Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome

Full-Length Transcriptome Profile of Apis cerana Revealed by Nanopore Sequencing

The Asian honey bee (Apis cerana) plays a crucial role in providing abundant bee products and in maintaining ecological balance. Despite the availability of the genomic sequence of the Asian honey bee, its transcriptomic information remains largely incomplete. To address this issue, here we constructed three pooled RNA samples from the queen, drone, and worker bees of A. cerana and performed full-length RNA sequencing using Nanopore single-molecule sequencing technology. Ultimately, we obtained 160,811 full-length transcript sequences from 19,859 genes, with 141,189 being novel transcripts, of which 130,367 were functionally annotated. We detected 520, 324, and 1823 specifically expressed transcripts in the queen, worker, and drone bees, respectively. Furthermore, we identified 38,799 alternative splicing (AS) events from 5710 genes, 44,243 alternative polyadenylation (APA) sites from 1649 gene loci, 88,187 simple sequence repeats (SSRs), and 17,387 long noncoding RNAs (lncRNAs). Leveraging these transcripts as references, we identified 6672, 7795, and 6804 differentially expressed transcripts (DETs) in comparisons of queen ovaries vs drone testes, worker ovaries vs drone testes, and worker ovaries vs queen ovaries, respectively. Our research results provide a comprehensive set of reference transcript datasets for Apis cerana, offering important sequence information for further exploration of its gene functions.

Comprehensive transcriptome sequencing of silkworm Midguts: Uncovering extensive isoform diversity and alternative splicing in BmNPV-Sensitive and BmNPV-resistant strains

The silkworm, Bombyx mori, stands out as one of the few economically valuable insects within the realm of model organisms. However, Bombyx mori nucleopolyhedrovirus (BmNPV) poses a significant threat, decreasing the quality and quantity of silkworm cocoons. Over the past few decades, a multitude of researchers has delved into the mechanisms that underlie silkworm resistance to BmNPV, employing diverse methodologies and approaching the problem from various angles. Despite this extensive research, the role of alternative splicing (AS) in the silkworm's response to BmNPV infection has been largely unexplored. This study leveraged both third-generation (Oxford Nanopore Technologies) and second-generation (Illumina) high-throughput sequencing technologies to meticulously identify and analyze AS patterns in the context of BmNPV response, utilizing two distinct silkworm strains-the susceptible strain 306 and the resistant strain NB. Consequently, we identified five crucial genes (Dsclp, LOC692903, LOC101743583, LOC101742498, LOC101743809) that are linked to the response to BmNPV infection through AS and differential expression. Additionally, a thorough comparative analysis was conducted on their diverse transcriptomic expression profiles, including alternative polyadenylation, simple sequence repeats, and transcription factors.

Multiple strategies, including 6mA methylation, affecting plant alternative splicing in allopolyploid peanut

Alternative splicing (AS), an important post-transcriptional regulation mechanism in eukaryotes, can significantly increase transcript diversity and contribute to gene expression regulation and many other complicated developmental processes. While plant gene AS events are well described, few studies have investigated the comprehensive regulation machinery of plant AS. Here, we use multi-omics to analyse peanut AS events. Using long-read isoform sequencing, 146 464 full-length non-chimeric transcripts were obtained, resulting in annotation corrections for 1782 genes and the identification of 4653 new loci. Using Iso-Seq RNA sequences, 271 776 unique splice junctions were identified, 82.49% of which were supported by transcriptome data. We characterized 50 977 polyadenylation sites for 23 262 genes, 12 369 of which had alternative polyadenylation sites. AS allows differential regulation of the same gene by miRNAs at the isoform level coupled with polyadenylation. In addition, we identified many long non-coding RNAs and fusion transcripts. There is a suppressed effect of 6mA on AS and gene expression. By analysis of chromatin structures, the genes located in the boundaries of topologically associated domains, proximal chromosomal telomere regions, inter- or intra-chromosomal loops were found to have more unique splice isoforms, higher expression, lower 6mA and more transposable elements (TEs) in their gene bodies than the other genes, indicating that chromatin interaction, 6mA and TEs play important roles in AS and gene expression. These results greatly refine the peanut genome annotation and contribute to the study of gene expression and regulation in peanuts. This work also showed AS is associated with multiple strategies for gene regulation.

