Biology subjects

Xiong, C.

Publications and source records attributed to Xiong, C..

54 records · Page 3Linked to original sources

bioRxiv2020

Light-Sheet Fluorescence Imaging Charts the Gastrula Origin of Vascular Endothelial Cells in Early Zebrafish Embryos

It remains challenging to construct a complete cell lineage map of the origin of vascular endothelial cells in any vertebrate embryo. Here, we report the application of in toto light-sheet fluorescence imaging of embryos to tracing the origin of vascular endothelial cells (ECs) at single-cell resolution in zebrafish. We first adapted a previously-reported method to mount embryos and light-sheet imaging, created an alignment, fusion, and extraction all-in-one software (AFEIO) for processing big data, and performed quantitative analysis of cell lineage relationships using commercially-available Imaris software. Our data revealed that vascular ECs originated from broad regions of the gastrula along the dorsal-ventral and anterior-posterior axes, of which the dorsal-anterior cells contributed to cerebral ECs, the dorsal-lateral cells to anterior trunk ECs, and the ventral-lateral cells to posterior trunk and tail ECs. Therefore, this work, to our knowledge, charts the first comprehensive map of the gastrula origin of vascular ECs in zebrafish, and has potential applications for studying the origin of any embryonic organs in zebrafish and other model organisms.

developmental biology↗

bioRxiv2020

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

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 DataO_LIThis 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. C_LIO_LIThe current data contributes to better understanding mechanisms regulating host-pathogen interaction during chalkbrood disease. C_LIO_LIOur data can provide novel insights into understanding non-coding RNA-mediated cross-kingdom regulation between Apis mellifera ligustica and A. apis. C_LI

molecular biology↗

bioRxiv2020

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

Apis 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 DataO_LIThe 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. C_LIO_LIThis data provides a valuable genetic resource for better understanding non-coding RNA-mediated cross-kingdom regulation of eastern honey larvae to A. apis. C_LIO_LIThe accessible data offers novel insights into understanding the molecular mechanism underlying interaction between eastern honeybee larvae and A. apis. C_LI

bioinformatics↗

bioRxiv2020

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

Nosema 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.

bioinformatics↗

bioRxiv2020

Genome-wide bisulfite sequencing data of normal and Ascosphaera apis-infected larval guts of eastern honeybee

Apis cerana cerana, a subspecies of eastern honey, Apis cerana, plays a specific role in beekeeping industry and ecosystem in China and other Asian countries. Larvae of A. c. cerana can be infected by Ascosphaera apis, the fungal pathogen of chalkbrood. In this article, normal 4-, 5-, and 6-day-old larval guts (AcCK1, AcCK2, AcCK3) and A. apis-infected 4-, 5- and 6-day-old larval guts (AcT1, AcT2, AcT3) of A. c. cerana workers were respectively harvested followed by DNA isolation, bisulfite conversion, cDNA library construction and Illumina sequencing. Based on genome-wide bisulfite sequencing, 79167210, 82175052, 79331489, 81051009, 74742842 and 74849091 raw reads were generated from AcCK1, AcCK2, AcCK3, AcT1, AcT2 and AcT3, and after quality control, 73417030 (92.73%), 76660370 (93.27%), 71804727 (90.44%), 75046507 (92.82%), 67487782 (90.30%) and 67367023 (90.04%) clean reads were obtained, respectively. Additionally, 73333333, 76533333, 71466667, 75066667, 67590965 and 67200000 clean reads were mapped to the reference genome of A. cerana, including 54656767, 58583415, 54127407, 57943220, 52547867 and 51295824 unique mapped clean reads, and 8624392, 8789458, 7531333, 7747337, 6249679 and 5394174 multiple mapped clean reads. The genome-wide bisulfite sequencing data reported here can be used for genome-wide identification of 5mC methylation sites in eastern honeybee larval guts and systematic investigation of DNA methylation-mediated host response to A. apis infection. Value of the dataO_LIThe current dataset contributes to genome-wide identification of 5mC methylation sites in normal and A. apis-infected larval guts of eastern honeybee. C_LIO_LIThe reported data could be used for systematic investigation of DNA methylation-mediated response of eastern honeybee larvae to A. apis infection. C_LIO_LIOur data offers a valuable genetic resource for better understanding epigenetic regulation mechanism involved in eastern honeybee larvae-A. apis interaction. C_LI

