while the numbers of unique DElncRNAs were 99 and 134, respectively. Functional annotation and pathway analysis showed that the DElncRNAs may regulate the expression of neighboring genes by acting in cis and trans fashion. Moreover, we discovered 27 lncRNAs harboring eight known miRNA precursors and 513 lncRNAs harboring 2257 novel miRNA precursors. Additionally, hundreds of DElncRNAs and their target miRNAs were found to form complex competitive endogenous RNA (ceRNA) networks, suggesting that these DElncRNAs may act as miRNA sponges. Furthermore, DElncRNA-miRNA-mRNA networks were constructed and investigated, the results demonstrated that a portion of the DElncRNAs were likely to participate in regulating the host material and energy metabolism as well as cellular and humoral immune host responses to N. ceranae invasion. Our findings revealed here offer not only a rich genetic resource for further investigation of the functional roles of lncRNAs involved in the A. m. ligustica response to N. ceranae infection, but also a novel insight into understanding the host-pathogen interaction during honeybee microsporidiosis.
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Affiliation(s)
- Dafu Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huazhi Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yu Du
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dingding Zhou
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sihai Geng
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haipeng Wang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jieqi Wan
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cuiling Xiong
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanzhen Zheng
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Rui Guo
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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37
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Chen X, Shi W, Chen C. Differential circular RNAs expression in ovary during oviposition in honey bees. Genomics 2019; 111:598-606. [DOI: 10.1016/j.ygeno.2018.03.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 03/10/2018] [Accepted: 03/19/2018] [Indexed: 02/02/2023]
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38
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Liu F, Shi T, Qi L, Su X, Wang D, Dong J, Huang ZY. lncRNA profile of Apis mellifera and its possible role in behavioural transition from nurses to foragers. BMC Genomics 2019; 20:393. [PMID: 31113365 PMCID: PMC6528240 DOI: 10.1186/s12864-019-5664-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/01/2019] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The behavioural transition from nurses to foragers in honey bees is known to be affected by intrinsic and extrinsic factors, including colony demography, hormone levels, brain chemistry and structure, and gene expression in the brain. However, the molecular mechanism underlying this behavioural transition of honey bees is still obscure. RESULTS Through RNA sequencing, we performed a comprehensive analysis of lncRNAs and mRNAs in honey bee nurses and foragers. Nurses and foragers from both typical colonies and single-cohort colonies were used to prepare six libraries to generate 49 to 100 million clear reads per sample. We obtained 6863 novel lncRNAs, 1480 differentially expressed lncRNAs between nurses and foragers, and 9308 mRNAs. Consistent with previous studies, lncRNAs showed features distinct from mRNAs, such as shorter lengths, lower exon numbers, and lower expression levels compared to mRNAs. Bioinformatic analysis showed that differentially expressed genes were mostly involved in the regulation of sensory-related events, such as olfactory receptor activity and odorant binding, and enriched Wnt and FoxO signaling pathways. Moreover, we found that lncRNAs TCONS_00356023, TCONS_00357367, TCONS_00159909 and mRNAs dop1, Kr-h1 and HR38 may play important roles in behavioural transition in honey bees. CONCLUSION This study characterized the expression profile of lncRNAs in nurses and foragers and provided a framework for further study of the role of lncRNAs in honey bee behavioural transition.