Evolutionary honing in and mutational replacement: how long-term directed mutational responses to specific environmental pressures are possible

Recent results have shown that the human malaria-resistant hemoglobin S mutation originates de novo more frequently in the gene and in the population where it is of adaptive significance, namely, in the hemoglobin subunit beta gene compared to the nonresistant but otherwise identical 20A[Formula: see text]T mutation in the hemoglobin subunit delta gene, and in sub-Saharan Africans, who have been subject to intense malarial pressure for many generations, compared to northern Europeans, who have not. This finding raises a fundamental challenge to the traditional notion of accidental mutation. Here, we address this finding with the replacement hypothesis, according to which preexisting genetic interactions can lead directly and mechanistically to mutations that simplify and replace them. Thus, an evolutionary process under selection can gradually hone in on interactions of importance for the currently evolving adaptations, from which large-effect mutations follow that are relevant to these adaptations. We exemplify this hypothesis using multiple types of mutation, including gene fusion mutations, gene duplication mutations, A[Formula: see text]G mutations in RNA-edited sites and transcription-associated mutations, and place it in the broader context of a system-level view of mutation origination called interaction-based evolution. Potential consequences include that similarity of mutation pressures may contribute to parallel evolution in genetically related species, that the evolution of genome organization may be driven by mutational mechanisms, that transposable element movements may also be explained by replacement, and that long-term directed mutational responses to specific environmental pressures are possible. Such mutational phenomena need to be further tested by future studies in natural and artificial settings.

A Global Survey of the Full-Length Transcriptome of Apis mellifera by Single-Molecule Long-Read Sequencing

As important pollinators, honey bees play a crucial role in both maintaining the ecological balance and providing products for humans. Although several versions of the western honey bee genome have already been published, its transcriptome information still needs to be refined. In this study, PacBio single-molecule sequencing technology was used to sequence the full-length transcriptome of mixed samples from many developmental time points and tissues of A. mellifera queens, workers and drones. A total of 116,535 transcripts corresponding to 30,045 genes were obtained. Of these, 92,477 transcripts were annotated. Compared to the annotated genes and transcripts on the reference genome, 18,915 gene loci and 96,176 transcripts were newly identified. From these transcripts, 136,554 alternative splicing (AS) events, 23,376 alternative polyadenylation (APA) sites and 21,813 lncRNAs were detected. In addition, based on the full-length transcripts, we identified many differentially expressed transcripts (DETs) between queen, worker and drone. Our results provide a complete set of reference transcripts for A. mellifera that dramatically expand our understanding of the complexity and diversity of the honey bee transcriptome.

Trans-splicing facilitated by RNA pairing greatly expands sDscam isoform diversity but not homophilic binding specificity

The Down syndrome cell adhesion molecule 1 (Dscam1) gene can generate tens of thousands of isoforms via alternative splicing, which is essential for nervous and immune functions. Chelicerates generate approximately 50 to 100 shortened Dscam (sDscam) isoforms by alternative promoters, similar to mammalian protocadherins. Here, we reveal that trans-splicing markedly increases the repository of sDscamβ isoforms in Tetranychus urticae. Unexpectedly, every variable exon cassette engages in trans-splicing with constant exons from another cluster. Moreover, we provide evidence that competing RNA pairing not only governs alternative cis-splicing but also facilitates trans-splicing. Trans-spliced sDscam isoforms mediate cell adhesion ability but exhibit the same homophilic binding specificity as their cis-spliced counterparts. Thus, we reveal a single sDscam locus that generates diverse adhesion molecules through cis- and trans-splicing coupled with alternative promoters. These findings expand understanding of the mechanism underlying molecular diversity and have implications for the molecular control of neuronal and/or immune specificity.

The Landscapes of Full-Length Transcripts and Splice Isoforms as Well as Transposons Exonization in the Lepidopteran Model System, Bombyx mori

The domesticated silkworm, Bombyx mori, is an important model system for the order Lepidoptera. Currently, based on third-generation sequencing, the chromosome-level genome of Bombyx mori has been released. However, its transcripts were mainly assembled by using short reads of second-generation sequencing and expressed sequence tags which cannot explain the transcript profile accurately. Here, we used PacBio Iso-Seq technology to investigate the transcripts from 45 developmental stages of Bombyx mori. We obtained 25,970 non-redundant high-quality consensus isoforms capturing ∼60% of previous reported RNAs, 15,431 (∼47%) novel transcripts, and identified 7,253 long non-coding RNA (lncRNA) with a large proportion of novel lncRNA (∼56%). In addition, we found that transposable elements (TEs) exonization account for 11,671 (∼45%) transcripts including 5,980 protein-coding transcripts (∼32%) and 5,691 lncRNAs (∼79%). Overall, our results expand the silkworm transcripts and have general implications to understand the interaction between TEs and their host genes. These transcripts resource will promote functional studies of genes and lncRNAs as well as TEs in the silkworm.

Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal

Hibernation is a physiological and behavioral phenotype that minimizes energy expenditure. Hibernators cycle between profound depression and rapid hyperactivation of multiple physiological processes, challenging our concept of mammalian homeostasis. How the hibernator orchestrates and survives these extremes while maintaining cell to organismal viability is unknown. Here, we enhance the genome integrity and annotation of a model hibernator, the 13-lined ground squirrel. Our new assembly brings this genome to near chromosome-level contiguity and adds thousands of previously unannotated genes. These new genomic resources were used to identify 6,505 hibernation-related, differentially-expressed and processed transcripts using RNA-seq data from three brain regions in animals whose physiological status was precisely defined using body temperature telemetry. A software tool, squirrelBox, was developed to foster further data analyses and visualization. SquirrelBox includes a comprehensive toolset for rapid visualization of gene level and cluster group dynamics, sequence scanning of k-mer and domains, and interactive exploration of gene lists. Using these new tools and data, we deconvolute seasonal from temperature-dependent effects on the brain transcriptome during hibernation for the first time, highlighting the importance of carefully timed samples for studies of differential gene expression in hibernation. The identified genes include a regulatory network of RNA binding proteins that are dynamic in hibernation along with the composition of the RNA pool. In addition to passive effects of temperature, we provide evidence for regulated transcription and RNA turnover during hibernation. Significant alternative splicing, largely temperature dependent, also occurs during hibernation. These findings form a crucial first step and provide a roadmap for future work toward defining novel mechanisms of tissue protection and metabolic depression that may 1 day be applied toward improving human health.

RNA structures in alternative splicing and back-splicing

Alternative splicing greatly expands the transcriptomic and proteomic diversities related to physiological and developmental processes in higher eukaryotes. Splicing of long noncoding RNAs, and back- and trans- splicing further expanded the regulatory repertoire of alternative splicing. RNA structures were shown to play an important role in regulating alternative splicing and back-splicing. Application of novel sequencing technologies made it possible to identify genome-wide RNA structures and interaction networks, which might provide new insights into RNA splicing regulation in vitro to in vivo. The emerging transcription-folding-splicing paradigm is changing our understanding of RNA alternative splicing regulation. Here, we review the insights into the roles and mechanisms of RNA structures in alternative splicing and back-splicing, as well as how disruption of these structures affects alternative splicing and then leads to human diseases. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.

SGID: a comprehensive and interactive database of the silkworm

Although the domestic silkworm (Bombyx mori) is an important model and economic animal, there is a lack of comprehensive database for this organism. Here, we developed the silkworm genome informatics database (SGID). It aims to bring together all silkworm-related biological data and provide an interactive platform for gene inquiry and analysis. The function annotation in SGID is thorough and covers 98% of the silkworm genes. The annotation details include function description, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway, subcellular location, transmembrane topology, protein secondary/tertiary structure, homologous group and transcription factor. SGID provides genome-scale visualization of population genetics test results based on high-depth resequencing data of 158 silkworm samples. It also provides interactive analysis tools of transcriptomic and epigenomic data from 79 NCBI BioProjects. SGID will be extremely useful to silkworm research in the future.

Combining next-generation sequencing and single-molecule sequencing to explore brown plant hopper responses to contrasting genotypes of japonica rice

BACKGROUND

The brown plant hopper (BPH), Nilaparvata lugens, is one of the major pest of rice (Oryza sativa). Plant defenses against insect herbivores have been extensively studied, but our understanding of insect responses to host plants' resistance mechanisms is still limited. The purpose of this study is to characterize transcripts of BPH and reveal the responses of BPH insects to resistant rice at transcription level by using the advanced molecular techniques, the next-generation sequencing (NGS) and the single-molecule, real-time (SMRT) sequencing.

RESULTS

The current study obtained 24,891 collapsed isoforms of full-length transcripts, and 20,662 were mapped to known annotated genes, including 17,175 novel transcripts. The current study also identified 915 fusion genes, 1794 novel genes, 2435 long non-coding RNAs (lncRNAs), and 20,356 alternative splicing events. Moreover, analysis of differentially expressed genes (DEGs) revealed that genes involved in metabolic and cell proliferation processes were significantly enriched in up-regulated and down-regulated sets, respectively, in BPH fed on resistant rice relative to BPH fed on susceptible wild type rice. Furthermore, the FoxO signaling pathway was involved and genes related to BPH starvation response (Nlbmm), apoptosis and autophagy (caspase 8, ATG13, BNIP3 and IAP), active oxygen elimination (catalase, MSR, ferritin) and detoxification (GST, CarE) were up-regulated in BPH responses to resistant rice.

CONCLUSIONS

The current study provides the first demonstrations of the full diversity and complexity of the BPH transcriptome, and indicates that BPH responses to rice resistance, might be related to starvation stress responses, nutrient transformation, oxidative decomposition, and detoxification. The current result findings will facilitate further exploration of molecular mechanisms of interaction between BPH insects and host rice.

