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Zang H, Guo S, Dong S, Song Y, Li K, Fan X, Qiu J, Zheng Y, Jiang H, Wu Y, Lü Y, Chen D, Guo R. Construction of a Full-Length Transcriptome of Western Honeybee Midgut Tissue and Improved Genome Annotation. Genes (Basel) 2024; 15:728. [PMID: 38927663 PMCID: PMC11202838 DOI: 10.3390/genes15060728] [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: 04/09/2024] [Revised: 05/22/2024] [Accepted: 05/26/2024] [Indexed: 06/28/2024] Open
Abstract
Honeybees are an indispensable pollinator in nature with pivotal ecological, economic, and scientific value. However, a full-length transcriptome for Apis mellifera, assembled with the advanced third-generation nanopore sequencing technology, has yet to be reported. Here, nanopore sequencing of the midgut tissues of uninoculated and Nosema ceranae-inoculated A. mellifera workers was conducted, and the full-length transcriptome was then constructed and annotated based on high-quality long reads. Next followed improvement of sequences and annotations of the current reference genome of A. mellifera. A total of 5,942,745 and 6,664,923 raw reads were produced from midguts of workers at 7 days post-inoculation (dpi) with N. ceranae and 10 dpi, while 7,100,161 and 6,506,665 raw reads were generated from the midguts of corresponding uninoculated workers. After strict quality control, 6,928,170, 6,353,066, 5,745,048, and 6,416,987 clean reads were obtained, with a length distribution ranging from 1 kb to 10 kb. Additionally, 16,824, 17,708, 15,744, and 18,246 full-length transcripts were respectively detected, including 28,019 nonredundant ones. Among these, 43,666, 30,945, 41,771, 26,442, and 24,532 full-length transcripts could be annotated to the Nr, KOG, eggNOG, GO, and KEGG databases, respectively. Additionally, 501 novel genes (20,326 novel transcripts) were identified for the first time, among which 401 (20,255), 193 (13,365), 414 (19,186), 228 (12,093), and 202 (11,703) were respectively annotated to each of the aforementioned five databases. The expression and sequences of three randomly selected novel transcripts were confirmed by RT-PCR and Sanger sequencing. The 5' UTR of 2082 genes, the 3' UTR of 2029 genes, and both the 5' and 3' UTRs of 730 genes were extended. Moreover, 17,345 SSRs, 14,789 complete ORFs, 1224 long non-coding RNAs (lncRNAs), and 650 transcription factors (TFs) from 37 families were detected. Findings from this work not only refine the annotation of the A. mellifera reference genome, but also provide a valuable resource and basis for relevant molecular and -omics studies.
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Affiliation(s)
- He Zang
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Sijia Guo
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
| | - Shunan Dong
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
| | - Yuxuan Song
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
| | - Kunze Li
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
| | - Xiaoxue Fan
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Jianfeng Qiu
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Yidi Zheng
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
| | - Haibin Jiang
- Apiculture Science Institute of Jilin Province, Jilin 132000, China; (H.J.); (Y.W.)
| | - Ying Wu
- Apiculture Science Institute of Jilin Province, Jilin 132000, China; (H.J.); (Y.W.)
| | - Yang Lü
- Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang 157000, China;
| | - Dafu Chen
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Rui Guo
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
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Tadano H, Kohno H, Takeuchi H, Kubo T. Unique spatially and temporary-regulated/sex-specific expression of a long ncRNA, Nb-1, suggesting its pleiotropic functions associated with honey bee lifecycle. Sci Rep 2024; 14:8701. [PMID: 38622193 PMCID: PMC11018616 DOI: 10.1038/s41598-024-59494-6] [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: 10/31/2023] [Accepted: 04/11/2024] [Indexed: 04/17/2024] Open
Abstract
Honey bees are social insects, and each colony member has unique morphological and physiological traits associated with their social tasks. Previously, we identified a long non-coding RNA from honey bees, termed Nb-1, whose expression in the brain decreases associated with the age-polyethism of workers and is detected in some neurosecretory cells and octopaminergic neurons, suggesting its role in the regulation of worker labor transition. Herein, we investigated its spatially and temporary-regulated/sex-specific expression. Nb-1 was expressed as an abundant maternal RNA during oogenesis and embryogenesis in both sexes. In addition, Nb-1 was expressed preferentially in the proliferating neuroblasts of the mushroom bodies (a higher-order center of the insect brain) in the pupal brains, suggesting its role in embryogenesis and mushroom body development. On the contrary, Nb-1 was expressed in a drone-specific manner in the pupal and adult retina, suggesting its role in the drone visual development and/or sense. Subcellular localization of Nb-1 in the brain during development differed depending on the cell type. Considering that Nb-1 is conserved only in Apidae, our findings suggest that Nb-1 potentially has pleiotropic functions in the expression of multiple developmental, behavioral, and physiological traits, which are closely associated with the honey bee lifecycle.
