OMIGA: Optimized Maker-Based Insect Genome Annotation

Genome assembly of the ectoparasitoid wasp Theocolax elegans

The ectoparasitoid wasp Theocolax elegans is a cosmopolitan and generalist pteromalid parasitoid of several major storage insect pests, and can effectively suppress a host population in warehouses. However, little molecular information about this wasp is currently available. In this study, we assembled the genome of T. elegans using PacBio long-read sequencing, Illumina sequencing, and Hi-C methods. The genome assembly is 662.73 Mb in length with contig and scaffold N50 values of 1.15 Mb and 88.8 Mb, respectively. The genome contains 56.4% repeat sequences and 23,212 protein-coding genes were annotated. Phylogenomic analyses revealed that T. elegans diverged from the lineage leading to subfamily Pteromalinae (Nasonia vitripennis and Pteromalus puparum) approximately 110.5 million years ago. We identified 130 significantly expanded gene families, 34 contracted families, 248 fast-evolving genes, and 365 positively selected genes in T. elegans. Additionally, 260 olfactory receptors and 285 venom proteins were identified. This genome assembly provides valuable genetic bases for future investigations on evolution, molecular biology and application of T. elegans.

Genome of the parasitoid wasp Cotesia chilonis sheds light on amino acid resource exploitation

Background

A fundamental feature of parasitism is the nutritional exploitation of host organisms by their parasites. Parasitoid wasps lay eggs on arthropod hosts, exploiting them for nutrition to support larval development by using diverse effectors aimed at regulating host metabolism. However, the genetic components and molecular mechanisms at the basis of such exploitation, especially the utilization of host amino acid resources, remain largely unknown. To address this question, here, we present a chromosome-level genome assembly of the parasitoid wasp Cotesia chilonis and reconstruct its amino acid biosynthetic pathway.

Results

Analyses of the amino acid synthetic pathway indicate that C. chilonis lost the ability to synthesize ten amino acids, which was confirmed by feeding experiments with amino acid-depleted media. Of the ten pathways, nine are known to have been lost in the common ancestor of animals. We find that the ability to synthesize arginine was also lost in C. chilonis because of the absence of two key genes in the arginine synthesis pathway. Further analyses of the genomes of 72 arthropods species show that the loss of arginine synthesis is common in arthropods. Metabolomic analyses by UPLC-MS/MS reveal that the temporal concentrations of arginine, serine, tyrosine, and alanine are significantly higher in host (Chilo suppressalis) hemolymph at 3 days after parasitism, whereas the temporal levels of 5-hydroxylysine, glutamic acid, methionine, and lysine are significantly lower. We sequence the transcriptomes of a parasitized host and non-parasitized control. Differential gene expression analyses using these transcriptomes indicate that parasitoid wasps inhibit amino acid utilization and activate protein degradation in the host, likely resulting in the increase of amino acid content in host hemolymph.

Conclusions

We sequenced the genome of a parasitoid wasp, C. chilonis, and revealed the features of trait loss in amino acid biosynthesis. Our work provides new insights into amino acid exploitation by parasitoid wasps, and this knowledge can specifically be used to design parasitoid artificial diets that potentially benefit mass rearing of parasitoids for pest control.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01313-3.

Chromosome-level genome assembly of the mirid predator Cyrtorhinus lividipennis Reuter (Hemiptera: Miridae), an important natural enemy in the rice ecosystem

Though the genomes of many rice herbivorous pests have recently been well characterized, little is known about the genome of their natural enemies. Here, by using the Illumina and PacBio platforms, we sequenced and assembled the whole genome of the mirid species Cyrtorhinus lividipennis Reuter (Hemiptera: Miridae), which is an economically and ecologically important natural enemy in the rice ecosystem acting as a dominant predator for planthoppers and leafhoppers in the field. Through Hi-C scaffolding, 1615 scaffolds with a total size of 338.08 Mb were successfully anchored onto 13 chromosomes. The assembled genome size was 345.75 Mb with a final scaffold N50 of 27.58 Mb. Approximately 107.51 Mb of sequences accounting for 31.10% of the genome were identified as repeat elements, and 14,644 protein-coding genes were annotated. Phylogenetic analysis showed that C. lividipennis clustered with other Hemipteran species and diverged from Apolygus lucorum about 66.7 million years ago. Gene families related to detoxification, environmental adaptation and digestion were analysed comparatively with other Hemipteran species, but no significant expansion or contraction was found in C. lividipennis. We also observed male meiosis in C. lividipennis, which showed a typical post-reduction of sex chromosomes and a karyotype of 2n = 22 + XY. As the first natural-enemy genome in the rice ecosystem, the genomic resource of C. lividipennis not only expands our understanding of the multitrophic interactions (host plant-prey-predator), but also provides a genomic basis for better understanding this dominant predator and therefore promotes sustainable rice pest management and food grain production.