Conserved sequences in the Drosophila mod(mdg4) intron promote poly(A)-independent transcription termination and trans-splicing

Alternative splicing (AS) is a regulatory mechanism of gene expression that greatly expands the coding capacities of genomes by allowing the generation of multiple mRNAs from a single gene. In Drosophila, the mod(mdg4) locus is an extreme example of AS that produces more than 30 different mRNAs via trans-splicing that joins together the common exons and the 3′ variable exons generated from alternative promoters. To map the regions required for trans-splicing, we have developed an assay for measuring trans-splicing events and identified a 73-bp region in the last common intron that is critical for trans-splicing of three pre-mRNAs synthesized from different DNA strands. We have also found that conserved sequences in the distal part of the last common intron induce polyadenylation-independent transcription termination and are enriched by paused RNA polymerase II (RNAP II). These results suggest that all mod(mdg4) mRNAs are formed by joining in trans the 5′ splice site in the last common exon with the 3′ splice site in one of the alternative exons.

Improving Silkworm Genome Annotation Using a Proteogenomics Approach

The silkworm genome has been deeply sequenced and assembled, but accurate genome annotation, which is important for modern biological research, remains far from complete. To improve silkworm genome annotation, we carried out a proteogenomics analysis using 9.8 million mass spectra collected from different tissues and developmental stages of the silkworm. The results confirmed the translational products of 4307 existing gene models and identified 1701 novel genome search-specific peptides (GSSPs). Using these GSSPs, 74 novel gene-coding sequences were identified, and 121 existing gene models were corrected. We also identified 1182 novel junction peptides based on an exon-skipping database that resulted in the identification of 973 alternative splicing sites. Furthermore, we performed RNA-seq analysis to improve silkworm genome annotation at the transcriptional level. A total of 1704 new transcripts and 1136 new exons were identified, 2581 untranslated regions (UTRs) were revised, and 1301 alternative splicing (AS) genes were identified. The transcriptomics results were integrated with the proteomics data to further complement and verify the new annotations. In addition, 14 incorrect genes and 10 skipped exons were verified using the two analysis methods. Altogether, we identified 1838 new transcripts and 1593 AS genes and revised 5074 existing genes using proteogenomics and transcriptome analyses. Data are available via ProteomeXchange with identifier PXD009672. The large-scale proteogenomics and transcriptome analyses in this study will greatly improve silkworm genome annotation and contribute to future studies.

Genome-wide profiling of the alternative splicing provides insights into development in Plutella xylostella

Background

The diamondback moth (DBM), Plutella xylostella (L.), is a major pest of cruciferous crops worldwide. While the species has become a model for genomics, post-transcriptional mechanisms associated with development and sex determination have not been comprehensively studied and the lack of complete structure of mRNA transcripts limits further research.

Results

Here, we combined the methods of single-molecule long-read sequencing technology (IsoSeq) and RNA-seq to re-annotate the published DBM genome and present the genome-wide identification of alternative splicing (AS) associated with development and sex determination of DBM. In total, we identified ~ 13,900 genes (~ 77%) annotated in the DBM genome (version-2), resulting in the correction of 1586 wrongly annotated genes and identification of 78,000 previously unannotated transcripts. We also identified 1804 genes showing alternative splicing (AS) in each of the developmental stages and sexes, suggesting that AS events are ubiquitous in DBM. Comparative analyses showed that these AS events were rarely shared among developmental stages, indicating that they may play key specific roles in regulation of insect development. Further, we found 156 genes showing different AS events and expression patterns between males and females, linking them to potential functions in sex determination.

Conclusion

Overall, the P. xylostella transcriptome provides the significant information about regulatory alternative splicing events, which are shown to be involved in development and sex determination. Our work presents a solid foundation to better understand the mechanism of post-transcriptional regulation, and offers wider insights into insect development and sex determination.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5838-3) contains supplementary material, which is available to authorized users.

Transcriptome-wide analysis of the difference of alternative splicing in susceptible and resistant silkworm strains after BmNPV infection

Novel alternative splicing events were identified from BmNPV-susceptible and -resistant silkworm strains after BmNPV infection using high-throughput RNA-sequencing strategy. In total, 12.82 Gb clean RNA-seq data were generated for the two midgut samples from BmNPV-susceptible and -resistant silkworm strains, and 14.78 Gb clean data for the two fat body samples. The number of alternative splicing events and isoforms in the BmNPV-susceptible silkworm strain was more than that in the BmNPV-resistant silkworm strain. Furthermore, alternative splicing genes uniquely present in BmNPV-resistant silkworm strain were involved in functions about ribosome, whereas, alternative splicing genes uniquely present in BmNPV-susceptible silkworm strain were implicated in functions like DNA helicase activity and signal transduction. Additionally, 33 expressed SR or SR-like proteins were identified, and three genes encoding SR or SR-like proteins (tetratricopeptide repeat protein 14 homolog, ubiquitin carboxyl-terminal hydrolase 32 and zinc finger CCCH domain-containing protein 18) have a higher number of different alternative splicing events between two silkworm strains. The present study suggested BmNPV treatment may have a smaller effect on the mRNA transcription in BmNPV-resistant silkworms than that in BmNPV-susceptible silkworms, and functions of alternative splicing genes are different between the two silkworm strains.