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Affiliation(s)
- Hiroto Tadano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroki Kohno
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hideaki Takeuchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Takeo Kubo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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Zafar J, Wu H, Xu Y, Lin L, Kang Z, Zhang J, Zhang R, Lu Y, Jin F, Xu X. Transcriptomic Analysis of Metarhizium anisopliae-Induced Immune-Related Long Non-Coding RNAs in Polymorphic Worker Castes of Solenopsis invicta. Int J Mol Sci 2023; 24:13983. [PMID: 37762284 PMCID: PMC10531276 DOI: 10.3390/ijms241813983] [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: 07/17/2023] [Revised: 09/03/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) represent a class of RNA molecules that do not encode proteins. Generally studied for their regulatory potential in model insects, relatively little is known about their immunoregulatory functions in different castes of eusocial insects, including Solenopsis invicta, a notoriously invasive insect pest. In the current study, we used Metarhizium anisopliae, an entomopathogenic fungus, to infect the polymorphic worker castes (Major and Minor Workers) and subjected them to RNA sequencing at different intervals (6, 24, and 48 h post-infection (hpi)). Comprehensive bioinformatic analysis identified 5719 (1869 known and 3850 novel) lncRNAs in all libraries. Genomic characteristics analysis showed that S. invicta lncRNAs exhibited structural similarities with lncRNAs from other eusocial insects, including lower exon numbers, shorter intron and exon lengths, and a lower expression profile. A comparison of lncRNAs in major and minor worker ants revealed that several lncRNAs were exclusively expressed in one worker caste and remained absent in the other. LncRNAs such as MSTRG.12029.1, XR_005575440.1 (6 h), MSTRG.16728.1, XR_005575440.1 (24 h), MSTRG.20263.41, and MSTRG.11994.5 (48 h) were only present in major worker ants, while lncRNAs such as MSTRG.8896.1, XR_005574239.1 (6 h), MSTRG.20289.8, XR_005575051.1 (24 h), MSTRG.20289.8, and MSTRG.6682.1 (48 h) were only detected in minor workers. Additionally, we performed real-time quantitative PCR and experimentally validated these findings. Functional annotation of cis-acting lncRNAs in major worker ants showed that lncRNAs targeted genes such as serine protease, trypsin, melanization protease-1, spaetzle-3, etc. In contrast, apoptosis and autophagy-related genes were identified as targets of lncRNAs in minor ants. Lastly, we identified several lncRNAs as precursors of microRNAs (miRNAs), such as miR-8, miR-14, miR-210, miR-6038, etc., indicating a regulatory relationship between lncRNAs, miRNAs, and mRNAs in antifungal immunity. These findings will serve as a genetic resource for lncRNAs in polymorphic eusocial ants and provide a theoretical basis for exploring the function of lncRNAs from a unique and novel perspective.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Fengliang Jin
- National Key Laboratory of Green Pesticide, “Belt and Road” Technology Industry and Innovation Institute for Green and Biological Control of Agricultural Pests, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (H.W.); (Y.X.); (L.L.); (Z.K.); (J.Z.); (R.Z.); (Y.L.)
| | - Xiaoxia Xu
- National Key Laboratory of Green Pesticide, “Belt and Road” Technology Industry and Innovation Institute for Green and Biological Control of Agricultural Pests, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (H.W.); (Y.X.); (L.L.); (Z.K.); (J.Z.); (R.Z.); (Y.L.)
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Mahanta DK, Bhoi TK, Komal J, Samal I, Nikhil RM, Paschapur AU, Singh G, Kumar PVD, Desai HR, Ahmad MA, Singh PP, Majhi PK, Mukherjee U, Singh P, Saini V, Shahanaz, Srinivasa N, Yele Y. Insect-pathogen crosstalk and the cellular-molecular mechanisms of insect immunity: uncovering the underlying signaling pathways and immune regulatory function of non-coding RNAs. Front Immunol 2023; 14:1169152. [PMID: 37691928 PMCID: PMC10491481 DOI: 10.3389/fimmu.2023.1169152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023] Open
Abstract
Multicellular organisms are constantly subjected to pathogens that might be harmful. Although insects lack an adaptive immune system, they possess highly effective anti-infective mechanisms. Bacterial phagocytosis and parasite encapsulation are some forms of cellular responses. Insects often defend themselves against infections through a humoral response. This phenomenon includes the secretion of antimicrobial peptides into the hemolymph. Specific receptors for detecting infection are required for the recognition of foreign pathogens such as the proteins that recognize glucans and peptidoglycans, together referred to as PGRPs and βGRPs. Activation of these receptors leads to the stimulation of signaling pathways which further activates the genes encoding for antimicrobial peptides. Some instances of such pathways are the JAK-STAT, Imd, and Toll. The host immune response that frequently accompanies infections has, however, been circumvented by diseases, which may have assisted insects evolve their own complicated immune systems. The role of ncRNAs in insect immunology has been discussed in several notable studies and reviews. This paper examines the most recent research on the immune regulatory function of ncRNAs during insect-pathogen crosstalk, including insect- and pathogen-encoded miRNAs and lncRNAs, and provides an overview of the important insect signaling pathways and effector mechanisms activated by diverse pathogen invaders.
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Affiliation(s)
- Deepak Kumar Mahanta
- Department of Entomology, Dr. Rajendra Prasad Central Agricultural University, Samastipur, Bihar, India
| | - Tanmaya Kumar Bhoi
- Forest Protection Division, Indian Council of Forestry Research and Education (ICFRE) - Arid Forest Research Institute (ICFRE-AFRI), Jodhpur, Rajasthan, India
| | - J. Komal
- Department of Entomology, Navsari Agricultural University, Navsari, Gujarat, India
| | - Ipsita Samal
- ICAR-National Research Centre on Litchi, Mushahari, Ramna, Muzaffarpur, Bihar, India
| | - R. M. Nikhil
- Division of Entomology, Indian Agricultural Research Institute, New Delhi, India
| | - Amit Umesh Paschapur
- Crop Protection Division, Indian Council of Agricultural Research (ICAR)-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand, India
| | - Gaurav Singh
- The Directorate of Research, Maharana Pratap Horticultural University, Karnal, Haryana, India
| | - P. V. Dinesh Kumar
- Department of Plant Pathology University of Agricultural Sciences, Bengaluru, Karnataka, India
| | - H. R. Desai
- Department of Entomology, Main Cotton Research Station, Navsari Agricultural University, Gujarat, India
| | - Mohammad Abbas Ahmad
- Department of Entomology, Dr. Rajendra Prasad Central Agricultural University, Samastipur, Bihar, India
| | - P. P. Singh
- Department of Entomology, Tirhut College of Agriculture, Dr. Rajendra Prasad Central Agricultural University, Samastipur, Bihar, India
| | - Prasanta Kumar Majhi
- Department of Plant Breeding and Genetics, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - U. Mukherjee
- Department of Entomology, Dr. Rajendra Prasad Central Agricultural University, Samastipur, Bihar, India
| | - Pushpa Singh
- Department of Entomology, Dr. Rajendra Prasad Central Agricultural University, Samastipur, Bihar, India
| | - Varun Saini
- Department of Entomology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Shahanaz
- Department of Entomology, College of Horticulture Mojerla, Sri Konda Laxman Telengana State Horticultural University, Wanaparthy, Telengana, India
| | - N. Srinivasa