molecular biology↗

bioRxiv2020

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

Chalkbrood, 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 dataO_LIThis dataset can be used for genome-wide identification of 5mC methylation sites in A. apis. C_LIO_LIThe accessible data could be used to systematically compare methylomes between mycelium and spore of A. apis. C_LIO_LICurrent 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. C_LI

molecular biology↗

bioRxiv2020

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

Apis 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.

bioinformatics↗

bioRxiv2020

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

Apis 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{diamondsuit} This dataset enables better understanding the complexity of A. c. cerana transcriptome. {diamondsuit}Current dataset contributes to identification of genes and transcripts engaged in response of eastern honeybee to N. ceranae stress. {diamondsuit}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. {diamondsuit}The reported data is beneficial for uncovering the molecular mechanism regulating interaction between eastern honeybee and microsporidian.

molecular biology↗

bioRxiv2020

PacBio SMRT-based full-length transcriptome data of Ascosphaera apis mycelium and spore

Ascosphaera apis is an entomopathogenic fungus that exclusively infects honeybee larvae, resulting in chalkbrood disease, a widespread fungal disease damaging the beekeeping industry all over the world. In this article, purified mycelia (Aam) and spores (Aas) of A. apis pure culture under lab condition were sequenced using PacBio Sequel platform. In total, 13,302,489 and 9,911,345 subreads were yielded from Aam and Aas, respectively; 394,142 and 274,928 circular consensus sequence (CCS) reads were identified as being full-length non-chimeric (FLNC) reads, with a mean length of 2820 bp and 2602 bp, respectively. Furthermore, 174,095 and 103,845 corrected isoforms were identified, with a N50 length of 3543 bp and 3262 bp, respectively. The reported full-length transcriptome data of A. apis mycelium and spore will provide a valuable resource for improvement of genome and transcriptome annotations as well as better understanding of transcript structure such as alternative splicing and polyadenylation. Value of the dataO_LICurrent dataset offers a set of high-quality full-length transcripts of A. apis. C_LIO_LIThe data can facilitate the improvement of A. apis genome and transcriptome annotations. C_LIO_LIThis dataset benefits further exploration of alternative splicing and polyadenylation of A. apis mRNAs. C_LI

evolutionary biology↗

bioRxiv2020

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

Ascosphaera 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 dataO_LIThe data can be used to investigate the relationship between the m6A modification extent and the transcript level in the A. apis transcriptome. C_LIO_LIThis dataset contributes to transcriptome-wide characterization of the m6A distributing patterns in mRNAs and non-coding RNAs in A. apis mycelium and spore. C_LIO_LICurrent data benefits new functions of m6A modification in the transcripts extensively modified by m6A in A. apis mycelium and spore. C_LIO_LIOur data could be used to characterize differential patterns of the m6A methylation between mycelium and spore of A. apis. C_LI

molecular biology↗

bioRxiv2020

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

Apis 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 DataO_LICurrent dataset offers a valuable resource for exploring mRNAs, lncRNAs and circRNAs involved in response of A. c. cerana worker to N. ceranae infection. C_LIO_LIThe 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. C_LIO_LIThis data will enable a better understanding of the molecular mechanism regulating eastern honeybee-N. ceranae interaction. C_LI

bioinformatics↗

bioRxiv2020

Nanopore long-read transcriptome data of fungal pathogen of chalkbrood disease, Ascosphaera apis