Alternative splicing regulation of doublesex gene by RNA-binding proteins in the silkworm Bombyx mori

Doublesex is highly conserved and sex-specifically spliced in insect sex-determination pathways, and its alternative splicing (AS) is regulated by Transformer, an exonic splicing activator, in the model system of Drosophila melanogaster. However, due to the lack of a transformer gene, AS regulation of doublesex remains unclear in Lepidoptera, which contain the economically important silkworm Bombyx mori and thousands of agricultural pests. Here, we use yeast three-hybrid system to screen for RNA-binding proteins that recognize sex-specific exons 3 and 4 of silkworm doublesex (Bm-dsx); this approach identified BxRBP1/Lark binding to the exon 3, and BxRBP2/TBPH and BxRBP3/Aret binding to the exon 4. Investigation of tissues shows that BxRBP1 and BxRBP2 have no sex specificity, but BxRBP3 has - three of its four isoforms are expressed with a sex-bias. Using novel sex-specific silkworm cell lines, we find that BxRBP1 and BxRBP3 directly interact with each other, and cooperatively function as splicing repressors. Over-expression of BxRBP1 and BxRBP3 isoforms efficiently inhibits splicing of the exons 3 and 4 in the female-specific cells and generates the male-specific isoform of Bm-dsx. We also demonstrate that the sex-determination upstream gene Masc regulates alternatively transcribed BxRBP3 isoforms. Thus, we identify a new regulatory mechanism of doublesex AS in the silkworm, revealing an evolutionary divergence in insect sex-determination.

Transcriptome analysis in different developmental stages of Batocera horsfieldi (Coleoptera: Cerambycidae) and comparison of candidate olfactory genes

The white-striped longhorn beetle Batocera horsfieldi (Coleoptera: Cerambycidae) is a polyphagous wood-boring pest that causes substantial damage to the lumber industry. Moreover olfactory proteins are crucial components to function in related processes, but the B. horsfieldi genome is not readily available for olfactory proteins analysis. In the present study, developmental transcriptomes of larvae from the first instar to the prepupal stage, pupae, and adults (females and males) from emergence to mating were built by RNA sequencing to establish a genetic background that may help understand olfactory genes. Approximately 199 million clean reads were obtained and assembled into 171,664 transcripts, which were classified into 23,380, 26,511, 22,393, 30,270, and 87, 732 unigenes for larvae, pupae, females, males, and combined datasets, respectively. The unigenes were annotated against NCBI’s non-redundant nucleotide and protein sequences, Swiss-Prot, Gene Ontology (GO), Pfam, Clusters of Eukaryotic Orthologous Groups (KOG), and KEGG Orthology (KO) databases. A total of 43,197 unigenes were annotated into 55 sub-categories under the three main GO categories; 25,237 unigenes were classified into 26 functional KOG categories, and 25,814 unigenes were classified into five functional KEGG Pathway categories. RSEM software identified 2,983, 3,097, 870, 2,437, 5,161, and 2,882 genes that were differentially expressed between larvae and males, larvae and pupae, larvae and females, males and females, males and pupae, and females and pupae, respectively. Among them, genes encoding seven candidate odorant binding proteins (OBPs) and three chemosensory proteins (CSPs) were identified. RT-PCR and RT-qPCR analyses showed that BhorOBP3, BhorCSP2, and BhorOBPC1/C3/C4 were highly expressed in the antenna of males, indicating these genes may may play key roles in foraging and host-orientation in B. horsfieldi. Our results provide valuable molecular information about the olfactory system in B. horsfieldi and will help guide future functional studies on olfactory genes.