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Affiliation(s)
- Fang Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230000 Anhui China
| | - Tengfei Shi
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230000 Anhui China
| | - Lei Qi
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230000 Anhui China
| | - Xin Su
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230000 Anhui China
| | - Deqian Wang
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
| | - Jie Dong
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
| | - Zachary Y. Huang
- Department of Entomology, Michigan State University, East Lansing, MI 48824 USA
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39
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Shields EJ, Petracovici AF, Bonasio R. lncRedibly versatile: biochemical and biological functions of long noncoding RNAs. Biochem J 2019; 476:1083-1104. [PMID: 30971458 PMCID: PMC6745715 DOI: 10.1042/bcj20180440] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/28/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) are transcripts that do not code for proteins, but nevertheless exert regulatory effects on various biochemical pathways, in part via interactions with proteins, DNA, and other RNAs. LncRNAs are thought to regulate transcription and other biological processes by acting, for example, as guides that target proteins to chromatin, scaffolds that facilitate protein-protein interactions and complex formation, and orchestrators of phase-separated compartments. The study of lncRNAs has reached an exciting time, as recent advances in experimental and computational methods allow for genome-wide interrogation of biochemical and biological mechanisms of these enigmatic transcripts. A better appreciation for the biochemical versatility of lncRNAs has allowed us to begin closing gaps in our knowledge of how they act in diverse cellular and organismal contexts, including development and disease.
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Affiliation(s)
- Emily J Shields
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
| | - Ana F Petracovici
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
- Graduate Group in Genetics and Epigenetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
| | - Roberto Bonasio
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A.
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
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40
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Glastad KM, Hunt BG, Goodisman MAD. Epigenetics in Insects: Genome Regulation and the Generation of Phenotypic Diversity. ANNUAL REVIEW OF ENTOMOLOGY 2019; 64:185-203. [PMID: 30285490 DOI: 10.1146/annurev-ento-011118-111914] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Epigenetic inheritance is fundamentally important to cellular differentiation and developmental plasticity. In this review, we provide an introduction to the field of molecular epigenetics in insects. Epigenetic information is passed across cell divisions through the methylation of DNA, the modification of histone proteins, and the activity of noncoding RNAs. Much of our knowledge of insect epigenetics has been gleaned from a few model species. However, more studies of epigenetic information in traditionally nonmodel taxa will help advance our understanding of the developmental and evolutionary significance of epigenetic inheritance in insects. To this end, we also provide a brief overview of techniques for profiling and perturbing individual facets of the epigenome. Doing so in diverse cellular, developmental, and taxonomic contexts will collectively help shed new light on how genome regulation results in the generation of diversity in insect form and function.
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Affiliation(s)
- Karl M Glastad
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| | - Brendan G Hunt
- Department of Entomology, University of Georgia, Griffin, Georgia 30223, USA;
| | - Michael A D Goodisman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
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41
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Wang GZ, Du K, Hu SQ, Chen SY, Jia XB, Cai MC, Shi Y, Wang J, Lai SJ. Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue. Lipids Health Dis 2018; 17:271. [PMID: 30486837 PMCID: PMC6263043 DOI: 10.1186/s12944-018-0915-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/15/2018] [Indexed: 02/06/2023] Open
Abstract
Background The rabbit is widely used as an important experimental model for biomedical research, and shows low adipose tissue deposition during growth. Long non-coding RNAs (lncRNAs) are associated with adipose growth, but little is known about the function of lncRNAs in the rabbit adipose tissue. Methods Deep RNA-sequencing and comprehensive bioinformatics analyses were used to characterize the lncRNAs of rabbit visceral adipose tissue (VAT) at 35, 85 and 120 days after birth. Differentially expressed (DE) lncRNAs were identified at the three growth stages by DESeq. The cis and trans prediction ways predicted the target genes of the DE lncRNAs. To explore the function of lncRNAs, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed on the candidate genes. Results A total of 991,157,544 clean reads were generated after RNA-Seq of the three growth stages, of which, 