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 First identification of long non-coding RNAs in fungal parasite Nosema ceranae

Apidologie ◽  
2018 ◽  
Vol 49 (5) ◽  
pp. 660-670 ◽  
Author(s):  
Rui Guo ◽  
Dafu Chen ◽  
Cuiling Xiong ◽  
Chunsheng Hou ◽  
Yanzhen Zheng ◽  
...  
Keyword(s):  
Nosema Ceranae ◽  
Fungal Parasite ◽  
Non Coding Rnas

scholarly journals Nanopore-based genome-wide DNA methylation sequencing data of Nosema ceranae-inoculated and un-inoculated eastern honeybee workers' midguts

2021 ◽  
Author(s):  
Jun Ke Yu ◽  
Da Fu Chen ◽  
Rui Guo
Keyword(s):  
Dna Methylation ◽  
Host Response ◽  
Reference Genome ◽  
Apis Cerana ◽  
Vital Role ◽  
Nosema Ceranae ◽  
Post Inoculation ◽  
Sequencing Data ◽  
Average Quality ◽  
Genome Wide

Apis cerana cerana is an excellent subspecies of Apis cerana, playing a vital role in pollination for wild flowers and crops as well as ecological balance. Nosema ceranae, an emergent fungal parasite infecting various bee species, originates from eastern honeybee. In this article, midguts of N. ceranae-inoculated A. c. cerana workers at 7 days post inoculation (dpi) and 10 dpi (AcT1 and AcT2) and un-inoculated workers' midguts (AcCK1, AcCK2) were subjected to Nanopore-based genome-wide DNA methylation sequencing. Totally, 1773258, 2151476, 1927874 and 2109961 clean reads were generated from AcCK1, AcCK2, AcT1, and AcT2 groups, with the N50 lengths of 7548, 7936, 7678, and 7291 and the average quality value of 8.97, 8.95, 9.24, and 8.98, respectively. Among these, 93.85%, 94.49%, 88.69%, and 81.27% clean reads could be mapped to the reference genome of A. c. cerana. In the aforementioned four groups, 2149685, 2614513, 1637018 and 2726985 CHG sites were identified; the numbers of CHH sites were 9581990, 11801082, 7178559, and 12342423, whereas those of CpG sites were 14325356, 15703508, 14856284 and 13956849, respectively. Additionally, there were 36114, 118867, 30249, and 82984 6mA methylation sites respectively discovered. These data can be used for identifying differential 5mC methylation and 6mA methylation engaged in response of eastern honeybee workers to N. ceranae infestation, and for investigating the 5mC or 6mA methylation-mediated mechanism underlying host response.

scholarly journals Genome-Wide Identification of Long Non-Coding RNAs and Their Regulatory Networks Involved in Apis mellifera ligustica Response to Nosema ceranae Infection

Insects ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 245 ◽  
Author(s):  
Dafu Chen ◽  
Huazhi Chen ◽  
Yu Du ◽  
Dingding Zhou ◽  
Sihai Geng ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Regulatory Networks ◽  
Expression Patterns ◽  
Structural Features ◽  
Nosema Ceranae ◽  
Post Inoculation ◽  
Form Complex ◽  
Apis Mellifera Ligustica ◽  
Wide Range ◽  
Non Coding Rnas