- Department of Entomology and Agricultural Zoology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Yogesh Yele
- School of Crop Health Management Research, Council of Agricultural Research-National Institute of Biotic Stress Management (ICAR)- National Institute of Biotic Stress Management, Raipur, India
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Shen Z, Yang Q, Luo L, Li T, Ke Z, Li T, Chen J, Meng X, Xiang H, Li C, Zhou Z, Chen P, Pan G. Non-coding RNAs identification and regulatory networks in pathogen-host interaction in the microsporidia congenital infection. BMC Genomics 2023; 24:420. [PMID: 37495972 PMCID: PMC10373312 DOI: 10.1186/s12864-023-09490-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/28/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND The interaction networks between coding and non-coding RNAs (ncRNAs) including long non-coding RNA (lncRNA), covalently closed circular RNA (circRNA) and miRNA are significant to elucidate molecular processes of biological activities and interactions between host and pathogen. Congenital infection caused by vertical transmission of microsporidia N. bombycis can result in severe economic losses in the silkworm-feeding industry. However, little is known about ncRNAs that take place in the microsporidia congenital infection. Here we conducted whole-transcriptome RNA-Seq analyses to identify ncRNAs and regulatory networks for both N. bombycis and host including silkworm embryos and larvae during the microsporidia congenital infection. RESULTS A total of 4,171 mRNAs, 403 lncRNA, 62 circRNAs, and 284 miRNAs encoded by N. bombycis were identified, among which some differentially expressed genes formed cross-talk and are involved in N. bombycis proliferation and infection. For instance, a lncRNA/circRNA competing endogenous RNA (ceRNA) network including 18 lncRNAs, one circRNA, and 20 miRNAs was constructed to describe 14 key parasites genes regulation, such as polar tube protein 3 (PTP3), ricin-B-lectin, spore wall protein 4 (SWP4), and heat shock protein 90 (HSP90). Regarding host silkworm upon N. bombycis congenital infection, a total of 14,889 mRNAs, 3,038 lncRNAs, 19,039 circRNAs, and 3,413 miRNAs were predicted based on silkworm genome with many differentially expressed coding and non-coding genes during distinct developmental stages. Different species of RNAs form interacting network to modulate silkworm biological processes, such as growth, metamorphosis and immune responses. Furthermore, a lncRNA/circRNA ceRNA network consisting of 140 lncRNAs, five circRNA, and seven miRNAs are constructed hypothetically to describe eight key host genes regulation, such as Toll-6, Serpin-6, inducible nitric oxide synthase (iNOS) and Caspase-8. Notably, cross-species analyses indicate that parasite and host miRNAs play a vital role in pathogen-host interaction in the microsporidia congenital infection. CONCLUSION This is the first comprehensive pan-transcriptome study inclusive of both N. bombycis and its host silkworm with a specific focus on the microsporidia congenital infection, and show that ncRNA-mediated regulation plays a vital role in the microsporidia congenital infection, which provides a new insight into understanding the basic biology of microsporidia and pathogen-host interaction.
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Affiliation(s)
- Zigang Shen
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, People's Republic of China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China
| | - Qiong Yang
- Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, People's Republic of China
| | - Lie Luo
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China
| | - Tangxin Li
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China
| | - Zhuojun Ke
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China
| | - Tian Li
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China
| | - Jie Chen
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China
| | - Xianzhi Meng
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China
| | - Heng Xiang
- College of Animal Science and Technology, Southwest University, Chongqing, People's Republic of China
| | - Chunfeng Li
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China
| | - Zeyang Zhou
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China
- College of Life Sciences, Chongqing Normal University, Chongqing, People's Republic of China
| | - Ping Chen
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China.
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, People's Republic of China.
| | - Guoqing Pan
- State Key Laboratory of Resource Insects, Southwest University, Tiansheng Street, Chongqing, 400715, People's Republic of China.
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, People's Republic of China.
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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: 4] [Impact Index Per Article: 4.0] [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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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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Unveiling the circRNA-Mediated Immune Responses of Western Honey Bee Larvae to Ascosphaera apis Invasion. Int J Mol Sci 2022; 24:ijms24010613. [PMID: 36614055 PMCID: PMC9820429 DOI: 10.3390/ijms24010613] [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: 11/23/2022] [Revised: 12/14/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022] Open
Abstract
Western honey bee (Apis mellifera), a eusocial insect with a superior economic and ecological value, is widely used in the beekeeping industry throughout the world. As a new class of non-coding RNAs (ncRNAs), circular RNAs (circRNAs) participate in the modulation of considerable biological processes, such as the immune response via diverse manners. Here, the identification, characteristic investigation, and molecular verification of circRNAs in the Apis mellifera ligustica larval guts were conducted, and the expression pattern of larval circRNAs during the Ascosphaera apis infection was analyzed, followed by the exploration of the potential regulatory part of differentially expressed circRNAs (DEcircRNAs) in host immune responses. A total of 2083 circRNAs in the larval guts of A. m. ligustcia were identified, with a length distribution ranging from 106 nt to 92,798 nt. Among these, exonic circRNAs were the most abundant type and LG1 was the most distributed chromosome. Additionally, 25, 14, and 30 up-regulated circRNAs as well as 26, 25, and 62 down-regulated ones were identified in the A. apis-inoculated 4-, 5-, and 6-day-old larval guts in comparison with the corresponding un-inoculated larval guts. These DEcircRNAs were predicted to target 35, 70, and 129 source genes, which were relative to 12, 23, and 20 GO terms as well as 11, 10, and 27 KEGG pathways, including 5 cellular and humoral immune pathways containing apoptosis, autophagy, endocytosis, MAPK, Toll, and Imd signaling pathways. Furthermore, complex competing endogenous RNA (ceRNA) regulatory networks were detected to be formed among DEcircRNAs, DEmiRNAs, and DEmRNAs. The Target DEmRNAs were engaged in 24, 20, and 25 functional terms as well as 62, 80, and 159 pathways, including several vital immune defense-associated pathways, namely the lysosome, endocytosis, phagosome, autophagy, apoptosis, MAPK, Jak-STAT, Toll, and Imd signaling pathways. Finally, back-splicing sites within 15 circRNAs and the difference in the 9 DEcircRNAs' expression between un-inoculated and A. apis-inoculated larval guts were confirmed utilizing molecular methods. These findings not only enrich our understanding of bee host-fungal pathogen interactions, but also lay a foundation for illuminating the mechanism underlying the DEcircRNA-mediated immune defense of A. m. ligustica larvae against A. apis invasion.
