scholarly journals Strand-specific cDNA library-based RNA sequencing dataset of un-infected and Ascosphaera apis-infected larval guts of Apis cerana cerana

2020 ◽  
Author(s):  
Huazhi Chen ◽  
Zhiwei Zhu ◽  
Jie Wang ◽  
Yuanchan Fan ◽  
Haibin Jiang ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Reference Genome ◽  
Apis Cerana ◽  
Gc Content ◽  
Current Data ◽  
Apis Cerana Cerana ◽  
List Type ◽  
Ascosphaera Apis ◽  
Intergenic Regions

ABSTRACTApis cerana cerana is a subspecies of eastern honeybee, Apis cerana. Ascosphaera apis is a widespread fungal pathogen of honeybee, leading to chalkbrood, which results in heavy losses for beekeeping industry. In this article, 4-, 5-, and 6-day-old larval guts of un-infected (AcCK1, AcCK2, and AcCK3) and A. apis-infected A. c. cerana (AcT1, AcT2, and AcT3) were sequenced by next generation sequencing. Totally, 73830148, 96586212, 94552744, 76672564, 90954858, and 83418832 raw reads were respectively produced from AcCK1, AcCK2, AcCK3, AcT1, AcT2, and AcT3. The sequencing depth was enough to detect all expressed genes. After strict quality control, 73775592, 96513798, 94495000, 76593924, 90870608 and 83339288 clean reads were obtained, with a mean GC content of 48.54%. Additionally, average Q20 and Q30 for aforementioned six groups were 98.10% and 94.36%, respectively. Moreover, 45302685, 65872823, 52709987, 49947838, 56476339, and 42657156 clean reads from above-mentioned six groups were mapped to the reference genome of Apis cerana, respectively. In addition, exons were the most abundant regions in reference genome mapped by clean reads, followed by intergenic regions and introns. Our data presented here can be used to identify long non-coding RNAs (lncRNAs), circlular RNAs (circRNAs), mRNAs and their regulatory networks engaged in response of eastern honeybee larvae to A. apis infection, and decipher molecular mechanisms underlying host-pathogen interaction.Value of the DataThe current data can be used for exploration of mRNAs, lncRNAs, circRNAs and their competing endogenous RNA (ceRNA) networks engaged in response of A. c. cerana larvae to A. apis infection.This data provides a valuable genetic resource for better understanding non-coding RNA-mediated cross-kingdom regulation of eastern honey larvae to A. apis.The accessible data offers novel insights into understanding the molecular mechanism underlying interaction between eastern honeybee larvae and A. apis.

scholarly journals MeRIP-seq and RNA-seq data of mycelium and spore of Ascosphaera apis, a widespread bee fungal pathogen

2020 ◽  
Author(s):  
Yu Du ◽  
Haibin Jiang ◽  
Zhiwei Zhu ◽  
Jie Wang ◽  
Huazhi Chen ◽  
...  
Keyword(s):  
Fungal Pathogen ◽  
Rna Isolation ◽  
Transcript Level ◽  
Current Data ◽  
List Type ◽  
Rna Seq ◽  
Ascosphaera Apis ◽  
Bee Health ◽  
Intergenic Regions