30,353 and 107 differentially expressed (DE) lncRNAs were identified. Compared to the protein-coding transcripts, the rabbit lncRNAs shared some characteristics such as shorter length and fewer exons. Cis and trans target gene prediction revealed, 43 and 64 DE lncRNAs respectively, corresponding to 72 and 20 protein-coding genes. GO enrichment and KEGG pathway analyses revealed that the candidate DE lncRNA target genes were involved in oxidative phosphorylation, glyoxylate and dicarboxylate metabolism, and other adipose growth-related pathways. Six DE lncRNAs were randomly selected and validated by q-PCR. Conclusions This study is the first to profile the potentially functional lncRNAs in the adipose tissue growth in rabbits, and contributes to our understanding of mammalian adipogenesis. Electronic supplementary material The online version of this article (10.1186/s12944-018-0915-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guo-Ze Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.,College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Kun Du
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shen-Qiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shi-Yi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xian-Bo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ming-Cheng Cai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Shi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Song-Jia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
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42
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Guo R, Chen D, Chen H, Xiong C, Zheng Y, Hou C, Du Y, Geng S, Wang H, Dingding Z, Yilong G. Genome-Wide Identification of Circular RNAs in Fungal Parasite Nosema ceranae. Curr Microbiol 2018; 75:1655-1660. [PMID: 30269253 DOI: 10.1007/s00284-018-1576-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/26/2018] [Indexed: 01/30/2023]
Abstract
Circular RNAs (circRNAs) are newly discovered endogenous non-coding RNAs (ncRNAs) that play key roles in microRNA function and transcriptional regulation. Though a large number of circRNAs had been identified in animals and plants, however, little is known regarding circRNAs in Nosema ceranae, a widespread fungal parasite of honeybee. In this study, using deep sequencing technology and bioinformatic analysis, we predicted 204 circRNAs from N. ceranae spore samples, including 174 exonic circRNAs and 30 intergenic circRNAs. In addition, the expression of seven N. ceranae circRNAs was confirmed by RT-PCR assay. Furthermore, regulation networks of circRNAs were constructed, and 15 circRNAs were found to act as sponges of the corresponding three miRNAs. GO categorization and pathway enrichment analysis suggested that the circRNAs are likely to play significant roles in N. ceranae spore. This is the first report of circRNAs generated by a microsporidia species. Our results provide novel insights into understanding the basic biology of N. ceranae.
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Affiliation(s)
- Rui Guo
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dafu Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Huazhi Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Cuiling Xiong
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yanzhen Zheng
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chunsheng Hou
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100093, China
| | - Yu Du
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Sihai Geng
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Haipeng Wang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhou Dingding
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Guo Yilong
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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43
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Kumar H, Panigrahi M, Chhotaray S, Bhanuprakash V, Shandilya R, Sonwane A, Bhushan B. Red flour beetle ( Tribolium castaneum): From population genetics to functional genomics. Vet World 2018; 11:1043-1046. [PMID: 30250361 PMCID: PMC6141300 DOI: 10.14202/vetworld.2018.1043-1046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 06/25/2018] [Indexed: 11/16/2022] Open
Abstract
Tribolium castaneum is a small and low maintenance beetle that has emerged as a most suitable insect model for studying developmental biology and functional genetic analysis. Diverse population genetic studies have been conducted using Tribolium as the principal model to establish basic facts and principles of inbreeding experiments and response to the selection and other quantitative genetics fundamentals. The advanced molecular genetic studies presently focused on the use of Tribolium as a typical invertebrate model for higher diploid eukaryotes. After a whole genome sequencing of Tribolium, many areas of functional genomics were unraveled, which enabled the use of it in many technical approaches of genomics. The present text reviews the use of Tribolium in techniques such as RNAi, transgenic studies, immune priming, immunohistochemistry, in situ hybridization, gene sequencing for characterization of microRNAs, and gene editing using engineered endonuclease. In contrast to Drosophila, the T. castaneum holds a robust systemic RNAi response, which makes it an excellent model for comparative functional genetic studies.