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9
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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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10
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Zhao X, Liu Y. Current Knowledge on Bee Innate Immunity Based on Genomics and Transcriptomics. Int J Mol Sci 2022; 23:ijms232214278. [PMID: 36430757 PMCID: PMC9692672 DOI: 10.3390/ijms232214278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/28/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
As important pollinators, bees play a critical role in maintaining the balance of the ecosystem and improving the yield and quality of crops. However, in recent years, the bee population has significantly declined due to various pathogens and environmental stressors including viruses, bacteria, parasites, and increased pesticide application. The above threats trigger or suppress the innate immunity of bees, their only immune defense system, which is essential to maintaining individual health and that of the colony. In addition, bees can be divided into solitary and eusocial bees based on their life traits, and eusocial bees possess special social immunities, such as grooming behavior, which cooperate with innate immunity to maintain the health of the colony. The omics approach gives us an opportunity to recognize the distinctive innate immunity of bees. In this regard, we summarize innate bee immunity from a genomic and transcriptomic perspective. The genetic characteristics of innate immunity were revealed by the multiple genomes of bees with different kinds of sociality, including honeybees, bumblebees, wasps, leaf-cutter bees, and so on. Further substantial transcriptomic data of different tissues from diverse bees directly present the activation or suppression of immune genes under the infestation of pathogens or toxicity of pesticides.
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Affiliation(s)
- Xiaomeng Zhao
- College of Engineering, Hebei Normal University, Shijiazhuang 050024, China
| | - Yanjie Liu
- Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
- Correspondence:
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11
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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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12
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Chen H, Fan X, Zhang W, Ye Y, Cai Z, Zhang K, Zhang K, Fu Z, Chen D, Guo R. Deciphering the CircRNA-Regulated Response of Western Honey Bee ( Apis mellifera) Workers to Microsporidian Invasion. BIOLOGY 2022; 11:biology11091285. [PMID: 36138764 PMCID: PMC9495892 DOI: 10.3390/biology11091285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/21/2022] [Accepted: 08/25/2022] [Indexed: 05/13/2023]
Abstract
Vairimorpha ceranae is a widespread fungal parasite of adult honey bees that leads to a serious disease called nosemosis. Circular RNAs (circRNAs) are newly discovered non-coding RNAs (ncRNAs) that regulate biological processes such as immune defense and development. Here, 8199 and 8711 circRNAs were predicted from the midguts of Apis mellifera ligustica workers at 7 d (Am7T) and 10 d (Am10T) after inoculation (dpi) with V. ceranae spores. In combination with transcriptome data from corresponding uninoculated midguts (Am7CK and Am10CK), 4464 circRNAs were found to be shared by these four groups. Additionally, 16 circRNAs were highly conserved among A. m. ligustica, Apis cerana cerana, and Homo sapiens. In the Am7CK vs. Am7T (Am10CK vs. Am10T) comparison group, 168 (306) differentially expressed circRNAs (DEcircRNAs) were identified. RT-qPCR results showed that the expression trend of eight DEcircRNAs was consistent with that in the transcriptome datasets. The source genes of DEcircRNAs in Am7CK vs. Am7T (Am10CK vs. Am10T) were engaged in 27 (35) GO functional terms, including 1 (1) immunity-associated terms. Moreover, the aforementioned source genes were involved in three cellular immune-related pathways. Moreover, 86 (178) DEcircRNAs in workers' midguts at 7 (10) dpi could interact with 75 (103) miRNAs, further targeting 215 (305) mRNAs. These targets were associated with cellular renewal, cellular structure, carbohydrate and energy metabolism, and cellular and humoral immunity. Findings in the present study unraveled the mechanism underlying circRNA-mediated immune responses of western honey bee workers to V. ceranae invasion, but also provided new insights into host-microsporidian interaction during nosemosis.
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Affiliation(s)
- Huazhi Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Xiaoxue Fan
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Wende Zhang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Yaping Ye
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Zongbing Cai
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Kaiyao Zhang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Kuihao Zhang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Zhongmin Fu
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
- Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Dafu Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
- Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Rui Guo
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 35002, China
- Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou 35002, China
- Correspondence: ; Tel./Fax: +86-0591-8764-0197
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13
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Moure UAE, Tan T, Sha L, Lu X, Shao Z, Yang G, Wang Y, Cui H. Advances in the Immune Regulatory Role of Non-Coding RNAs (miRNAs and lncRNAs) in Insect-Pathogen Interactions. Front Immunol 2022; 13:856457. [PMID: 35464405 PMCID: PMC9020863 DOI: 10.3389/fimmu.2022.856457] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/10/2022] [Indexed: 11/30/2022] Open
Abstract
Insects are by far the most abundant and diverse living organisms on earth and are frequently prone to microbial attacks. In other to counteract and overcome microbial invasions, insects have in an evolutionary way conserved and developed immune defense mechanisms such as Toll, immune deficiency (Imd), and JAK/STAT signaling pathways leading to the expression of antimicrobial peptides. These pathways have accessory immune effector mechanisms, such as phagocytosis, encapsulation, melanization, nodulation, RNA interference (RNAi), lysis, autophagy, and apoptosis. However, pathogens evolved strategies that circumvent host immune response following infections, which may have helped insects further sophisticate their immune response mechanisms. The involvement of ncRNAs in insect immunity is undeniable, and several excellent studies or reviews have investigated and described their roles in various insects. However, the functional analyses of ncRNAs in insects upon pathogen attacks are not exhaustive as novel ncRNAs are being increasingly discovered in those organisms. This article gives an overview of the main insect signaling pathways and effector mechanisms activated by pathogen invaders and summarizes the latest findings of the immune modulation role of both insect- and pathogen-encoded ncRNAs, especially miRNAs and lncRNAs during insect–pathogen crosstalk.