ABSTRACTAscosphaera apis is widespread fungal pathogen of honeybee larvae, causing chalkbrood, a chronic disease that weakens bee health and colony productivity. In this article, mecylia and spores of A. apis were respectively purified followed by RNA isolation, cDNA library construction, MeRIP-seq and RNA-seq. A total of 62,551,172, 41,773,158, 49,535,092 and 61,569,610 raw reads were produced from Aam_IP, Aas_IP, Aam_input and Aas_input groups, respectively. After quality control, 58,484,368, 37,381,432, 44,655,434 and 58,739,742 clean reads were obtained. Furthermore, 47,706,205, 31,356,690, 35,259,810 and 44,319,061 clean reads were mapped to the reference genome of A. apis, including 39,337,036, 26,731,957, 31,987,396 and 40,017,855 unique mapped reads, and 8,369,169, 4,624,733, 3,272,414 and 4,301,206 multiple mapped reads. Among them, 96.31%, 96.51%, 96.82% and 97.11% of clean reads were mapped to exons; 2.09%, 2.31%,1.83% and 1.81% to introns; 1.60%, 1.18%, 1.35% and 1.08% to intergenic regions.Value of the dataThe data can be used to investigate the relationship between the m6A modification extent and the transcript level in the A. apis transcriptome.This dataset contributes to transcriptome-wide characterization of the m6A distributing patterns in mRNAs and non-coding RNAs in A. apis mycelium and spore.Current data benefits new functions of m6A modification in the transcripts extensively modified by m6A in A. apis mycelium and spore.Our data could be used to characterize differential patterns of the m6A methylation between mycelium and spore of A. apis.

scholarly journals Whole transcriptome data of uninfected and Nosema ceranae-infected midguts of eastern honeybee workers

2020 ◽  
Author(s):  
Huazhi Chen ◽  
Dingding Zhou ◽  
Yu Du ◽  
Cuiling Xiong ◽  
Yanzhen Zheng ◽  
...  
Keyword(s):  
Apis Cerana ◽  
Gc Content ◽  
Nosema Ceranae ◽  
Post Inoculation ◽  
List Type ◽  
Valuable Resource ◽  
Fungal Parasite ◽  
Differential Expression Pattern ◽  
Non Coding Rnas ◽  
Whole Transcriptome

ABSTRACTApis cerana cerana is a subspecies of eastern honeybee, Apis cerana. Nosema ceranae is a widespread fungal parasite of honeybee, causing heavy losses for beekeeping industry all over the world. In this article, total RNA of normal midguts (AcCK1, AcCK2) and N. ceranae-infected midguts of A. c. cerana workers at 7 d and 10 d post inoculation (AcT1, AcT2) were respectively isolated followed by strand-specific cDNA library construction and next-generation RNA sequencing. In tolal, 56270223688, 44860946964, 78991623806, and 92712308296 raw reads were derived from AcCK1, AcCK2, AcT1 and AcT2, respectively. Following strict quality control, 54495191388, 43570608753, 76708161525, and 89467858351 clean reads were obtained, with Q30 value of 95.80%, 95.99%, 96.07% and 96.04%, and GC content of 44.20%, 43.44%, 44.83% and 43.63%, respectively. The raw data were submitted to the NCBI Sequence Read Archive database and connected to BioProject PRJNA562784. These data offers a valuable resource for deep investigation of mechanisms underlying eastern honeybee responding to N. ceranae infection and host-fungal parasite interaction during microsporidiosis.Value of the DataCurrent dataset offers a valuable resource for exploring mRNAs, lncRNAs and circRNAs involved in response of A. c. cerana worker to N. ceranae infection.The accessible data can be used to investigate differential expression pattern and regulatory network of non-coding RNAs in A. c. cerana workers’ midguts responding to N. ceranae challenge.This data will enable a better understanding of the molecular mechanism regulating eastern honeybee-N. ceranae interaction.

scholarly journals Comparative Identification of MicroRNAs in Apis cerana cerana Workers’ Midguts in Responseto Nosema ceranae Invasion

Insects ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 258 ◽  
Author(s):  
Chen ◽  
Du ◽  
Chen ◽  
Fan ◽  
Fan ◽  
...  
Keyword(s):  
Immune System ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Apis Cerana ◽  
Apis Cerana Cerana ◽  
Host Responses ◽  
Small Rna Sequencing ◽  
Post Inoculation ◽  
Stem Loop ◽  
Target Mrnas