Long non-coding RNAs (lncRNAs) are a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins, and lncRNAs have been proven to play pivotal roles in a wide range of biological processes in animals and plants. However, knowledge of expression patterns and potential roles of honeybee lncRNA response to Nosema ceranae infection is completely unknown. Here, we performed whole transcriptome strand-specific RNA sequencing of normal midguts of Apis mellifera ligustica workers (Am7CK, Am10CK) and N. ceranae-inoculated midguts (Am7T, Am10T), followed by comprehensive analyses using bioinformatic and molecular approaches. A total of 6353 A. m. ligustica lncRNAs were identified, including 4749 conserved lncRNAs and 1604 novel lncRNAs. These lncRNAs had minimal sequence similarities with other known lncRNAs in other species; however, their structural features were similar to counterparts in mammals and plants, including shorter exon and intron length, lower exon number, and lower expression level, compared with protein-coding transcripts. Further, 111 and 146 N. ceranae-responsive lncRNAs were identified from midguts at 7-days post-inoculation (dpi) and 10 dpi compared with control midguts. Twelve differentially expressed lncRNAs (DElncRNAs) were shared by Am7CK vs. Am7T and Am10CK vs. Am10T comparison groups, while the numbers of unique DElncRNAs were 99 and 134, respectively. Functional annotation and pathway analysis showed that the DElncRNAs may regulate the expression of neighboring genes by acting in cis and trans fashion. Moreover, we discovered 27 lncRNAs harboring eight known miRNA precursors and 513 lncRNAs harboring 2257 novel miRNA precursors. Additionally, hundreds of DElncRNAs and their target miRNAs were found to form complex competitive endogenous RNA (ceRNA) networks, suggesting that these DElncRNAs may act as miRNA sponges. Furthermore, DElncRNA-miRNA-mRNA networks were constructed and investigated, the results demonstrated that a portion of the DElncRNAs were likely to participate in regulating the host material and energy metabolism as well as cellular and humoral immune host responses to N. ceranae invasion. Our findings revealed here offer not only a rich genetic resource for further investigation of the functional roles of lncRNAs involved in the A. m. ligustica response to N. ceranae infection, but also a novel insight into understanding the host-pathogen interaction during honeybee microsporidiosis.

scholarly journals Genome-wide identification of long non-coding RNAs and their regulatory networks involved in Apis mellifera ligustica response to Nosema ceranae infection

2019 ◽  
Author(s):  
Rui Guo ◽  
Huazhi Chen ◽  
Yu Du ◽  
Dingding Zhou ◽  
Sihai Geng ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Expression Pattern ◽  
Structural Features ◽  
Nosema Ceranae ◽  
Post Inoculation ◽  
Sequencing Data ◽  
Form Complex ◽  
Apis Mellifera Ligustica ◽  
Wide Range ◽  
Non Coding Rnas

AbstractLong non-coding RNAs (lncRNAs) are a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins, and lncRNAs have been proved to play pivotal roles in a wide range of biological processes in animals and plants. However, knowledge of expression pattern and potential role of honeybee lncRNAs response to Nosema ceranae infection is completely unknown. Here, we performed whole transcriptome strand-specific RNA sequencing of normal midguts of Apis mellifera ligustica workers (Am7CK, Am10CK) and N. ceranae-inoculated midguts (Am7T, Am10T), followed by comprehensive analyses using bioinformatic and molecular approaches. A total of 6353 A. m. ligustica lncRNAs were identified, including 4749 conserved lncRNAs and 1604 novel lncRNAs. These lncRNAs had low sequence similarities with other known lncRNAs in other species; however, their structural features were similar with counterparts in mammals and plants, including shorter exon and intron length, lower exon number, and lower expression level, compared with protein-coding transcripts. Further, 111 and 146 N. ceranae-responsive lncRNAs were identified from midguts at 7 day post inoculation (dpi) and 10 dpi compared with control midguts. 12 differentially expressed lncRNAs (DElncRNAs) were shared by Am7CK vs Am7T and Am10CK vs Am10T comparison groups, while the numbers of unique ones were 99 and 134, respectively. Functional annotation and pathway analysis showed the DElncRNAs may regulate the expression of neighboring genes by acting in cis. Moreover, we discovered 27 lncRNAs harboring eight known miRNA precursors and 513 lncRNAs harboring 2257 novel miRNA precursors. Additionally, hundreds of DElncRNAs and their target miRNAs were found to form complex competitive endogenous RNA (ceRNA) networks, suggesting these DElncRNAs may act as miRNA sponges. Furthermore, DElncRNA-miRNA-mRNA networks were constructed and investigated, the result demonstrated that part of DElncRNAs were likely to participate in regulating the material and energy metabolism as well as cellular and humoral immune during host responses to N. ceranae invasion. Finally, the expression pattern of 10 DElncRNAs was validated using RT-qPCR, confirming the reliability of our sequencing data. Our findings revealed here offer not only a rich genetic resource for further investigation of the functional roles of lncRNAs involved in A. m. ligustica response to N. ceranae infection, but also a novel insight into understanding host-pathogen interaction during microsporidiosis of honeybee.