Single molecule RNA sequencing uncovers trans-splicing and improves annotations in Anopheles stephensi

Single molecule real-time (SMRT) sequencing has recently been used to obtain full-length cDNA sequences that improve genome annotation and reveal RNA isoforms. Here, we used one such method called isoform sequencing from Pacific Biosciences (PacBio) to sequence a cDNA library from the Asian malaria mosquito Anopheles stephensi. More than 600 000 full-length cDNAs, referred to as reads of insert, were identified. Owing to the inherently high error rate of PacBio sequencing, we tested different approaches for error correction. We found that error correction using Illumina RNA sequencing (RNA-seq) generated more data than using the default SMRT pipeline. The full-length error-corrected PacBio reads greatly improved the gene annotation of Anopheles stephensi: 4867 gene models were updated and 1785 alternatively spliced isoforms were added to the annotation. In addition, six trans-splicing events, where exons from different primary transcripts were joined together, were identified in An. stephensi. All six trans-splicing events appear to be conserved in Culicidae, as they are also found in Anopheles gambiae and Aedes aegypti. The proteins encoded by trans-splicing events are also highly conserved and the orthologues of these proteins are cis-spliced in outgroup species, indicating that trans-splicing may arise as a mechanism to rescue genes that broke up during evolution.

Genome-Wide Analysis of Alternative Splicing Provides Insights into Stress Adaptation of the Pacific Oyster

Alternative splicing (AS) is thought to enhance transcriptome diversity dramatically and play an important role in stress adaptation. While well studied in vertebrates, AS remains poorly understood in invertebrates. Here, we used high-throughput RNA-sequencing data to perform a genome-wide survey of AS in the Pacific oyster (Crassostrea gigas), an economically important mollusk that is cultivated worldwide. This analysis identified 8223 AS events corresponding to 4480 genes in the Pacific oyster, suggesting that about 16 % of oyster multiexonic genes undergo AS. We observed that a majority of the identified AS events were related to skipped exons (37.8 %). Then Gene Ontology analysis was conducted to analyze the function of the genes that undergo AS and the genes that produce more than five AS isoforms. After that, the expression of AS isoforms facing temperature, salinity, and air exposure challenge were examined. To validate our bioinformatic-predicted results and examine whether AS affects stress adaptation, we selected heat-shock protein 60 (HSP60) and HSP90 genes, both of which experience AS, for reverse transcription PCR (RT-PCR). We also performed quantitative real-time PCR (qRT-PCR) to determine the relative expression of each AS isoform among different stress adapted populations. Our study indicates that AS events are likely complex in the Pacific oyster and may be related to stress adaptation. These results will complement the predicted gene database of C. gigas and provide an invaluable resource for future functional genomic studies on molluscs.

BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori

BACKGROUND

Long non-coding RNAs (lncRNAs) may play critical roles in a wide range of developmental processes of higher organisms. Recently, lncRNAs have been widely identified across eukaryotes and many databases of lncRNAs have been developed for human, mouse, fruit fly, etc. However, there is rare information about them in the only completely domesticated insect, silkworm (Bombyx mori).

DESCRIPTION

In this study, we systematically scanned lncRNAs using the available silkworm RNA-seq data and public unigenes. Finally, we identified and collected 6281 lncRNAs in the silkworm. Besides, we also collected 1986 microRNAs (miRNAs) from previous studies. Then, we organized them into a comprehensive and web-based database, BmncRNAdb. This database offers a user-friendly interface for data browse and online analysis as well as the three online tools for users to predict the target genes of lncRNA or miRNA.

CONCLUSIONS

We have systematically identified and collected the silkworm lncRNAs and constructed a comprehensive database of the silkworm lncRNAs and miRNAs. This work gives a glimpse into lncRNAs of the silkworm and lays foundations for the ncRNAs study of the silkworm and other insects in the future. The BmncRNAdb is freely available at http://gene.cqu.edu.cn/BmncRNAdb/index.php .

Evolutionary Insights into RNA trans-Splicing in Vertebrates

Pre-RNA splicing is an essential step in generating mature mRNA. RNA trans-splicing combines two separate pre-mRNA molecules to form a chimeric non-co-linear RNA, which may exert a function distinct from its original molecules. Trans-spliced RNAs may encode novel proteins or serve as noncoding or regulatory RNAs. These novel RNAs not only increase the complexity of the proteome but also provide new regulatory mechanisms for gene expression. An increasing amount of evidence indicates that trans-splicing occurs frequently in both physiological and pathological processes. In addition, mRNA reprogramming based on trans-splicing has been successfully applied in RNA-based therapies for human genetic diseases. Nevertheless, clarifying the extent and evolution of trans-splicing in vertebrates and developing detection methods for trans-splicing remain challenging. In this review, we summarize previous research, highlight recent advances in trans-splicing, and discuss possible splicing mechanisms and functions from an evolutionary viewpoint.