Here, the expression profiles and differentially expressed miRNAs (DEmiRNAs) in the midguts of Apis cerana cerana workers at 7 d and 10 d post-inoculation (dpi) with N. ceranae were investigated via small RNA sequencing and bioinformatics. Five hundred and twenty nine (529) known miRNAs and 25 novel miRNAs were identified in this study, and the expression of 16 predicted miRNAs was confirmed by Stem-loop RT-PCR. A total of 14 DEmiRNAs were detected in the midgut at 7 dpi, including eight up-regulated and six down-regulated miRNAs, while 12 DEmiRNAs were observed in the midgut at 10 dpi, including nine up-regulated and three down-regulated ones. Additionally, five DEmiRNAs were shared, while nine and seven DEmiRNAs were specifically expressed in midguts at 7 dpi and 10 dpi. Gene ontology analysis suggested some DEmiRNAs and corresponding target mRNAs were involved in various functions including immune system processes and response to stimulus. KEGG pathway analysis shed light on the potential functions of some DEmiRNAs in regulating target mRNAs engaged in material and energy metabolisms, cellular immunity and the humoral immune system. Further investigation demonstrated a complex regulation network between DEmiRNAs and their target mRNAs, with miR-598-y, miR-252-y, miR-92-x and miR-3654-y at the center. Our results can facilitate future exploration of the regulatory roles of miRNAs in host responses to N. ceranae, and provide potential candidates for further investigation of the molecular mechanisms underlying eastern honeybee-microsporidian interactions.

Transcriptomic investigation of immune responses of the Apis cerana cerana larval gut infected by Ascosphaera apis

2019 ◽  
Vol 166 ◽  
pp. 107210 ◽  
Author(s):  
Rui Guo ◽  
Dafu Chen ◽  
Qingyun Diao ◽  
Cuiling Xiong ◽  
Yanzhen Zheng ◽  
...  
Keyword(s):  
Immune Responses ◽  
Apis Cerana ◽  
Apis Cerana Cerana ◽  
Ascosphaera Apis

Morphological and molecular identification of chalkbrood disease pathogen Ascosphaera apis in Apis cerana cerana

2018 ◽  
Vol 57 (4) ◽  
pp. 516-521 ◽  
Author(s):  
Dafu Chen ◽  
Rui Guo ◽  
Cuiling Xiong ◽  
Yanzhen Zheng ◽  
Chunsheng Hou ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Apis Cerana ◽  
Apis Cerana Cerana ◽  
Ascosphaera Apis

scholarly journals Systematic identification of circular RNAs and corresponding regulatory networks unveil their potential roles in the midgut ofApis cerana ceranaworkers

2019 ◽  
Author(s):  
Dafu Chen ◽  
Huazhi Chen ◽  
Yu Du ◽  
Sihai Geng ◽  
Cuiling Xiong ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Apis Cerana ◽  
Regulation Of Gene Expression ◽  
Functional Study ◽  
Circular Rnas ◽  
Kegg Pathways ◽  
Midgut Development ◽  
Go Terms