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Affiliation(s)
- Harshit Kumar
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Bareilly - 243 122, Uttar Pradesh, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Bareilly - 243 122, Uttar Pradesh, India
| | - Supriya Chhotaray
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Bareilly - 243 122, Uttar Pradesh, India
| | - V Bhanuprakash
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Bareilly - 243 122, Uttar Pradesh, India
| | - Rahul Shandilya
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Bareilly - 243 122, Uttar Pradesh, India
| | - Arvind Sonwane
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Bareilly - 243 122, Uttar Pradesh, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Bareilly - 243 122, Uttar Pradesh, India
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44
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Zhou QZ, Fang SM, Zhang Q, Yu QY, Zhang Z. Identification and comparison of long non-coding RNAs in the silk gland between domestic and wild silkworms. INSECT SCIENCE 2018; 25:604-616. [PMID: 28111905 DOI: 10.1111/1744-7917.12443] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 12/03/2016] [Accepted: 12/29/2016] [Indexed: 06/06/2023]
Abstract
Under long-term artificial selection, the domestic silkworm (Bombyx mori) has increased its silk yield tremendously in comparison with its wild progenitor, Bombyx mandarina. However, the molecular mechanism of silk yield increase is still unknown. Comparative analysis of long non-coding RNAs (lncRNAs) may provide some insights into understanding this phenotypic variation. In this study, using RNA sequencing technology data of silk gland in domestic and wild silkworms, we identified 599 lncRNAs in the silk gland of the silkworm. Compared with protein-coding genes, the silk gland lncRNA genes tend to have fewer exon numbers, shorter transcript length and lower GC-content. Moreover, we found that three lncRNA genes are significantly and differentially expressed between domestic and wild silkworms. The potential targets of two differentially expressed lncRNAs (DELs) (dw4sg_0040 and dw4sg_0483) and the expression-correlated genes with the two DELs are mainly enriched in the related processes of silk protein translation. This implies that these DELs may affect the phenotypic variation in silk yield between the domestic and wild silkworms through the post-transcriptional regulation of silk protein.
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Affiliation(s)
- Qiu-Zhong Zhou
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, China
| | - Shou-Min Fang
- College of Life Science, China West Normal University, Nanchong, Sichuan, China
| | - Qiang Zhang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, China
| | - Quan-You Yu
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, China
| | - Ze Zhang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, China
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45
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Guo R, Chen D, Xiong C, Hou C, Zheng Y, Fu Z, Diao Q, Zhang L, Wang H, Hou Z, Li W, Kumar D, Liang Q. Identification of long non-coding RNAs in the chalkbrood disease pathogen Ascospheara apis. J Invertebr Pathol 2018; 156:1-5. [PMID: 29894727 DOI: 10.1016/j.jip.2018.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 06/04/2018] [Accepted: 06/08/2018] [Indexed: 01/14/2023]
Abstract
Ascospheara apis is a widespread fungal pathogen that exclusively invades honeybee larvae. Thus far, non-coding RNA in A. apis has not yet been documented. In this study, we sequenced A. apis using strand specific cDNA library construction and Illumina RNA sequencing methods, and identified 379 lncRNAs, including antisense lncRNAs, lincRNAs, intronic lncRNAs and sense lncRNAs. Additionally, these lncRNAs were found to be shorter in length and have fewer exons and transcript isoforms than protein-coding genes, similar to those identified in mammals and plants. Furthermore, the existence of 15 predicted lncRNAs of A. apis was confirmed using RT-PCR and expression levels of 11 were lower than those of adjacent protein-coding genes. Our findings not only enlarge the lncRNA database for fungi, but also lay a foundation for further investigation of potential lncRNA-mediated regulation of genes in A. apis.