The evolutionary landscape of intergenic trans-splicing events in insects

To explore the landscape of intergenic trans-splicing events and characterize their functions and evolutionary dynamics, we conduct a mega-data study of a phylogeny containing eight species across five orders of class Insecta, a model system spanning 400 million years of evolution. A total of 1,627 trans-splicing events involving 2,199 genes are identified, accounting for 1.58% of the total genes. Homology analysis reveals that mod(mdg4)-like trans-splicing is the only conserved event that is consistently observed in multiple species across two orders, which represents a unique case of functional diversification involving trans-splicing. Thus, evolutionarily its potential for generating proteins with novel function is not broadly utilized by insects. Furthermore, 146 non-mod trans-spliced transcripts are found to resemble canonical genes from different species. Trans-splicing preserving the function of 'breakup' genes may serve as a general mechanism for relaxing the constraints on gene structure, with profound implications for the evolution of genes and genomes.

A conserved intronic U1 snRNP-binding sequence promotes trans-splicing in Drosophila

Gao et al. investigate mod(mdg4), a classic trans-spliced gene in Drosophila, and report that two critical RNA sequences in the middle of the last 5′ intron, TSA and TSB, promote trans-splicing of mod(mdg4). In TSA, a 13-nt core motif is conserved across Drosophila species and is essential and sufficient for trans-splicing, which binds U1 snRNP through strong base-pairing with U1 snRNA. In TSB, a conserved secondary structure acts as an enhancer. Deletions of TSA and TSB result in developmental defects in flies.

Unlike typical cis-splicing, trans-splicing joins exons from two separate transcripts to produce chimeric mRNA and has been detected in most eukaryotes. Trans-splicing in trypanosomes and nematodes has been characterized as a spliced leader RNA-facilitated reaction; in contrast, its mechanism in higher eukaryotes remains unclear. Here we investigate mod(mdg4), a classic trans-spliced gene in Drosophila, and report that two critical RNA sequences in the middle of the last 5′ intron, TSA and TSB, promote trans-splicing of mod(mdg4). In TSA, a 13-nucleotide (nt) core motif is conserved across Drosophila species and is essential and sufficient for trans-splicing, which binds U1 small nuclear RNP (snRNP) through strong base-pairing with U1 snRNA. In TSB, a conserved secondary structure acts as an enhancer. Deletions of TSA and TSB using the CRISPR/Cas9 system result in developmental defects in flies. Although it is not clear how the 5′ intron finds the 3′ introns, compensatory changes in U1 snRNA rescue trans-splicing of TSA mutants, demonstrating that U1 recruitment is critical to promote trans-splicing in vivo. Furthermore, TSA core-like motifs are found in many other trans-spliced Drosophila genes, including lola. These findings represent a novel mechanism of trans-splicing, in which RNA motifs in the 5′ intron are sufficient to bring separate transcripts into close proximity to promote trans-splicing.

PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data

The vast majority of multi-exon genes in higher eukaryotes are alternatively spliced and changes in alternative splicing (AS) can impact gene function or cause disease. High-throughput RNA sequencing (RNA-seq) has become a powerful technology for transcriptome-wide analysis of AS, but RT-PCR still remains the gold-standard approach for quantifying and validating exon splicing levels. We have developed PrimerSeq, a user-friendly software for systematic design and visualization of RT-PCR primers using RNA-seq data. PrimerSeq incorporates user-provided transcriptome profiles (i.e., RNA-seq data) in the design process, and is particularly useful for large-scale quantitative analysis of AS events discovered from RNA-seq experiments. PrimerSeq features a graphical user interface (GUI) that displays the RNA-seq data juxtaposed with the expected RT-PCR results. To enable primer design and visualization on user-provided RNA-seq data and transcript annotations, we have developed PrimerSeq as a stand-alone software that runs on local computers. PrimerSeq is freely available for Windows and Mac OS X along with source code at http://primerseq.sourceforge.net/. With the growing popularity of RNA-seq for transcriptome studies, we expect PrimerSeq to help bridge the gap between high-throughput RNA-seq discovery of AS events and molecular analysis of candidate events by RT-PCR.

Transcriptomic analysis of differentially expressed genes in the Ras1(CA)-overexpressed and wildtype posterior silk glands

Background

Using the piggyBac-mediated GAL4/UAS transgenic system established in the silkworm, Bombyx mori, we have previously reported that overexpression of the Ras1^CA oncogene specifically in the posterior silk gland (PSG) improved cell growth, fibroin synthesis, and thus silk yield. However, the detailed molecular mechanism remains to be fully elucidated. To achieve this goal, Illumina sequencing was used in the present study to compare the transcriptomes of the Ras1^CA-overexpressed and wildtype PSGs.

