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

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.

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Genome-Wide Identification of Circular RNAs in Fungal Parasite Nosema ceranae

Current Microbiology ◽

10.1007/s00284-018-1576-z ◽

2018 ◽

Vol 75 (12) ◽

pp. 1655-1660 ◽

Cited By ~ 5

Author(s):

Rui Guo ◽

Dafu Chen ◽

Huazhi Chen ◽

Cuiling Xiong ◽

Yanzhen Zheng ◽

...

Keyword(s):

Nosema Ceranae ◽

Circular Rnas ◽

Fungal Parasite ◽

Genome Wide

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

Insects ◽

10.3390/insects10080245 ◽

2019 ◽

Vol 10 (8) ◽

pp. 245 ◽

Cited By ~ 6

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.

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

10.1101/643627 ◽

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.

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

10.1101/2020.04.05.026849 ◽

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.

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Identification of microRNA-like small RNAs from fungal parasite Nosema ceranae

Journal of Invertebrate Pathology ◽

10.1016/j.jip.2015.12.005 ◽

2016 ◽

Vol 133 ◽

pp. 107-109 ◽

Cited By ~ 11

Author(s):

Qiang Huang ◽

Jay D. Evans

Keyword(s):

Small Rnas ◽

Nosema Ceranae ◽

Fungal Parasite

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Long-read transcriptome data of bee fungal parasite, Nosema ceranae

10.1101/2020.03.11.987271 ◽

2020 ◽

Author(s):

Huazhi Chen ◽

Yu Du ◽

Yuanchan Fan ◽

Haibin Jiang ◽

Cuiling Xiong ◽

...

Keyword(s):

Length Distribution ◽

Nosema Ceranae ◽

Full Length ◽

Score Distribution ◽

Fungal Parasite ◽

Third Generation Sequencing ◽

Bee Health ◽

Long Read ◽

Generation Sequencing

ABSTRACTNosema ceranae, a widespread fungal parasite that infects honeybee and many other bee species, can seriously affect bee health and colony productivity. In this article, N. ceranae spores were purified followed by third-generation sequencing using Nanopore PromethION platform. Totally, 6988795 raw reads were yielded from purified spores, with a length distribution among 1 kb~10 kb and a quality (Q) score distribution among Q6~Q12. A total of 6953469 clean reads were obtained, and among them 73.98% were identified as being full-length. The length of redundant reads-removed full-length transcripts was ranged from 1 kb to 5 kb, with the most abundant length of 1 kb. These data will improve transcriptome quality of N. ceranae significantly.

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

10.1101/2020.03.21.001958 ◽

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.

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