A chromosome-level assembly of the harlequin ladybird Harmonia axyridis as a genomic resource to study beetle and invasion biology

The harlequin ladybird, Harmonia axyridis (Pallas), is a well-known model organism for genetic studies and is also a well-studied natural enemy used for pest control. It became an invasive species after being introduced to North America and Europe as a pest control agent. Though two genome assemblies for this insect have been previously reported, a high-quality genome assembly at the chromosome level is still not available. Here, we obtained a new chromosome-level genome assembly of H. axyridis by combining various sequencing technologies, namely Illumina short reads, PacBio long reads, 10X Genomics and Hi-C. The chromosome-level genome assembly is 423 Mb with a scaffold N50 of 45.92 Mb. Using Hi-C data 1,897 scaffolds were anchored to eight chromosomes. A total of 730,068 repeat sequences were identified, making up 51.2% of the assembled genome. After masking these repeat sequences, we annotated 22,810 protein-encoding genes. The X chromosome and Y-linked scaffolds were also identified by resequencing male and female genomes and calculating the male to female coverage ratios. Two gene families associated with environmental adaptation, odorant receptor and cytochrome P450, were analysed and showed no obvious expansion in H. axyridis. We successfully constructed a putative biosynthesis pathway of harmonine, a defence compound in the haemolymph of H. axyridis, which is a key factor for H. axyridis strong immunity. The chromosome-level genome assembly of H. axyridis is a helpful resource for studies of beetle biology and invasive biology.

InsectOR-Webserver for sensitive identification of insect olfactory receptor genes from non-model genomes

Insect Olfactory Receptors (ORs) are diverse family of membrane protein receptors responsible for most of the insect olfactory perception and communication, and hence they are of utmost importance for developing repellents or pesticides. Accurate gene prediction of insect ORs from newly sequenced genomes is an important but challenging task. We have developed a dedicated webserver, 'insectOR', to predict and validate insect OR genes using multiple gene prediction algorithms, accompanied by relevant validations. It is possible to employ this server nearly automatically and perform rapid prediction of the OR gene loci from thousands of OR-protein-to-genome alignments, resolve gene boundaries for tandem OR genes and refine them further to provide more complete OR gene models. InsectOR outperformed the popular genome annotation pipelines (MAKER and NCBI eukaryotic genome annotation) in terms of overall sensitivity at base, exon and locus level, when tested on two distantly related insect genomes. It displayed more than 95% nucleotide level precision in both tests. Finally, given the same input data and parameters, InsectOR missed less than 2% gene loci, in contrast to 55% loci missed by MAKER for Drosophila melanogaster. The webserver is freely available on the web at http://caps.ncbs.res.in/insectOR/ and the basic package can be downloaded from https://github.com/sdk15/insectOR for local use. This tool will allow biologists to perform quick preliminary identification of insect olfactory receptor genes from newly sequenced genomes and also assist in their further detailed annotation. Its usage can also be extended to other divergent gene families.