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Affiliation(s)
- Ulrich Aymard Ekomi Moure
- Affiliated Hospital of Southwest University, the Ninth People's Hospital of Chongqing, Chongqing, China.,Medical Research Institute, Southwest University, Chongqing, China
| | - Tingshan Tan
- Affiliated Hospital of Southwest University, the Ninth People's Hospital of Chongqing, Chongqing, China
| | - Lin Sha
- Affiliated Hospital of Southwest University, the Ninth People's Hospital of Chongqing, Chongqing, China
| | - Xiaoqin Lu
- Affiliated Hospital of Southwest University, the Ninth People's Hospital of Chongqing, Chongqing, China
| | - Zhi Shao
- Affiliated Hospital of Southwest University, the Ninth People's Hospital of Chongqing, Chongqing, China
| | - Guang Yang
- Affiliated Hospital of Southwest University, the Ninth People's Hospital of Chongqing, Chongqing, China
| | - Yi Wang
- Affiliated Hospital of Southwest University, the Ninth People's Hospital of Chongqing, Chongqing, China.,Department of Gastrointestinal Surgery, the Ninth People's Hospital of Chongqing, Chongqing, China
| | - Hongjuan Cui
- Medical Research Institute, Southwest University, Chongqing, China.,State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
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14
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Fan Y, Wang J, Yu K, Zhang W, Cai Z, Sun M, Hu Y, Zhao X, Xiong C, Niu Q, Chen D, Guo R. Comparative Transcriptome Investigation of Nosema ceranae Infecting Eastern Honey Bee Workers. INSECTS 2022; 13:insects13030241. [PMID: 35323539 PMCID: PMC8952433 DOI: 10.3390/insects13030241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 02/04/2023]
Abstract
Simple Summary At present, interaction between Nosema ceranae and Apis cerana is poorly understood, though A. cerana is the original host for N. ceranae. Here, comparative investigation was conducted using transcriptome data from N. ceranae infecting Apis cerana cerana workers at seven days post inoculation (dpi) and 10 dpi (NcT1 and NcT2 groups) as well as N. ceranae spores (NcCK group). There were 1411, 604, and 38 DEGs identified in NcCK vs. NcT1, NcCK vs. NcT2, and NcT1 vs. NcT2 comparison groups. Additionally, 10 upregulated genes and nine downregulated ones were shared by above-mentioned comparison groups. GO classification and KEGG pathway analysis suggested that these DEGs were engaged in a number of key functional terms and pathways such as cell part and glycolysis. Further analysis indicated that most of virulence factor-encoding genes were upregulated, while a few were downregulated during the fungal infection. Findings in this current work provide a basis for clarifying the molecular mechanism udnerlying N. ceranae infection and host-microsporidian interaction during bee nosemosis. Abstract Apis cerana is the original host for Nosema ceranae, a widespread fungal parasite resulting in honey bee nosemosis, which leads to severe losses to the apiculture industry throughout the world. However, knowledge of N. ceranae infecting eastern honey bees is extremely limited. Currently, the mechanism underlying N. ceranae infection is still largely unknown. Based on our previously gained high-quality transcriptome datasets derived from N. ceranae spores (NcCK group), N. ceranae infecting Apis cerana cerana workers at seven days post inoculation (dpi) and 10 dpi (NcT1 and NcT2 groups), comparative transcriptomic investigation was conducted in this work, with a focus on virulence factor-associated differentially expressed genes (DEGs). Microscopic observation showed that the midguts of A. c. cerana workers were effectively infected after inoculation with clean spores of N. ceranae. In total, 1411, 604, and 38 DEGs were identified from NcCK vs. NcT1, NcCK vs. NcT2, and NcT1 vs. NcT2 comparison groups. Venn analysis showed that 10 upregulated genes and nine downregulated ones were shared by the aforementioned comparison groups. The GO category indicated that these DEGs were involved in a series of functional terms relevant to biological process, cellular component, and molecular function such as metabolic process, cell part, and catalytic activity. Additionally, KEGG pathway analysis suggested that the DEGs were engaged in an array of pathways of great importance such as metabolic pathway, glycolysis, and the biosynthesis of secondary metabolites. Furthermore, expression clustering analysis demonstrated that the majority of genes encoding virulence factors such as ricin B lectins and polar tube proteins displayed apparent upregulation, whereas a few virulence factor-associated genes such as hexokinase gene and 6-phosphofructokinase gene presented downregulation during the fungal infection. Finally, the expression trend of 14 DEGs was confirmed by RT-qPCR, validating the reliability of our transcriptome datasets. These results together demonstrated that an overall alteration of the transcriptome of N. ceranae occurred during the infection of A. c. cerana workers, and most of the virulence factor-related genes were induced to activation to promote the fungal invasion. Our findings not only lay a foundation for clarifying the molecular mechanism underlying N. ceranae infection of eastern honey bee workers and microsporidian–host interaction.