AbstractBackgroundCircular RNAs (circRNAs) are newly discovered noncoding RNAs (ncRNAs) that play key roles in various biological functions, such as the regulation of gene expression and alternative splicing. CircRNAs have been identified in some species, including western honeybees. However, the understanding of honeybee circRNA is still very limited, and to date, no study on eastern honeybee circRNA has been conducted. Here, the circRNAs in the midguts ofApis cerana ceranaworkers were identified and validated, and the regulatory networks were constructed. Differentially expressed circRNAs (DEcircRNAs) and the corresponding competitively endogenous RNA (ceRNA) networks in the development of the worker’s midgut were further investigated.ResultsHere, 7- and 10-day-oldA. c. ceranaworkers’ midguts (Ac1 and Ac2) were sequenced using RNA-seq, and a total of 9589 circRNAs were predicted using bioinformatics. These circRNAs were approximately 201-800 nt in length and could be classified into six types; the annotated exonic circRNAs were the most abundant. Additionally, five novelA. c. ceranacircRNAs were confirmed by PCR amplification and Sanger sequencing, indicating the authenticity ofA. c. ceranacircRNAs. Interestingly, novel_circ_003723, novel_circ_002714, novel_circ_002451 and novel_circ_001980 were the most highly expressed circRNAs in both Ac1 and Ac2, which is indicative of their key roles in the development of the midgut. Moreover, 55 DEcircRNAs were identified in the Ac1 vs Ac2 comparison group, including 34 upregulated and 21 downregulated circRNAs. Further investigation showed that the source genes of circRNAs were classified into 34 GO terms and were involved in 141 KEGG pathways. In addition, the source genes of DEcircRNAs were categorized into 10 GO terms and 15 KEGG pathways, which demonstrated that the corresponding DEcircRNAs may affect the growth, development, and material and energy metabolisms of the worker’s midgut by regulating the expression of the related source genes. Additionally, the circRNA-miRNA regulatory networks were constructed and analyzed, and the results demonstrated that 1060 circRNAs can bind to 74 miRNAs and that 71.51% of circRNAs can be linked to only one miRNA. Furthermore, the DEcircRNA-miRNA-mRNA networks were constructed and explored, and the results indicate that the 13 downregulated circRNAs can bind to eight miRNAs and to 29 target genes. In addition, the results indicate that the 16 upregulated circRNAs can bind to 9 miRNAs and to 29 target genes, demonstrating that DEcircRNAs are likely involved in the regulation of midgut development via ceRNA mechanisms. Moreover, the regulatory networks of miR-6001-y-targeted DEcircRNAs were analyzed, and the results showed that eight DEcircRNAs may affect the development ofA. c. ceranaworkers’ midguts by targeting miR-6001-y. Finally, four randomly selected DEcircRNAs were verified via RT-qPCR, confirming the reliability of our sequencing data.ConclusionThis is the first systematic investigation of circRNAs and their corresponding regulatory networks in eastern honeybees. The identified circRNAs from theA. c. ceranaworker’s midgut will enrich the known reservoir of honeybee ncRNAs. DEcircRNAs may play a comprehensive role during the development of the worker’s midgut via the regulation of source genes and the interaction with miRNAs by acting as ceRNAs. The eight DEcircRNAs that targeted miR-6001-y were likely to be vital for the development of the worker’s midgut. Our results provide a valuable resource for the future studies ofA. c. ceranacircRNA and lay a foundation to reveal the molecular mechanisms underlying the regulatory networks of circRNAs responsible for the worker’s midgut development; in addition, these findings facilitate a functional study on the key circRNAs involved in the developmental process.Graphical Abstract

scholarly journals Whole genome bisulfite sequencing dataset of mycelium and spore of chalkbrood disease pathogen Ascosphaera apis

2020 ◽  
Author(s):  
Yu Du ◽  
Haibin Jiang ◽  
Huazhi Chen ◽  
Jie Wang ◽  
Yuanchan Fan ◽  
...  
Keyword(s):  
Bisulfite Sequencing ◽  
Current Data ◽  
List Type ◽  
Whole Genome ◽  
Mycelium Growth ◽  
Ascosphaera Apis ◽  
Whole Genome Bisulfite Sequencing ◽  
Bisulfite Treatment ◽  
Genome Wide ◽  
Genome Bisulfite Sequencing

ABSTRACTChalkbrood, a widespread fungal disease of bee larvae, is caused by the fungus Ascosphaera apis. In this article, mecylia and spores of A. apis were respectively collected followed by DNA isolation, bisulfite conversion, cDNA library construction and next-generation sequencing. Using whole genome bisulfite sequencing (WGBS), 69,844,360 and 60,570,990 raw reads were yielded from Aam and Aas, and after quality control, 9,982,386,951 and 8,825,601,434 clean reads were obtained, respectively. In addition, 67,685,866 and 58,886,072 clean reads were mapped to the reference genome of A. apis, including 37,643,592 and 31,568,442 unique mapped clean reads, and 49,686 and 13,348 multiple mapped clean reads. Furthermore, after bisulfite treatment, the conversion ratio of clean reads from Aam and Aas were 99.38% and 99.51%, respectively. The WGBS data ducumented here contributes to genome-wide identification of 5mC methylation sites in A. apis and comparison of methylomes between mycelium and spore.Value of the dataThis dataset can be used for genome-wide identification of 5mC methylation sites in A. apis.The accessible data could be used to systematically compare methylomes between mycelium and spore of A. apis.Current data provides a useful resource for further study on DNA methylation-mediated mechanism underlying mycelium growth, spore germination and sexual reproduction of mycelium with the opposite sex.