Chromosomal-level genomes of three rice planthoppers provide new insights into sex chromosome evolution

The brown planthopper Nilaparvata lugens, white-backed planthopper Sogatella furcifera, and small brown planthopper Laodelphax striatellus are three major insect pests of rice. They are genetically close; however, they differ in several ecological traits such as host range, migration capacity, and in their sex chromosomes. Though the draft genome of these three planthoppers have been previously released, the quality of genome assemblies need to be improved. The absence of chromosome-level genome resources has hindered in-depth research of these three species. Here, we performed a de novo genome assembly for N. lugens to increase its genome assembly quality with PacBio and Illumina platforms, increasing the contig N50 to 589.46 Kb. Then, with the new N. lugens genome and previously reported S. furcifera and L. striatellus genome assemblies, we generated chromosome-level scaffold assemblies of these three planthopper species using HiC scaffolding technique. The scaffold N50s significantly increased to 77.63 Mb, 43.36 Mb and 29.24 Mb for N. lugens, S. furcifera and L. striatellus, respectively. To identify sex chromosomes of these three planthopper species, we carried out genome re-sequencing of males and females and successfully determined the X and Y chromosomes for N. lugens, and X chromosome for S. furcifera and L. striatellus. The gene content of the sex chromosomes showed high diversity among these three planthoppers suggesting the rapid evolution of sex-linked genes, and all chromosomes showed high synteny. The chromosome-level genome assemblies of three planthoppers would provide a valuable resource for a broad range of future research in molecular ecology, and subsequently benefits development of modern pest control strategies.

A chromosome-level genome assembly of rice leaffolder, Cnaphalocrocis medinalis

The rice leaffolder, Cnaphalocrocis medinalis Guenée (Crambidae, Lepidoptera), is an important agricultural pest that causes serious losses to rice production in rice-growing regions with high humidity and temperature. However, a lack of genomic resources limits in-depth understanding of its biological characteristics and ecological adaptation. Here, we sequenced the genome of rice leaffolder using the Illumina and PacBio platforms, yielding a genome assembly of 528.3 Mb with a contig N50 of 524.6 kb. A high percentage (96.4%) of Benchmarking Universal Single-Copy Orthologs (BUSCOs) were successfully detected, suggesting high-level completeness of the genome assembly. In total, 39.5% of the genome consists of repeat sequences and 15,045 protein-coding genes were annotated. Comparative phylogenomic analysis showed that some gene families associated with hormone biosynthesis expanded in rice leaffolder. Next, we used the Hi-C technique to produce a chromosome-level genome assembly with a scaffold N50 of 16.1 Mb by anchoring 3,248 scaffolds to 31 chromosomes. The rice leaffolder genome showed high chromosomal synteny with the genome of four other lepidopteran insects. By comparing coverage ratios from the genome resequencing of male and female pupae, we identified near intact Z and W chromosomes. The W chromosome is estimated as 20.75 Mb, which is the most complete known W chromosome in Lepidoptera. The protein-coding genes on the W chromosome were significantly enriched in metabolic pathways. In all, the high-quality genome assembly and the near-intact W chromosome of rice leaffolder should be a useful resource for the fields of insect migration, chromosome evolution and pest control.

Amino acid synthesis loss in parasitoid wasps and other hymenopterans

Insects utilize diverse food resources which can affect the evolution of their genomic repertoire, including leading to gene losses in different nutrient pathways. Here, we investigate gene loss in amino acid synthesis pathways, with special attention to hymenopterans and parasitoid wasps. Using comparative genomics, we find that synthesis capability for tryptophan, phenylalanine, tyrosine, and histidine was lost in holometabolous insects prior to hymenopteran divergence, while valine, leucine, and isoleucine were lost in the common ancestor of Hymenoptera. Subsequently, multiple loss events of lysine synthesis occurred independently in the Parasitoida and Aculeata. Experiments in the parasitoid Cotesia chilonis confirm that it has lost the ability to synthesize eight amino acids. Our findings provide insights into amino acid synthesis evolution, and specifically can be used to inform the design of parasitoid artificial diets for pest control.