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Affiliation(s)
- Yuanchan Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.F.); (J.W.); (K.Y.); (W.Z.); (Z.C.); (M.S.); (Y.H.); (X.Z.); (C.X.)
| | - Jie Wang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.F.); (J.W.); (K.Y.); (W.Z.); (Z.C.); (M.S.); (Y.H.); (X.Z.); (C.X.)
| | - Kejun Yu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.F.); (J.W.); (K.Y.); (W.Z.); (Z.C.); (M.S.); (Y.H.); (X.Z.); (C.X.)
| | - Wende Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.F.); (J.W.); (K.Y.); (W.Z.); (Z.C.); (M.S.); (Y.H.); (X.Z.); (C.X.)
| | - Zongbing Cai
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.F.); (J.W.); (K.Y.); (W.Z.); (Z.C.); (M.S.); (Y.H.); (X.Z.); (C.X.)
| | - Minghui Sun
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.F.); (J.W.); (K.Y.); (W.Z.); (Z.C.); (M.S.); (Y.H.); (X.Z.); (C.X.)
| | - Ying Hu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.F.); (J.W.); (K.Y.); (W.Z.); (Z.C.); (M.S.); (Y.H.); (X.Z.); (C.X.)
| | - Xiao Zhao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.F.); (J.W.); (K.Y.); (W.Z.); (Z.C.); (M.S.); (Y.H.); (X.Z.); (C.X.)
| | - Cuiling Xiong
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.F.); (J.W.); (K.Y.); (W.Z.); (Z.C.); (M.S.); (Y.H.); (X.Z.); (C.X.)
| | - Qingsheng Niu
- Jilin Province Institute of Apicultural Science, Jilin 132000, China;
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.F.); (J.W.); (K.Y.); (W.Z.); (Z.C.); (M.S.); (Y.H.); (X.Z.); (C.X.)
- Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (D.C.); (R.G.); Tel./Fax: +86-0591-87640197 (R.G.)
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.F.); (J.W.); (K.Y.); (W.Z.); (Z.C.); (M.S.); (Y.H.); (X.Z.); (C.X.)
- Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (D.C.); (R.G.); Tel./Fax: +86-0591-87640197 (R.G.)
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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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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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Feng W, Huang J, Zhang Z, Nie H, Lin Y, Li Z, Su S. Understanding of Waggle Dance in the Honey Bee (Apis mellifera) from the Perspective of Long Non-Coding RNA. INSECTS 2022; 13:insects13020111. [PMID: 35206685 PMCID: PMC8878125 DOI: 10.3390/insects13020111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/08/2022] [Accepted: 01/11/2022] [Indexed: 01/03/2023]
Abstract
The ethological study of dance behaviour has yielded some findings since Karl Von Frisch discovered and interpreted the ‘dance language’ in the honey bee. However, the function and role of long non-coding RNAs on dance behaviour are hardly known until now. In this study, the differential expression patterns of lncRNAs in the brains of waggling dancers and non-dancing bees were analysed by RNA sequencing. Furthermore, lncRNA-mRNA association analysis was constructed to decipher the waggle dance. The results of RNA sequencing indicated that a total of 2877 lncRNAs and 9647 mRNAs were detected from honey bee brains. Further comparison analysis displayed that two lncRNAs, MSTRG.6803.3 and XR_003305156.1, may be involved in the waggle dance. The lncRNA-mRNA association analysis showed that target genes of differentially expressed lncRNAs in the brains between waggling dancers and non-dancing bees were mainly annotated in biological processes related to metabolic process, signalling and response to stimulus and in molecular function associated with signal transducer activity, molecular transducer activity and binding. Nitrogen metabolism was likely implicated in the modulation of the waggle dance. Our findings contribute to further understanding the occurrence and development of waggle dance.
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Affiliation(s)
- Wangjiang Feng
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.F.); (J.H.); (H.N.); (Y.L.)
| | - Jingnan Huang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.F.); (J.H.); (H.N.); (Y.L.)
| | - Zhaonan Zhang
- Laboratory of Evolution and Diversity Biology (EDB), UMR5174, University Toulouse III Paul Sabatier, CNRS, 31062 Toulouse, France;
| | - Hongyi Nie
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.F.); (J.H.); (H.N.); (Y.L.)
| | - Yan Lin
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.F.); (J.H.); (H.N.); (Y.L.)
| | - Zhiguo Li
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.F.); (J.H.); (H.N.); (Y.L.)
- Correspondence: (Z.L.); (S.S.); Tel.: +86-150-0591-7215 (Z.L.); +86-136-6500-5782 (S.S.)
| | - Songkun Su
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.F.); (J.H.); (H.N.); (Y.L.)
- Correspondence: (Z.L.); (S.S.); Tel.: +86-150-0591-7215 (Z.L.); +86-136-6500-5782 (S.S.)
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18
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Xing W, Zhou D, Long Q, Sun M, Guo R, Wang L. Immune Response of Eastern Honeybee Worker to Nosema ceranae Infection Revealed by Transcriptomic Investigation. INSECTS 2021; 12:insects12080728. [PMID: 34442293 PMCID: PMC8396959 DOI: 10.3390/insects12080728] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/29/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Currently, knowledge regarding Apis cerana–Nosema ceranae interaction is very limited, though A. cerana is the original host of N. ceranae. Apis cerana cerana is a subspecies of A. cerana and a major bee species used in the beekeeping industry in China and other countries. Here, the effective infection of A. c. cerana workers by N. ceranae was verified, followed by transcriptomic investigation of host responses. Furthermore, immune responses between A. c. cerana and Apis mellifera ligustica were deeply compared and discussed. In total, 1127 and 957 N. ceranae-responsive genes were identified in the infected midguts at 7 d post-inoculation (dpi) and 10 dpi, respectively. Additionally, DEGs in workers’ midguts at both 7 dpi and 10 dpi were associated with six cellular immune pathways and three humoral immune pathways. Noticeably, one up-regulated gene was enriched in the NF-κB signaling pathway in the midgut at 10 dpi. Further analysis indicated that different cellular and humoral immune responses were employed by A. c. cerana and A. m. ligustica workers to combat N. ceranae. Our findings provide a foundation for clarifying the mechanisms regulating the immune response of A. c. cerana workers to N. ceranae invasion and developing new approaches to control bee microsporidiosis. Abstract Here, a comparative transcriptome investigation was conducted based on high-quality deep sequencing data from the midguts of Apis cerana cerana workers at 7 d post-inoculation (dpi) and 10 dpi with Nosema ceranae and corresponding un-inoculated midguts. PCR identification and microscopic observation of paraffin sections confirmed the effective infection of A. c. cerana worker by N. ceranae. In total, 1127 and 957 N. ceranae-responsive genes were identified in the infected midguts at 7 dpi and 10 dpi, respectively. RT-qPCR results validated the reliability of our transcriptome data. GO categorization indicated the differentially expressed genes (DEGs) were respectively engaged in 34 and 33 functional terms associated with biological processes, cellular components, and molecular functions. Additionally, KEGG pathway enrichment analysis showed that DEGs at 7 dpi and 10 dpi could be enriched in 231 and 226 pathways, respectively. Moreover, DEGs in workers’ midguts at both 7 dpi and 10 dpi were involved in six cellular immune pathways such as autophagy and phagosome and three humoral immune pathways such as the Toll/Imd signaling pathway and Jak-STAT signaling pathway. In addition, one up-regulated gene (XM_017055397.1) was enriched in the NF-κB signaling pathway in the workers’ midgut at 10 dpi. Further investigation suggested the majority of these DEGs were engaged in only one immune pathway, while a small number of DEGs were simultaneously involved in two immune pathways. These results together demonstrated that the overall gene expression profile in host midgut was altered by N. ceranae infection and some of the host immune pathways were induced to activation during fungal infection, whereas some others were suppressed via host–pathogen interaction. Our findings offer a basis for clarification of the mechanism underlying the immune response of A. c. cerana workers to N. ceranae infection, but also provide novel insights into eastern honeybee-microsporodian interaction.