scholarly journals Pacific Biosciences long reads-based genome sequencing data from a widespread bee fungal parasite, Nosema ceranae

2020 ◽  
Author(s):  
Huazhi Chen ◽  
Wende Zhang ◽  
Yu Du ◽  
Xiaoxue Fan ◽  
Jie Wang ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Average Length ◽  
Length Distribution ◽  
Gc Content ◽  
Nosema Ceranae ◽  
Sequencing Data ◽  
Smrt Sequencing ◽  
Fungal Parasite ◽  
Total Length ◽  
Pacific Biosciences

ABSTRACTNosema ceranae is a widespread fungal parasite that infects both adult honeybee and honeybee larvae, leading to microsporidiosis, which seriously affects bee health and apicultural industry. In this article, genome sequencing of clean spores of N. ceranae was conducted using third-generation Pacific Biosciences (PacBio) single molecule real time (SMRT) sequencing technology. In total, 152671 subreads were obtained after quality control of raw reads from PacBio SMRT sequencing, with a N50 and average length of 14422 bp and 11310 bp, respectively. Additionally, the length distribution of subreads was from 10000 bp to more than 50000 bp. Nineteen scaffords with a total length of 7354221 bp were assembled, and the N50, N90 and maximum scafford length were 728543 bp, 198795 bp and 1917792 bp, respectively. The GC content was 25.97%. Furthermore, by integration of genes predicted from de novo and homology-based methods, 3112 N. ceranae genes were finally assembled, with a total length of 2730179 bp and mean length of 877.31 bp. In addition, the total length and mean length of exons were 2657637 bp and 854 bp, respectively; and the total length and mean length of introns were 72542 bp and 23.31 bp, respectively. The genome sequencing data documented here will give deep insights into the molecular biology of N. ceranae, facilitate exploration of genes and pathways associated with toxin factors and infection-related factors, and benefit research on comparative genomics and phylogenetic diversity of Nosema species.

scholarly journals A full-length transcriptome dataset of normal and Nosema ceranae-challenged midgut tissues of eastern honeybee workers

2020 ◽  
Author(s):  
Yu Du ◽  
Yuanchan Fan ◽  
Huazhi Chen ◽  
Jie Wang ◽  
Cuiling Xiong ◽  
...  
Keyword(s):  
Apis Cerana ◽  
Length Distribution ◽  
Vital Role ◽  
Nosema Ceranae ◽  
Full Length ◽  
List Type ◽  
Sequencing Technology ◽  
Score Distribution ◽  
Long Read ◽  
Reported Data