Contact Chemosensory Genes Identified in Leg Transcriptome of Apis cerana cerana (Hymenoptera: Apidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2015-2029 ◽  
Author(s):  
Yali Du ◽  
Kai Xu ◽  
Weihua Ma ◽  
Wenting Su ◽  
Miaomiao Tai ◽  
...  
Keyword(s):  
Honey Bees ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Apis Cerana ◽  
In Silico Analysis ◽  
Apis Cerana Cerana ◽  
Specific Expression ◽  
Genes Encoding ◽  
Honey Bee Workers ◽  
Selection Of

Abstract Correct gustatory recognition and selection of foods both within and outside the hive by honey bee workers are fundamental to the maintenance of colonies. The tarsal chemosensilla located on the legs of workers are sensitive to nonvolatile compounds and proposed to be involved in gustatory detection. However, little is known about the molecular mechanisms underlying the gustatory recognition of foods in honey bees. In the present study, RNA-seq was performed with RNA samples extracted from the legs of 1-, 10-, and 20-d-old workers of Apis cerana cerana Fabricius, a dominant indigenous crop pollinator with a keen perception ability for phytochemicals. A total of 124 candidate chemosensory proteins (CSPs), including 15 odorant-binding proteins (OBPs), 5 CSPs, 7 gustatory receptors (GRs), 2 sensory neuron membrane proteins (SNMPs), and 95 odorant receptors (ORs), were identified from the assembled leg transcriptome. In silico analysis of expression showed that 36 of them were differentially expressed among the three different ages of A. c. cerana workers. Overall, the genes encoding OBPs and CSPs had great but extremely variable FPKM values and thus were highly expressed in the legs of workers, whereas the genes encoding ORs, GRs, and SNMPs (except SNMP2) were expressed at low levels. Tissue-specific expression patterns indicated that two upregulated genes, AcerOBP15 and AcerCSP3, were predominately expressed in the legs of 20-d-old foragers, suggesting they may play an essential role in gustatory recognition and selection of plant nectars and pollens. This study lays a foundation for further research on the feeding preferences of honey bees.

scholarly journals Comparative identification of microRNAs in Apis cerana cerana workers’ midguts responding to Nosema ceranae invasion

2019 ◽  
Author(s):  
Dafu Chen ◽  
Yu Du ◽  
Huazhi Chen ◽  
Haipeng Wang ◽  
Cuiling Xiong ◽  
...  
Keyword(s):  
Immune System ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Apis Cerana ◽  
Mapk Signaling ◽  
Nosema Ceranae ◽  
Apis Cerana Cerana ◽  
Small Rna Sequencing ◽  
Biological Processes