Results

The transcriptomic sequencing results in 56 million reads following filtering steps. Most of the reads (~70%) are successfully mapped to the Bombyx genome. The mapped reads are situated within at least 9,133 predicted genes, covering 62.46% genes of the Bombyx genome. GO annotation shows that 2512 of the 2,636 differentially expressed genes (DEGs) are mostly distributed in metabolic process, cell and cell part, and binding, and KEGG annotation shows that 1,941 DEGs are mapped into 277 pathways. Importantly, Ras1^CA overexpression in the PSG upregulated many DEGs distributed in “pathways in cancer”, “insulin signaling pathway”, and “MAPK signaling pathway” as well as “purine metabolism” and “pyrimidine metabolism”. Transcriptional regulation of these DEGs was verified by quantitative real-time PCR. Moreover, injection of small-molecule chemical inhibitors of the Ras1 downstream effectors into the Ras1^CA-overexpressed silkworms revealed that both Raf-MAPK and PI3K-TORC1 pathways are required for the Ras1-induced DEG expression.

Conclusion

The transcriptomic analysis illustrates that, apart from phosphorylational regulation, Ras1 activates its downstream Raf-MAPK and PI3K-TORC1 pathways at the transcriptional level. Meanwhile, Ras1 increases DNA content and induces endoreplication, at least in part, by upregulating genes in “nucleotide metabolism” and “cell cycle”. This study provides further insights into the molecular mechanism of how Ras1^CA overexpression in the PSG improves silk yield.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-182) contains supplementary material, which is available to authorized users.

New insights into the genomic organization and splicing of the doublesex gene, a terminal regulator of sexual differentiation in the silkworm Bombyx mori

Sex-determination mechanisms differ among organisms. The primary mechanism is diverse, whereas the terminal regulator is relatively-conserved. We analyzed the transcripts of the Bombyx mori doublesex gene (Bmdsx), and reported novel results concerning the genomic organization and expression of Bmdsx. Bmdsx consists of nine exons and eight introns, of which two exons are novel and have not been reported previously. Bmdsx transcripts are spliced to generate seventeen alternatively-spliced forms and eleven putative trans-spliced variants. Thirteen of the alternatively-spliced forms and five of the putative trans-spliced forms are reported here for the first time. Sequence analysis predicts that ten female-specific, six male-specific splice forms and one splice form found in males and females will result in four female-specific, two male-specific Dsx proteins and one Dsx protein common to males and females. The Dsx proteins are expected to be functional and regulate downstream target genes. Some of the predicted Dsx proteins are described here for the first time. Therefore the expression of the dsx gene in B. mori results in a variety of cis- and trans-spliced transcripts and multiple Dsx proteins. These findings show that in B. mori there is a complicated pattern of dsx splicing, and that the regulation of splicing and sex-specific functions of lepidopteran dsx have evolved complexity.

Successive gain of insulator proteins in arthropod evolution

Alteration of regulatory DNA elements or their binding proteins may have drastic consequences for morphological evolution. Chromatin insulators are one example of such proteins and play a fundamental role in organizing gene expression. While a single insulator protein, CTCF (CCCTC-binding factor), is known in vertebrates, Drosophila melanogaster utilizes six additional factors. We studied the evolution of these proteins and show here that—in contrast to the bilaterian-wide distribution of CTCF—all other D. melanogaster insulators are restricted to arthropods. The full set is present exclusively in the genus Drosophila whereas only two insulators, Su(Hw) and CTCF, existed at the base of the arthropod clade and all additional factors have been acquired successively at later stages. Secondary loss of factors in some lineages further led to the presence of different insulator subsets in arthropods. Thus, the evolution of insulator proteins within arthropods is an ongoing and dynamic process that reshapes and supplements the ancient CTCF-based system common to bilaterians. Expansion of insulator systems may therefore be a general strategy to increase an organism’s gene regulatory repertoire and its potential for morphological plasticity.

Novel female-specific trans-spliced and alternative splice forms of dsx in the silkworm Bombyx mori

The Bombyx mori doublesex gene (Bmdsx) plays an important role in somatic sexual development. Its pre-mRNA splices in a sex-specific manner to generate two female-specific and one male-specific splice forms. The present study investigated six novel dsx variants generated by trans-splicing between female dsx transcripts and two additional novel genes, dsr1 and dsr2. Expression analysis indicated that Bmdsx-dsr1 represented splicing noise, whereas dsr2, which trans-spliced with dsx to generate five variants, regulated the expression of the female-specific B. mori dsx transcript Bmdsx(F)s. We unexpectedly found a novel exon 2n insertion during Bmdsx transcription, which did not influence the validity of the novel protein, BmDSX(F3). Ectopic expression of BmDSX(F3) repressed the pheromone-binding protein gene and the testis-specific gene A2 in males, and activated of the storage protein 1 gene. Our findings suggest that trans-splicing is a novel regulatory function of Bmdsx, which participates in female sexual development by regulating the expression of three BmDSX(F) proteins.