A chromosome-level genome assembly provides new insights into paternal genome elimination in the cotton mealybug Phenacoccus solenopsis

Mealybugs (Hemiptera: Pseudococcidae) are economically important agricultural pests with several compelling biological phenomena including paternal genome elimination (PGE). However, limited high-quality genome assemblies of mealybugs hinder a full understanding of this striking and unusual biological phenomenon. Here, we generated a chromosome-level genome assembly of cotton mealybug, Phenacoccus solenopsis, by combining Illumina short reads, PacBio long reads and Hi-C scaffolding. The assembled genome was 292.54 Mb with a contig N50 of 489.8 kb and a scaffold N50 of 49.0 Mb. Hi-C scaffolding assigned 84.42% of the bases to five chromosomes. A total of 110.75 Mb (37.9%) repeat sequences and 11,880 protein-coding genes were predicted. The completeness of the genome assembly was estimated to be 95.5% based on BUSCO genes. In addition, 27,086 (95.3%) full-length PacBio transcripts were uniquely mapped to the assembled scaffolds, suggesting the high quality of the genome assembly. We showed that cotton mealybugs lack differentiated sex chromosomes by analysing genome resequencing data of males and females. DAPI staining confirmed that one chromosome set in males becomes heterochromatin at an early embryo stage. Chromatin immunoprecipitation assays with sequencing analysis demonstrated that the epigenetic modifications H3K9me3 and H3K27me3 are distributed across the whole genome in males, suggesting that these two modifications might be involved in maintaining heterochromatin status. Both markers were more likely to be distributed in repeat regions, while H3K27me3 had higher overall enrichment. Our results provide a valuable genomic resource and shed new light on the genomic and epigenetic basis of PGE in cotton mealybugs.

Insect genomes: progress and challenges

In the wake of constant improvements in sequencing technologies, numerous insect genomes have been sequenced. Currently, 1219 insect genome-sequencing projects have been registered with the National Center for Biotechnology Information, including 401 that have genome assemblies and 155 with an official gene set of annotated protein-coding genes. Comparative genomics analysis showed that the expansion or contraction of gene families was associated with well-studied physiological traits such as immune system, metabolic detoxification, parasitism and polyphagy in insects. Here, we summarize the progress of insect genome sequencing, with an emphasis on how this impacts research on pest control. We begin with a brief introduction to the basic concepts of genome assembly, annotation and metrics for evaluating the quality of draft assemblies. We then provide an overview of genome information for numerous insect species, highlighting examples from prominent model organisms, agricultural pests and disease vectors. We also introduce the major insect genome databases. The increasing availability of insect genomic resources is beneficial for developing alternative pest control methods. However, many opportunities remain for developing data-mining tools that make maximal use of the available insect genome resources. Although rapid progress has been achieved, many challenges remain in the field of insect genomics.

A chromosome-level genome assembly of Cydia pomonella provides insights into chemical ecology and insecticide resistance

The codling moth Cydia pomonella, a major invasive pest of pome fruit, has spread around the globe in the last half century. We generated a chromosome-level scaffold assembly including the Z chromosome and a portion of the W chromosome. This assembly reveals the duplication of an olfactory receptor gene (OR3), which we demonstrate enhances the ability of C. pomonella to exploit kairomones and pheromones in locating both host plants and mates. Genome-wide association studies contrasting insecticide-resistant and susceptible strains identify hundreds of single nucleotide polymorphisms (SNPs) potentially associated with insecticide resistance, including three SNPs found in the promoter of CYP6B2. RNAi knockdown of CYP6B2 increases C. pomonella sensitivity to two insecticides, deltamethrin and azinphos methyl. The high-quality genome assembly of C. pomonella informs the genetic basis of its invasiveness, suggesting the codling moth has distinctive capabilities and adaptive potential that may explain its worldwide expansion.

The codling moth, Cydia pomonella, is one of the major pests of pome fruit (apples and pears) and walnuts. Here, the authors sequence and analyze its genome, providing insights on olfactory and detoxification processes that may underlie its worldwide expansion.

The genomic features of parasitism, Polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum

BACKGROUND

Parasitoid wasps are well-known natural enemies of major agricultural pests and arthropod borne diseases. The parasitoid wasp Macrocentrus cingulum (Hymenoptera: Braconidae) has been widely used to control the notorious insect pests Ostrinia furnacalis (Asian Corn Borer) and O. nubilalis (European corn borer). One striking phenomenon exhibited by M. cingulum is polyembryony, the formation of multiple genetically identical offspring from a single zygote. Moreover, M. cingulum employs a passive parasitic strategy by preventing the host's immune system from recognizing the embryo as a foreign body. Thus, the embryos evade the host's immune system and are not encapsulated by host hemocytes. Unfortunately, the mechanism of both polyembryony and immune evasion remains largely unknown.