Ascosphaera apis is a fungal pathogen that exclusively infects honeybee larvae, leading to chalkbrood disease, which damages the number of adult honeybees and colony productivity. In this article, A. apis mecylia and spores were respectively purified followed by Oxford Nanopore sequencing via PromethION platform. In total, 6,321,704 and 6,259,727 raw reads were generated from Aam and Aas, with a length distribution among 1 kb~10 kb. The quality (Q) scores of majority of raw reads were Q9 (Aam) and Q11 (Aas). Additionally, 5,669,436 and 6,233,159 clean reads were gained, among them 79.32% and 79.62% were identified as being full-length. The lengths of redundant reads-removed full-length transcripts were among 1 kb~8 kb and 1 kb~9 kb, and most abundant length for both was 1 kb. Furthermore, the length of redundant transcripts-removed clean reads was ranged from 1 kb~7 kb, with the largest group of 1 kb. The data reported here provides a beneficial genetic resource for improving genome and transcriptome annotations of A. apis and for exploring alternative splicing and polyadenylation of A. apis mRNAs. Value of the resultO_LICurrent dataset enables better understanding of the complexity of A. apis transcriptome. C_LIO_LIThe long-read transcriptome data can be used to identify of genes and transcripts associated with A. apis infection mechanism. C_LIO_LIThe accessible data provides full-length transcripts for improving gene structure and functional annotation of A. apis transcriptome. C_LIO_LIThis dataset could be utilized for investigation of alternative splicing and polyadenylation of A. apis mRNAs. C_LI

molecular biology↗

bioRxiv2020

The ACE2 expression of maternal-fetal interface and fetal organs indicates potential risk of vertical transmission of SARS-COV-2

Recent studies have demonstrated that SARS-CoV-2 cell entry depends on both ACE2 and TMPRSS2 genes (DOI: 10.1016/j.cell.2020.02.052), but our current work only focus on ACE2, which is insufficient to support the conclusion of this paper. So the authors have withdrawn their manuscript whilst they perform additional experiments and analysis to test some of their conclusions further. Therefore, the authors do not wish this work to be cited as reference for the project.

genomics↗

bioRxiv2020

Evolution and variation of 2019-novel coronavirus

BackgroundThe current outbreak caused by novel coronavirus (2019-nCoV) in China has become a worldwide concern. As of 28 January 2020, there were 4631 confirmed cases and 106 deaths, and 11 countries or regions were affected. MethodsWe downloaded the genomes of 2019-nCoVs and similar isolates from the Global Initiative on Sharing Avian Influenza Database (GISAID and nucleotide database of the National Center for Biotechnology Information (NCBI). Lasergene 7.0 and MEGA 6.0 softwares were used to calculate genetic distances of the sequences, to construct phylogenetic trees, and to align amino acid sequences. Bayesian coalescent phylogenetic analysis, implemented in the BEAST software package, was used to calculate the molecular clock related characteristics such as the nucleotide substitution rate and the most recent common ancestor (tMRCA) of 2019-nCoVs. ResultsAn isolate numbered EPI_ISL_403928 showed different phylogenetic trees and genetic distances of the whole length genome, the coding sequences (CDS) of ployprotein (P), spike protein (S), and nucleoprotein (N) from other 2019-nCoVs. There are 22, 4, 2 variations in P, S, and N at the level of amino acid residues. The nucleotide substitution rates from high to low are 1{middle dot}05 x 10-2 (nucleotide substitutions/site/year, with 95% HPD interval being 6.27 x 10-4 to 2.72 x 10-2) for N, 5.34 x 10-3 (5.10 x 10-4, 1.28 x 10-2) for S, 1.69 x 10-3 (3.94 x 10-4, 3.60 x 10-3) for P, 1.65 x 10-3 (4.47 x 10-4, 3.24 x 10-3) for the whole genome, respectively. At this nucleotide substitution rate, the most recent common ancestor (tMRCA) of 2019-nCoVs appeared about 0.253-0.594 year before the epidemic. ConclusionOur analysis suggests that at least two different viral strains of 2019-nCoV are involved in this outbreak that might occur a few months earlier before it was officially reported.