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Affiliation(s)
- Rui Guo
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dafu Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Cuiling Xiong
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chunsheng Hou
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Yanzhen Zheng
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongmin Fu
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qingyun Diao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Lu Zhang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hongquan Wang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhixian Hou
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wendong Li
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dhiraj Kumar
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Qin Liang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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46
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Gaiti F, Degnan BM, Tanurdžić M. Long non-coding regulatory RNAs in sponges and insights into the origin of animal multicellularity. RNA Biol 2018; 15:696-702. [PMID: 29616867 PMCID: PMC6152434 DOI: 10.1080/15476286.2018.1460166] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/26/2018] [Accepted: 03/28/2018] [Indexed: 02/01/2023] Open
Abstract
How animals evolved from a single-celled ancestor over 700 million years ago is poorly understood. Recent transcriptomic and chromatin analyses in the sponge Amphimedon queenslandica, a morphologically-simple representative of one of the oldest animal phyletic lineages, have shed light on what innovations in the genome and its regulation underlie the emergence of animal multicellularity. Comparisons of the regulatory genome of this sponge with those of more complex bilaterian model species and even simpler unicellular relatives have revealed that fundamental changes in genome regulatory complexity accompanied the evolution of animal multicellularity. Here, we review and discuss the results of these recent investigations by specifically focusing on the contribution of long non-coding RNAs to the evolution of the animal regulatory genome.
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Affiliation(s)
- Federico Gaiti
- School of Biological Sciences, University of Queensland, Brisbane, Australia
| | - Bernard M. Degnan
- School of Biological Sciences, University of Queensland, Brisbane, Australia
| | - Miloš Tanurdžić
- School of Biological Sciences, University of Queensland, Brisbane, Australia
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47
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Aumer D, Mumoki FN, Pirk CWW, Moritz RFA. The transcriptomic changes associated with the development of social parasitism in the honeybee Apis mellifera capensis. Naturwissenschaften 2018; 105:22. [PMID: 29557991 DOI: 10.1007/s00114-018-1552-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/06/2018] [Accepted: 03/08/2018] [Indexed: 02/07/2023]
Abstract
Social insects are characterized by the division of labor. Queens usually dominate reproduction, whereas workers fulfill non-reproductive age-dependent tasks to maintain the colony. Although workers are typically sterile, they can activate their ovaries to produce their own offspring. In the extreme, worker reproduction can turn into social parasitism as in Apis mellifera capensis. These intraspecific parasites occupy a host colony, kill the resident queen, and take over the reproductive monopoly. Because they exhibit a queenlike behavior and are also treated like queens by the fellow workers, they are so-called pseudoqueens. Here, we compare the development of parasitic pseudoqueens and social workers at different time points using fat body transcriptome data. Two complementary analysis methods-a principal component analysis and a time course analysis-led to the identification of a core set of genes involved in the transition from a social worker into a highly fecund parasitic pseudoqueen. Comparing our results on pseudoqueens with gene expression data of honeybee queens revealed many similarities. In addition, there was a set of specific transcriptomic changes in the parasitic pseudoqueens that differed from both, queens and social workers, which may be typical for the development of the social parasitism in A. m. capensis.
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Affiliation(s)
- Denise Aumer
- Department of Molecular Ecology, Martin-Luther University Halle-Wittenberg, Hoher Weg 4, 06099, Halle (Saale), Germany.