RESULTS

We report the genome of the parasitoid wasp M. cingulum. Comparative genomics analysis of M. cingulum and other 11 insects were conducted, finding some gene families with apparent expansion or contraction which might be linked to the parasitic behaviors or polyembryony of M. cingulum. Moreover, we present the evidence that the microRNA miR-14b regulates the polyembryonic development of M. cingulum by targeting the c-Myc Promoter-binding Protein 1 (MBP-1), histone-lysine N-methyltransferase 2E (KMT2E) and segmentation protein Runt. In addition, Hemomucin, an O-glycosylated transmembrane protein, protects the endoparasitoid wasp larvae from being encapsulated by host hemocytes. Motif and domain analysis showed that only the hemomucin in two endoparasitoids, M. cingulum and Venturia canescens, possessing the ability of passive immune evasion has intact mucin domain and similar O-glycosylation patterns, indicating that the hemomucin is a key factor modulating the immune evasion.

CONCLUSIONS

The microRNA miR-14b participates in the regulation of polyembryonic development, and the O-glycosylation of the mucin domain in the hemomucin confers the passive immune evasion in this wasp. These key findings provide new insights into the polyembryony and immune evasion.

WaspBase: a genomic resource for the interactions among parasitic wasps, insect hosts and plants

Insect pests reduce yield and cause economic losses, which are major problems in agriculture. Parasitic wasps are the natural enemies of many agricultural pests and thus have been widely used as biological control agents. Plants, phytophagous insects and parasitic wasps form a tritrophic food chain. Understanding the interactions in this tritrophic system should be helpful for developing parasitic wasps for pest control and deciphering the mechanisms of parasitism. However, the genomic resources for this tritrophic system are not well organized. Here, we describe the WaspBase, a new database that contains 573 transcriptomes of 35 parasitic wasps and the genomes of 12 parasitic wasps, 5 insect hosts and 8 plants. In addition, we identified long non-coding RNA, untranslated regions and 25 widely studied gene families from the genome and transcriptome data of these species. WaspBase provides conventional web services such as Basic Local Alignment Search Tool, search and download, together with several widely used tools such as profile hidden Markov model, Multiple Alignment using Fast Fourier Transform, automated alignment trimming and JBrowse. We also present a collection of active researchers in the field of parasitic wasps, which should be useful for constructing scientific networks in this field.

Draft genome of the honey bee ectoparasitic mite, Tropilaelaps mercedesae, is shaped by the parasitic life history

The number of managed honey bee colonies has considerably decreased in many developed countries in recent years and ectoparasitic mites are considered as major threats to honey bee colonies and health. However, their general biology remains poorly understood. We sequenced the genome of Tropilaelaps mercedesae, the prevalent ectoparasitic mite infesting honey bees in Asia, and predicted 15 190 protein-coding genes that were well supported by the mite transcriptomes and proteomic data. Although amino acid substitutions have been accelerated within the conserved core genes of two mites, T. mercedesae and Metaseiulus occidentalis, T. mercedesae has undergone the least gene family expansion and contraction between the seven arthropods we tested. The number of sensory system genes has been dramatically reduced, but T. mercedesae contains all gene sets required to detoxify xenobiotics. T. mercedesae is closely associated with a symbiotic bacterium (Rickettsiella grylli-like) and Deformed Wing Virus, the most prevalent honey bee virus. T. mercedesae has a very specialized life history and habitat as the ectoparasitic mite strictly depends on the honey bee inside a stable colony. Thus, comparison of the genome and transcriptome sequences with those of a tick and free-living mites has revealed the specific features of the genome shaped by interaction with the honey bee and colony environment. Genome and transcriptome sequences of T. mercedesae, as well as Varroa destructor (another globally prevalent ectoparasitic mite of honey bee), not only provide insights into the mite biology, but may also help to develop measures to control the most serious pests of the honey bee.