ABSTRACTApis cerana cerana is a subspecies of eastern honeybee, Apis cerana, and it plays a vital role in ecological maintenance in China. However, A. c. cerana is threatened by many pathogenic microorganisms including Nosema ceranae, a widespread fungal parasite that infected worldwide colonies. In this article, un-challenged (AcCK1, AcCK2) and N. ceranae-challenged midguts of A. c. cerana workers (AcT1, AcT2) were sequenced utilizing Nanopore long-read sequencing technology. Totally, 11,727,628, 6,996,395, 14,383,735 and 11,580,154 raw reads were yielded from AcCK1, AcCK2, AcT1 and AcT2; the average lengths were 1147 bp, 908 bp, 992 bp and 1077 bp, and the average N50 were 1308 bp, 911 bp, 1079 bp and 1192 bp. The length distribution of was ranged 1 kb to more than 10 kb. Additionally, the quality (Q) score distribution of raw reads was among Q7~Q17. Further, 11,617,144, 6,940,895, 14,277,240 and 11,501,562 clean reads were respectively obtained from AcCK1, AcCK2, AcT1 and AcT2, and among them 78.40%, 82.50%, 79.05% and 80.20% were identified as full-length clean reads. In addition, full-length clean reads from AcCK1, AcT1, AcT2 and AcCK2 were ranged from 1 kb to more than 10 kb in length. Finally, the length distribution of redundant reads-removed full-length transcripts was among 1 kb~5 kb.Value of the data♦This dataset enables better understanding the complexity of A. c. cerana transcriptome.♦Current dataset contributes to identification of genes and transcripts engaged in response of eastern honeybee to N. ceranae stress.♦The data provides a valuable genetic resource for deciphering alternative splicing and polyadenylation of A. c. cerana mRNAs involved in host response to N. ceranae challenge.♦The reported data is beneficial for uncovering the molecular mechanism regulating interaction between eastern honeybee and microsporidian.

scholarly journals Nanopore-based long-read transcriptome data of Nosema ceranae-infected and un-infected western honeybee workers’ midguts

2020 ◽  
Author(s):  
Huazhi Chen ◽  
Xiaoxue Fan ◽  
Yu Du ◽  
Yuanchan Fan ◽  
Jie Wang ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Length Distribution ◽  
Quality Score ◽  
Nosema Ceranae ◽  
Full Length ◽  
Post Inoculation ◽  
Transcriptome Data ◽  
Fungal Parasite ◽  
Long Read ◽  
Colony Productivity

ABSTRACTApis mellifera ligustica is a subspecies of western honeybee, Apis mellifera. Nosema ceranae is known to cause bee microspodiosis, which seriously affects bee survival and colony productivity. In this article, Nanopore long-read sequencing was used to sequence N. ceranae-infected and un-infected midguts of A. m. ligustica workers at 7 d and 10 d post inoculation (dpi). In total, 5942745, 6664923, 7100161 and 6506665 raw reads were respectively yielded from AmT1, AmT2, AmCK1 and AmCK2, with average lengths of 1148, 1196, 1178 and 1201 bp, and N50 of 1328, 1394, 1347 and 1388 bp. The length distribution of raw reads from AmT1, AmT2, AmCK1 and AmCK2 was ranged from 1 kb to more than 10 kb. Additionally, the distribution of quality score of raw reads from AmT1 and AmT2 was among Q6∼Q12, while that from AmCK1 and AmCK2 was among Q6∼Q16. Further, 5745048, 6416987, 6928170, 6353066 clean reads were respectively gained from AmT1, AmT2, AmCK1 and AmCK2, and among them 4172542, 4638289, 5068270 and 4857960 were identified as being full-length. After removing redundant reads, the length distribution of remaining full-length transcripts was among 1 kb∼8 kb, with the most abundant length of 2 kb. The long-read transcriptome data reported here contributes to a deeper understanding of the molecular regulating N. ceranae-response of A. m. ligustica and host-fungal parasite interaction during microsporidiosis.

scholarly journals Immune Response of Eastern Honeybee Worker to Nosema ceranae Infection Revealed by Transcriptomic Investigation

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 728
Author(s):  
Wenhao Xing ◽  
Dingding Zhou ◽  
Qi Long ◽  
Minghui Sun ◽  
Rui Guo ◽  
...  
Keyword(s):  
Immune Response ◽  
Signaling Pathway ◽  
Apis Cerana ◽  
Enrichment Analysis ◽  
Nosema Ceranae ◽  
Pathway Enrichment Analysis ◽  
Post Inoculation ◽  
Sequencing Data ◽  
Humoral Immune ◽  
Immune Pathways

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.

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.

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