AbstractMicroRNAs (miRNAs) are endogenous small noncoding RNAs that post transcriptionally regulate gene expression and are involved in many biological processes including host-pathogen interactions. However, the potential role of miRNAs in the responses of eastern honeybees to Nosema ceranae invasion is completely unknown. Here, the expression profiles and differentially expressed miRNAs (DEmiRNAs) in the midguts of Apis cerana cerana workers 7 and 10 days post infection (dpi) with N. ceranae were investigated via small RNA sequencing and bioinformatics. In total, 529 miRNAs highly conserved between various species and 25 novel miRNAs with varied expressions were identified for the first time. In addition, stem-loop RT-PCR confirmed the expression of 16 predicted miRNAs, validating their existence. Eight up-regulated miRNAs and six down-regulated miRNAs were detected in midguts at 7 dpi, while nine and three miRNAs were significantly up-regulated and down-regulated, respectively, in midguts at 10 dpi. In addition, Venn analysis showed that five DEmiRNAs were shared, while nine and seven DEmiRNAs were specifically expressed in midguts at 7 and 10 dpi, respectively. Gene ontology analysis suggested that a portion of the DEmiRNAs and corresponding target genes were involved in various biological processes, cellular components, and molecular functions including immune system processes and response to stimulus and signaling. Moreover, KEGG pathway analysis shed light on the potential functions of some DEmiRNAs in the regulation of target genes engaged in material and energy metabolism, cellular immunity such as endocytosis and phagosome, and the humoral immune system, including the Jak-STAT and MAPK signaling pathways. Further investigation demonstrated a complex regulation network between DEmiRNAs and their target mRNAs, with miR-598-y, miR-252-y, miR-92-x and miR-3654-y at the center of the network, implying their key parts in host responses. This comprehensive miRNA transcriptome analysis demonstrated that N. ceranae invasion influenced the expression of miRNAs in the midguts of A. c. ceranae workers; the results can not only facilitate future exploration of the regulatory roles and mechanisms of miRNAs in hosts’ responses, especially their immune responses to N. ceranae, but also provide potential candidates for further investigation of the molecular mechanisms underlying eastern honeybee-microsporidian interactions.

scholarly journals Comprehensive transcriptome data of normal and Ascosphaera apis-infected western honeybee larval guts

2020 ◽  
Author(s):  
Yu Du ◽  
Jie Wang ◽  
Zhiwei Zhu ◽  
Haibin Jiang ◽  
Xiaoxue Fan ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Gc Content ◽  
List Type ◽  
Sequencing Data ◽  
Illumina Hiseq ◽  
Ascosphaera Apis ◽  
Apis Mellifera Ligustica ◽  
Host Pathogen Interaction ◽  
Non Coding Rna ◽  
Host Pathogen

ABSTRAmTApis mellifera ligustica is a well-known subspecies of western honeybee, Apis mellifera. Ascosphaera apis is a common fungal pathogen of honeybee larvae, resulting in Chalkbrood disease. In this article, deep sequencing of un-treated 4-, 5-, and 6-day-old larval guts (AmCK1, AmCK2, AmCK3) and A. apis-treated 4-, 5- and 6-day-old larval guts (AmT1, AmT2, AmT3) of Apis mellifera ligustica were conducted using Illumina HiSeq™ 4000 platform. In total, 85811046, 81962296, 85636572, 79267686, 82889882, and 100211796 raw reads were respectively yielded from above-mentioned six groups. The result of sequencing satuation analysis suggested that the sequencing depth in this work was enough to detect nearly all expressed genes. After quality control, 85739414, 81896402, 85573798, 79202304, 82828926, and 100128692 clean reads were obtained. Additionally, the GC content of each group was above 45.26%. Furthermore, 47035852, 65612676, 71803878, 62560904, 65018360, and 56278272 clean reads were mapped to the Apis mellifera genome, including 41221479, 61172916, 66724233, 57531335, 60245732, and 52638986 unique mapped clean reads, and 2078427, 986825, 915375, 1082925, 1097130, and 716436 multiple mapped clean reads. In addition, exons were the most abundant regions mapped by clean reads, follow by intergenic regions and introns. The strand-specific cDNA library-based RNA sequencing data documented here will faciliate study on molecualr mechanisms underlying host immune response and host-pathogen interaction during chalkbrood disease, and benefit understanding of non-coding RNA-mediated cross-kingdom regulation between A. m. ligustica larvae and A. apis.Value of the DataThis data reported here could be used to explore circRNAs, lncRNAs, mRNAs and their competing endogenous RNA networks involved in response of western honeybee larvae to Ascosphaera apis infection.The current data contributes to better understanding mechanisms regulating host-pathogen interaction during chalkbrood disease.Our data can provide novel insights into understanding non-coding RNA-mediated cross-kingdom regulation between Apis mellifera ligustica and A. apis.

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