Genome-wide analysis of chitinase genes and their varied functions in larval moult, pupation and eclosion in the rice striped stem borer, Chilo suppressalis

Some insect chitinases are required to degrade chitin and ensure successful metamorphosis. Although chitinase genes have been well characterized in several model insects, no reports exist for the rice striped stem borer, Chilo suppressalis, a highly destructive pest that causes huge yield losses in rice production. Here, we conducted a genome-level analysis of chitinase genes in C. suppressalis. After amplification of full-length transcripts with rapid amplification of cDNA ends, we identified 12 chitinase genes in C. suppressalis. All these genes had the conserved domains and motifs of glycoside hydrolase family 18 and grouped phylogenetically into five subgroups. C. suppressalis chitinase 1 (CsCht1) was highly expressed in late pupae, whereas CsCht3 was abundant in early pupae. Both CsCht2 and CsCht4 were highly expressed in larvae. CsCht2 was abundant specifically in the third-instar larvae and CsCht4 showed periodic high expression in 2- to 5-day-old larvae in each instar. Tissue specific expression analysis indicated that CsCht1 and CsCht3 were highly expressed in epidermis whereas CsCht2 and CsCht4 were specifically abundant in the midgut. Knockdown of CsCht1 resulted in adults with curled wings, indicating that CsCht1 might have an important role in wing expansion. Silencing of CsCht2 or CsCht4 arrested moulting, suggesting essential roles in larval development. When the expression of CsCht3 was interfered, defects in pupation occurred. Overall, we provide here the first catalogue of chitinase genes in the rice striped stem borer and have elucidated the functions of four chitinases in metamorphosis.

InsectBase: a resource for insect genomes and transcriptomes

The genomes and transcriptomes of hundreds of insects have been sequenced. However, insect community lacks an integrated, up-to-date collection of insect gene data. Here, we introduce the first release of InsectBase, available online at http://www.insect-genome.com. The database encompasses 138 insect genomes, 116 insect transcriptomes, 61 insect gene sets, 36 gene families of 60 insects, 7544 miRNAs of 69 insects, 96 925 piRNAs of Drosophila melanogaster and Chilo suppressalis, 2439 lncRNA of Nilaparvata lugens, 22 536 pathways of 78 insects, 678 881 untranslated regions (UTR) of 84 insects and 160 905 coding sequences (CDS) of 70 insects. This release contains over 12 million sequences and provides search functionality, a BLAST server, GBrowse, insect pathway construction, a Facebook-like network for the insect community (iFacebook), and phylogenetic analysis of selected genes.

Genome-wide identification of long noncoding RNA genes and their potential association with fecundity and virulence in rice brown planthopper, Nilaparvata lugens

Background

The functional repertoire of long noncoding RNA (lncRNA) has been characterized in several model organisms, demonstrating that lncRNA plays important roles in fundamental biological processes. However, they remain largely unidentified in most species. Understanding the characteristics and functions of lncRNA in insects would be useful for insect resources utilization and sustainable pest control.

Methods

A computational pipeline was developed to identify lncRNA genes in the rice brown planthopper, Nilaparvata lugens, a destructive rice pest causing huge yield losses. Strand specific RT-PCR were used to determine the transcription orientation of lncRNAs.

Results

In total, 2,439 lncRNA transcripts corresponding to 1,882 loci were detected from 12 whole transcriptomes (RNA-seq) datasets, including samples from high fecundity (HFP), low fecundity (LFP), I87i and C89i populations, in addition Mudgo and TN1 virulence strains. The identified N. lugens lncRNAs had low sequence similarities with other known lncRNAs. However, their structural features were similar with mammalian counterparts. N. lugens lncRNAs had shorter transcripts than protein-coding genes due to the lower exon number though their exons and introns were longer. Only 19.9% of N. lugens lncRNAs had multiple alternatively spliced isoforms. We observed biases in the genome location of N. lugens lncRNAs. More than 30% of the lncRNAs overlapped with known protein-coding genes. These lncRNAs tend to be co-expressed with their neighboring genes (Pearson correlation, p < 0.01, T-test) and might interact with adjacent protein-coding genes. In total, 19-148 lncRNAs were specifically-expressed in the samples of HFP, LFP, Mudgo, TN1, I87i and C89i populations. Three lncRNAs specifically expressed in HFP and LFP populations overlapped with reproductive-associated genes.