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Affiliation(s)
- Wenhao Xing
- College of Animal Science, Guizhou University, Guiyang 550025, China;
| | - Dingding Zhou
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (D.Z.); (Q.L.); (M.S.)
| | - Qi Long
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (D.Z.); (Q.L.); (M.S.)
| | - Minghui Sun
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (D.Z.); (Q.L.); (M.S.)
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (D.Z.); (Q.L.); (M.S.)
- Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: ; Tel./Fax: +86-0591-8764-0197
| | - Limei Wang
- Dongying Vocational Institute, Dongying 257000, China;
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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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20
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Zhou Y, Yang P, Xie S, Shi M, Huang J, Wang Z, Chen X. Comparative Transcriptome Analysis Reveals Sex-Based Differences during the Development of the Adult Parasitic Wasp Cotesia vestalis (Hymenoptera: Braconidae). Genes (Basel) 2021; 12:genes12060896. [PMID: 34200644 PMCID: PMC8228208 DOI: 10.3390/genes12060896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 12/19/2022] Open
Abstract
The endoparasitic wasp Cotesia vestalis is an important biological agent for controlling the population of Plutella xylostella, a major pest of cruciferous crops worldwide. Though the genome of C. vestalis has recently been reported, molecular mechanisms associated with sexual development have not been comprehensively studied. Here, we combined PacBio Iso-Seq and Illumina RNA-Seq to perform genome-wide profiling of pharate adult and adult development of male and female C. vestalis. Taking advantage of Iso-Seq full-length reads, we identified 14,466 novel transcripts as well as 8770 lncRNAs, with many lncRNAs showing a sex- and stage-specific expression pattern. The differentially expressed gene (DEG) analyses showed 2125 stage-specific and 326 sex-specific expressed genes. We also found that 4819 genes showed 11,856 alternative splicing events through combining the Iso-Seq and RNA-Seq data. The results of comparative analyses showed that most genes were alternatively spliced across developmental stages, and alternative splicing (AS) events were more prevalent in females than in males. Furthermore, we identified six sex-determining genes in this parasitic wasp and verified their sex-specific alternative splicing profiles. Specifically, the characterization of feminizer and doublesex splicing between male and female implies a conserved regulation mechanism of sexual development in parasitic wasps.
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Affiliation(s)
- Yuenan Zhou
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
| | - Pei Yang
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
| | - Shuang Xie
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
| | - Min Shi
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
| | - Jianhua Huang
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Lab of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Zhizhi Wang
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, China
- Correspondence: (Z.W.); (X.C.)
| | - Xuexin Chen
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Lab of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou 310058, China
- Correspondence: (Z.W.); (X.C.)
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21
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Chen X, Lai H, Li R, Yao Y, Liu J, Yuan S, Fu S, Hu X, Guo J. Character changes and Transcriptomic analysis of a cassava sexual Tetraploid. BMC PLANT BIOLOGY 2021; 21:188. [PMID: 33874893 PMCID: PMC8056498 DOI: 10.1186/s12870-021-02963-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Cassava (Manihot esculenta Crantz) is an important food crop known for its high starch content. Polyploid breeding is effective in its genetic improvement, and use of 2n gametes in sexual polyploid breeding is one of the potential methods for cassava breeding and improvement. In our study, the cassava sexual tetraploid (ST), which carries numerous valuable traits, was successfully generated by hybridizing 2n female gametes SC5 (♀) and 2n male gametes SC10 (♂). However, the molecular mechanisms remain unclear. To understand these underlying molecular mechanisms behind the phenotypic alterations and heterosis in ST plants, we investigated the differences in gene expression between polyploids and diploids by determining the transcriptomes of the ST plant and its parents during the tuber root enlargement period. We also compared the characters and transcriptomes of the ST plant with its parents. RESULTS The ST plant was superior in plant height, stem diameter, leaf area, petiole length, plant weight, and root weight than the parent plants, except the leaf number, which was lower. The number of starch granules was higher in the roots of ST plants than those in the parent plants after five months (tuber root enlargement period), which could be due to a higher leaf net photosynthetic rate leading to early filling of starch granules. Based on transcriptome analysis, we identified 2934 and 3171 differentially expressed genes (DEGs) in the ST plant as compared to its female and male parents, respectively. Pathway enrichment analyses revealed that flavonoid biosynthesis and glycolysis/gluconeogenesis were significantly enriched in the ST plants, which might contribute to the colors of petiole (purple-red), root epidermis (dark brown), and tuber starch accumulation, respectively. CONCLUSIONS After sexual polyploidization, the phenotype of ST has changed significantly in comparison to their diploid parents, mainly manifest as enlarged biomass, yield, early starch filling, deep colored petiole and root epidermis. The tetraploid plants were also mature early due to early starch grain filling. Owing to enriched flavonoid biosynthesis and glycolysis/gluconeogenesis, they are possibly resistant to adversity stresses and provide better yield, respectively.