microbiology↗

bioRxiv2019

Reconstruction and functional annotation of Ascosphaera apis full-length transcriptome via PacBio single-molecule long-read sequencing

Ascosphaera apis is a widespread fungal pathogen of honeybee larvae that results in chalkbrood disease, leading to heavy losses for the beekeeping industry in China and many other countries. This work was aimed at generating a full-length transcriptome of A. apis using PacBio single-molecule real-time (SMRT) sequencing. Here, more than 23.97 Gb of clean reads was generated from long-read sequencing of A. apis mecylia, including 464,043 circular consensus sequences (CCS) and 394,142 full-length non-chimeric (FLNC) reads. In total, we identified 174,095 high-confidence transcripts covering 5141 known genes with an average length of 2728 bp. We also discovered 2405 genic loci and 11,623 isoforms that have not been annotated yet within the current reference genome. Additionally, 16,049, 10,682, 4520 and 7253 of the discovered transcripts have annotations in the Non-redundant protein (Nr), Clusters of Eukaryotic Orthologous Groups (KOG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Moreover, 1205 long non-coding RNAs (lncRNAs) were identified, which have less exons, shorter exon and intron lengths, shorter transcript lengths, lower GC percent, lower expression levels, and fewer alternative splicing (AS) evens, compared with protein-coding transcripts. A total of 253 members from 17 transcription factor (TF) families were identified from our transcript datasets. Finally, the expression of A. apis isoforms was validated using a molecular approach. Overall, this is the first report of a full-length transcriptome of entomogenous fungi including A. apis. Our data offer a comprehensive set of reference transcripts and hence contributes to improving the genome annotation and transcriptomic study of A. apis.

molecular biology↗

bioRxiv2019

Systematic identification of circular RNAs and corresponding regulatory networks unveil their potential roles in the midgut of Apis cerana cerana workers

BackgroundCircular 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 of Apis cerana cerana workers 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 workers midgut were further investigated. ResultsHere, 7- and 10-day-old A. c. cerana workers 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 novel A. c. cerana circRNAs were confirmed by PCR amplification and Sanger sequencing, indicating the authenticity of A. c. cerana circRNAs. 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 workers 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 of A. c. cerana workers 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 the A. c. cerana workers midgut will enrich the known reservoir of honeybee ncRNAs. DEcircRNAs may play a comprehensive role during the development of the workers 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 workers midgut. Our results provide a valuable resource for the future studies of A. c. cerana circRNA and lay a foundation to reveal the molecular mechanisms underlying the regulatory networks of circRNAs responsible for the workers midgut development; in addition, these findings facilitate a functional study on the key circRNAs involved in the developmental process. Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

molecular biology↗

bioRxiv2019

Comparative identification of microRNAs in Apis cerana cerana workers'midguts responding to Nosema ceranae invasion

MicroRNAs (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.

bioinformatics↗

bioRxiv2018

Saturation mutagenesis of disease-associated regulatory elements

The majority of common variants associated with common diseases, as well as an unknown proportion of causal mutations for rare diseases, fall in noncoding regions of the genome. Although catalogs of noncoding regulatory elements are steadily improving, we have a limited understanding of the functional effects of mutations within them. Here, we performed saturation mutagenesis in conjunction with massively parallel reporter assays on 20 disease-associated gene promoters and enhancers, generating functional measurements for over 30,000 single nucleotide substitution and deletion mutations. We find that the density of putative transcription factor binding sites varies widely between regulatory elements, as does the extent to which evolutionary conservation or various integrative scores predict functional effects. These data provide a powerful resource for interpreting the pathogenicity of clinically observed mutations in these disease-associated regulatory elements, and also comprise a gold-standard dataset for the further development of algorithms that aim to predict the regulatory effects of noncoding mutations.

genetics↗