Discussion

The structural features of N. lugens lncRNAs are similar to mammalian counterparts. Coexpression and function analysis suggeste that N. lugens lncRNAs might have important functions in high fecundity and virulence adaptability.

Conclusions

This study provided the first catalog of lncRNA genes in rice brown planthopper. Gene expression and genome location analysis indicated that lncRNAs might play important roles in high fecundity and virulence adaptation in N. lugens.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1953-y) contains supplementary material, which is available to authorized users.

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts

BACKGROUND

The impact of gene annotation quality on functional and comparative genomics makes gene prediction an important process, particularly in non-model species, including many fungi. Sets of homologous protein sequences are rarely complete with respect to the fungal species of interest and are often small or unreliable, especially when closely related species have not been sequenced or annotated in detail. In these cases, protein homology-based evidence fails to correctly annotate many genes, or significantly improve ab initio predictions. Generalised hidden Markov models (GHMM) have proven to be invaluable tools in gene annotation and, recently, RNA-seq has emerged as a cost-effective means to significantly improve the quality of automated gene annotation. As these methods do not require sets of homologous proteins, improving gene prediction from these resources is of benefit to fungal researchers. While many pipelines now incorporate RNA-seq data in training GHMMs, there has been relatively little investigation into additionally combining RNA-seq data at the point of prediction, and room for improvement in this area motivates this study.

RESULTS

CodingQuarry is a highly accurate, self-training GHMM fungal gene predictor designed to work with assembled, aligned RNA-seq transcripts. RNA-seq data informs annotations both during gene-model training and in prediction. Our approach capitalises on the high quality of fungal transcript assemblies by incorporating predictions made directly from transcript sequences. Correct predictions are made despite transcript assembly problems, including those caused by overlap between the transcripts of adjacent gene loci. Stringent benchmarking against high-confidence annotation subsets showed CodingQuarry predicted 91.3% of Schizosaccharomyces pombe genes and 90.4% of Saccharomyces cerevisiae genes perfectly. These results are 4-5% better than those of AUGUSTUS, the next best performing RNA-seq driven gene predictor tested. Comparisons against whole genome Sc. pombe and S. cerevisiae annotations further substantiate a 4-5% improvement in the number of correctly predicted genes.

CONCLUSIONS

We demonstrate the success of a novel method of incorporating RNA-seq data into GHMM fungal gene prediction. This shows that a high quality annotation can be achieved without relying on protein homology or a training set of genes. CodingQuarry is freely available ( https://sourceforge.net/projects/codingquarry/ ), and suitable for incorporation into genome annotation pipelines.

ChiloDB: a genomic and transcriptome database for an important rice insect pest Chilo suppressalis

ChiloDB is an integrated resource that will be of use to the rice stem borer research community. The rice striped stem borer (SSB), Chilo suppressalis Walker, is a major rice pest that causes severe yield losses in most rice-producing countries. A draft genome of this insect is available. The aims of ChiloDB are (i) to store recently acquired genomic sequence and transcriptome data and integrate them with protein-coding genes, microRNAs, piwi-interacting RNAs (piRNAs) and RNA sequencing (RNA-Seq) data and (ii) to provide comprehensive search tools and downloadable data sets for comparative genomics and gene annotation of this important rice pest. ChiloDB contains the first version of the official SSB gene set, comprising 80 479 scaffolds and 10 221 annotated protein-coding genes. Additionally, 262 SSB microRNA genes predicted from a small RNA library, 82 639 piRNAs identified using the piRNApredictor software, 37 040 transcripts from a midgut transcriptome and 69 977 transcripts from a mixed sample have all been integrated into ChiloDB. ChiloDB was constructed using a data structure that is compatible with data resources, which will be incorporated into the database in the future. This resource will serve as a long-term and open-access database for research on the biology, evolution and pest control of SSB. To the best of our knowledge, ChiloDB is one of the first genomic and transcriptome database for rice insect pests.

Database URL: http://ento.njau.edu.cn/ChiloDB.