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Affiliation(s)
- Xia Chen
- Agricultural College of Hainan University, Haikou, 571104 China
| | - Hanggui Lai
- Agricultural College of Hainan University, Haikou, 571104 China
| | - Ruimei Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 China
| | - Yuan Yao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 China
| | - Jiao Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 China
| | - Shuai Yuan
- Agricultural College of Hainan University, Haikou, 571104 China
| | - Shaoping Fu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 China
| | - Xinwen Hu
- Agricultural College of Hainan University, Haikou, 571104 China
| | - Jianchun Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 China
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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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Hong F, Mo SH, Lin XY, Niu J, Yin J, Wei D. The PacBio Full-Length Transcriptome of the Tea Aphid as a Reference Resource. Front Genet 2020; 11:558394. [PMID: 33304379 PMCID: PMC7693467 DOI: 10.3389/fgene.2020.558394] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 10/09/2020] [Indexed: 12/30/2022] Open
Abstract
The tea aphid, Aphis aurantii, has become one of the destructive pests in tea plantations in the tropics and subtropics. Very few functional studies have so far focused on the developmental and reproductive biology at a molecular level, because of the lack of comprehensive genetic information. Full-length transcriptomes represent a very highly efficient approach to obtain reference gene sequences in non-model insects. In the present study, the transcriptome of A. aurantii was comprehensively sequenced using PacBio Iso-Seq technology. A total of 46.8 Gb nucleotides and 15,938 non-redundant full-length transcripts were obtained, 13,498 (84.69%) of which were annotated into seven databases. Of these transcripts, 2,029 alternative splicing events and 15,223 simple sequence repeats were detected. Among these transcripts, 4,571 (28.68%) and 11,367 (71.32%) were long non-coding RNAs (lncRNAs) and protein-coding genes, respectively. Five hundred and ninety transcription factors were detected. The first full-length transcriptome represents a significant increase in the known genetic information of A. aurantii. It will assist the future functional study of genes involved in its development and reproduction.
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Affiliation(s)
- Feng Hong
- College of Agriculture, Xinyang Agriculture and Forestry University, Xinyang, China
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Si-Hua Mo
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Xing-Yu Lin
- College of Agriculture, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Jinzhi Niu
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jian Yin
- College of Agriculture, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Dong Wei
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
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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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Li WJ, Song YJ, Han HL, Xu HQ, Wei D, Smagghe G, Wang JJ. Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett). BMC Genomics 2020; 21:600. [PMID: 32867696 PMCID: PMC7457495 DOI: 10.1186/s12864-020-07014-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are involved in many fundamental biological processes, such as transcription regulation, protein degradation, and cell differentiation. Information on lncRNA in the melon fly, Zeugodacus cucurbitae (Coquillett) is currently limited. Results We constructed 24 RNA-seq libraries from eight tissues (midgut, Malpighian tubules, fat body, ovary, and testis) of Z. cucurbitae adults. A total of 3124 lncRNA transcripts were identified. Among those, 1464 were lincRNAs, 1037 were intronic lncRNAs, 301 were anti-sense lncRNAs, and 322 were sense lncRNAs. The majority of lncRNAs contained two exons and one isoform. Differentially expressed lncRNAs were analyzed between tissues, and Malpighian tubules versus testis had the largest number. Some lncRNAs exhibited strong tissue specificity. Specifically expressed lncRNAs were identified and filtered in tissues of female and male Z. cucurbitae based on their expression levels. Four midgut-specific lncRNAs were validated by quantitative real-time polymerase chain reaction (RT-qPCR), and the data were consistent with RNA-seq data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of targets of midgut-specific lncRNAs indicated an enrichment of the metabolic process. Conclusions This was the first systematic identification of lncRNA in the melon fly. Expressions of lncRNAs in multiple adult tissues were evaluated by quantitative transcriptomic analysis. These qualitative and quantitative analyses of lncRNAs, especially the tissue-specific lncRNAs in Z. cucurbitae, provide useful data for further functional studies.
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Affiliation(s)
- Wei-Jun Li
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, 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
| | - Yu-Jia Song
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, 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
| | - Hong-Liang Han
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, 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
| | - Hui-Qian Xu
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, 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
| | - Dong Wei
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, 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
| | - Guy Smagghe
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, 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. .,Department of Plants and Crops, Ghent University, 9000, Ghent, Belgium.
| | - Jin-Jun Wang
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, 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.
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Chen H, Du Y, Xiong C, Zheng Y, Chen D, Guo R. A comprehensive transcriptome data of normal and Nosema ceranae-stressed midguts of Apis mellifera ligustica workers. Data Brief 2019; 26:104349. [PMID: 31516938 PMCID: PMC6727036 DOI: 10.1016/j.dib.2019.104349] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 11/24/2022] Open
Abstract
Honeybees are pivotal pollinators of crops and wild flora, and of great importance in supporting critical ecosystem balance. Nosema ceranae, a unicellular fungal parasite that infects midgut epithelial cells of honeybees, can dramatically reduce honeybee population and productivity. Here, midguts of Apis mellifera ligustica workers at 7 d and 10 d post inoculation (dpi) with sucrose solution (Ac7CK and Ac10CK) and midguts at 7 dpi and 10 dpi with sucrose solution containing N. ceranae spores (Ac7T and Ac10T) were sequenced using strand-specific cDNA library construction and next-generation sequencing. A total of 1956129858 raw reads were gained in this article, and after quality control, 1946489304 high-quality clean reads with a mean Q30 of 93.82% were obtained. The rRNA-removed clean reads were then aligned to the reference genome of Apis mellifera with TopHat2. For more insight please see “Genome-wide identification of long non-coding RNAs and their regulatory networks involved in Apis mellifera ligustica response to Nosema ceranae infection” [1]. Raw data were deposited in NCBI Sequence Read Archive (SRA) database under the BioProject number PRJNA406998. These data can be used for comparative analysis to identify differentially expressed coding RNAs and non-coding RNAs involved in A. m. ligustica responses to N. ceranae stress, and for investigation of molecular mechanisms regulating host N. ceranae -response.
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