| | - Fiona N Mumoki
- Social Insect Research Group, Department of Zoology and Entomology, University of Pretoria, Private Bag X20 Hatfield, Pretoria, 0002, South Africa
| | - Christian W W Pirk
- Social Insect Research Group, Department of Zoology and Entomology, University of Pretoria, Private Bag X20 Hatfield, Pretoria, 0002, South Africa
| | - Robin F A Moritz
- Department of Molecular Ecology, Martin-Luther University Halle-Wittenberg, Hoher Weg 4, 06099, Halle (Saale), Germany.,Social Insect Research Group, Department of Zoology and Entomology, University of Pretoria, Private Bag X20 Hatfield, Pretoria, 0002, South Africa.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
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48
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Gaiti F, Hatleberg WL, Tanurdžić M, Degnan BM. Sponge Long Non-Coding RNAs Are Expressed in Specific Cell Types and Conserved Networks. Noncoding RNA 2018; 4:ncrna4010006. [PMID: 29657303 PMCID: PMC5890393 DOI: 10.3390/ncrna4010006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/05/2018] [Accepted: 02/27/2018] [Indexed: 02/06/2023] Open
Abstract
Although developmental regulation by long non-coding RNAs (lncRNAs) appears to be a widespread feature amongst animals, the origin and level of evolutionary conservation of this mode of regulation remain unclear. We have previously demonstrated that the sponge Amphimedon queenslandica—a morphologically-simple animal—developmentally expresses an array of lncRNAs in manner akin to more complex bilaterians (insects + vertebrates). Here, we first show that Amphimedon lncRNAs are expressed in specific cell types in larvae, juveniles and adults. Thus, as in bilaterians, sponge developmental regulation involves the dynamic, cell type- and context-specific regulation of specific lncRNAs. Second, by comparing gene co-expression networks between Amphimedon queenslandica and Sycon ciliatum—a distantly-related calcisponge—we identify several putative co-expression modules that appear to be shared in sponges; these network-embedded sponge lncRNAs have no discernable sequence similarity. Together, these results suggest sponge lncRNAs are developmentally regulated and operate in conserved gene regulatory networks, as appears to be the case in more complex bilaterians.
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Affiliation(s)
- Federico Gaiti
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia.
- Department of Medicine, Weill Cornell Medicine, and New York Genome Center, New York, NY 10021, USA.
| | - William L Hatleberg
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia.
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Miloš Tanurdžić
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia.
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49
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Lopez-Ezquerra A, Mitschke A, Bornberg-Bauer E, Joop G. Tribolium castaneum gene expression changes after Paranosema whitei infection. J Invertebr Pathol 2018; 153:92-98. [DOI: 10.1016/j.jip.2018.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/10/2018] [Accepted: 02/12/2018] [Indexed: 12/24/2022]
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50
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Liu F, Guo D, Yuan Z, Chen C, Xiao H. Genome-wide identification of long non-coding RNA genes and their association with insecticide resistance and metamorphosis in diamondback moth, Plutella xylostella. Sci Rep 2017; 7:15870. [PMID: 29158595 PMCID: PMC5696462 DOI: 10.1038/s41598-017-16057-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/06/2017] [Indexed: 01/17/2023] Open
Abstract
Long non-coding RNA (lncRNA) is a class of noncoding RNA >200 bp in length that has essential roles in regulating a variety of biological processes. Here, we constructed a computational pipeline to identify lncRNA genes in the diamondback moth (Plutella xylostella), a major insect pest of cruciferous vegetables. In total, 3,324 lncRNAs corresponding to 2,475 loci were identified from 13 RNA-Seq datasets, including samples from parasitized, insecticide-resistant strains and different developmental stages. The identified P. xylostella lncRNAs had shorter transcripts and fewer exons than protein-coding genes. Seven out of nine randomly selected lncRNAs were validated by strand-specific RT-PCR. In total, 54-172 lncRNAs were specifically expressed in the insecticide resistant strains, among which one lncRNA was located adjacent to the sodium channel gene. In addition, 63-135 lncRNAs were specifically expressed in different developmental stages, among which three lncRNAs overlapped or were located adjacent to the metamorphosis-associated genes. These lncRNAs were either strongly or weakly co-expressed with their overlapping or neighboring mRNA genes. In summary, we identified thousands of lncRNAs and presented evidence that lncRNAs might have key roles in conferring insecticide resistance and regulating the metamorphosis development in P. xylostella.
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Affiliation(s)
- Feiling Liu
- College of Life Sciences and Resource Environment, Yichun University, Yichun, 336000, China
| | - Dianhao Guo
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhuting Yuan
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chen Chen
- College of Life Sciences and Resource Environment, Yichun University, Yichun, 336000, China
| | - Huamei Xiao
- College of Life Sciences and Resource Environment, Yichun University, Yichun, 336000, China.
- The Center for Translational Medicine, Yichun University, Yichun, 336000, China.
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