InsectBase 2.0: a comprehensive gene resource for insects

Yang, Mei; Dong, Jing; Tang, Shenyang; Chen, Xi; Chen, Hao; Duanmu, Haonan; Cong, Yuyang; Chen, Mengyao; Ye, Xinhai; Zhou, Huaqiang; He, Kang; Li, Fēi

doi:10.1093/nar/gkab1090

Cited by 103 publications

(80 citation statements)

References 56 publications

(67 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The Ruminant Genome Database ( 72 ) paper reports significant expansion of its multi-omics content throughout. Insects are the focus of three returning database: InsectBase ( 73 ) reports dramatic increases in content as well as new features focusing on ncRNA–mRNA interactions and likely horizontal gene transfer; Hymenoptera Genome Database ( 74 ) covers a tripling of covered species and a focus on better Gene Ontology ( 75 ) assignments allowing, for example, better on-site GO enrichment analysis; and FlyAtlas 2 ( 76 ) enhances its (sub-) tissue-specific gene expression data and introduces a new co-expression tool. As usual, aspects of human genomics feature strongly.…”

Section: New and Updated Databasesmentioning

confidence: 99%

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Rigden

Fernández

2021

Nucleic Acids Research

View full text Add to dashboard Cite

The 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide updates on databases most recently published elsewhere. Seven new databases focus specifically on COVID-19 and SARS-CoV-2, including SCoV2-MD, the first of the Issue's Breakthrough Articles. Major nucleic acid databases reporting updates include MODOMICS, JASPAR and miRTarBase. The AlphaFold Protein Structure Database, described in the second Breakthrough Article, is the stand-out in the protein section, where the Human Proteoform Atlas and GproteinDb are other notable new arrivals. Updates from DisProt, FuzDB and ELM comprehensively cover disordered proteins. Under the metabolism and signalling section Reactome, ConsensusPathDB, HMDB and CAZy are major returning resources. In microbial and viral genomes taxonomy and systematics are well covered by LPSN, TYGS and GTDB. Genomics resources include Ensembl, Ensembl Genomes and UCSC Genome Browser. Major returning pharmacology resource names include the IUPHAR/BPS guide and the Therapeutic Target Database. New plant databases include PlantGSAD for gene lists and qPTMplants for post-translational modifications. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Our latest update to the NAR online Molecular Biology Database Collection brings the total number of entries to 1645. Following last year's major cleanup, we have updated 317 entries, listing 89 new resources and trimming 80 discontinued URLs. The current release is available at http://www.oxfordjournals.org/nar/database/c/.

show abstract

Section: New and Updated Databasesmentioning

confidence: 99%

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Rigden

Fernández

2021

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…The GC content of the F. auricularia genome is 31.03%, markedly greater than that the 19.3% GC observed in the genome of the earwig A. maritima (Mei et al . 2022).…”

Section: Resultsmentioning

confidence: 62%

“…Using the insect database (n=1,367) it has 83.4% complete and 10.8% fragmented Busco scores. The A. maritima assembly has an N50 of 1.4Mb with a genome size of 649.7 Mb (Mei et al . 2022).…”

Section: Resultsmentioning

confidence: 99%

A high-quality genome assembly and annotation of the European earwig Forficula auricularia

Bhattarai

Katuwal

Poulin

et al. 2022

Preprint

View full text Add to dashboard Cite

The European earwig Forficula auricularia is an important model for studies of maternal care, sexual selection, sociality and host-parasite interactions. However, detailed genetic investigations of this species are hindered by a lack of genomic resources. Here we present a high-quality hybrid genome assembly for F. auricularia. The genome was assembled using nanopore long-reads and 10x chromium link-reads. The final assembly is 1.06Gb in length with 31.03% GC content. It consists of 919 scaffolds with an N50 of 12.55Mb. Half of the genome is present in only 20 scaffolds. Benchmarking Universal Single-Copy Orthologs scores are ∼90% from three sets of single-copy orthologs (eukaryotic, insect, and arthropod). The total repeat elements in the genome are 64.62%. The MAKER2 pipeline annotated 12,876 protein-coding genes and 21,031 mRNAs. The genome assembly, annotation, and associated resources will be of high value to a large and diverse group of researchers working on Dermapterans.

show abstract

“…Using SOAPdenovo (http://soap.genomics.org.cn/, v1.05) [68], we performed preliminary assembling with multiple trials of different Kmer parameters, and then we used the GapCloser software to perform local gap lling and base correction [69]. We also used the PacBio sequel II platform to de novo sequence the genome and we used the HiFiasm software (v0.14) (with the parameters -t32 and -f39) [79] to de novo assemble the genome. The Illumina short reads were then aligned to the corrected HiFiasm contigs using BWA-MEM (v0.7.17) [71], and Pilon (v1.2) [72] was used to correct errors in the contigs.…”

Section: Genome Assembly and Quality Controlmentioning

confidence: 99%

“…Ortho nder v. 2.3.3 [78] was used to cluster the protein-coding genes of A. nilaparvatae, Ceratosolen solmsi, Pteromalus puparum, Trichomalopsis sarcophagae, Nasonia vitripennis, Copidosoma oridanum, Trichogramma pretisum, Trichogramma brassicaem, Diachasma alloeum, Fopius arisanus, Microplitis demolitor, Belonocnema treatae, and Apis mellifera into orthologous groups [79]. We identi ed 205 single-copy groups (with one member for each species).…”

Section: Phylogenetic Analysis and Gene Family Analysesmentioning

confidence: 99%

The Genome of Rice Planthopper Egg Parasitoid Wasps Anagrus Nilaparvatae (Hymenoptera: Mymaridae) Casts Light on the Chemo- and Mechano-Sensing in Parasitism

Ying¹,

Guo²,

Wang³

et al. 2022

Preprint

View full text Add to dashboard Cite

Background Mymaridae is an ancient insect group, which is a basal lineage in the Chalcidoidea phylogeny. The species of Mymaridae have great potential for biological control. Anagrus nilaparvatae, a representative specie of Mymaridae, is ideal for controlling rice planthopper due to its high rate of parasitism by finding hosts efficiently from paddy ridges to fields. Results Using both single-molecule real-time and Illumina sequencing, we sequenced and assembled the whole genome of A. nilaparvatae, which is the first genome sequenced in family Mymaridae. The assembly consists of 394 scaffolds accumulated to 488.8Mb. The assembly is of high continuity and completeness, indicated by the N50 value of 25,368,259bp and 98.4% mapping rate of BUSCO orthologs. 16894 protein-coding genes in the genome were annotated. The phylogenomic tree constructed for A. nilaparvatae and other 12 species of Hymenoptera confirmed that family Mymaridae is basal in the Chalcidoidea superfamily and sister to all the remaining Chalcidoidea species. The divergence between A. nilaparvatae and the other seven Chalcidoidea species was dated at ~ 126.9 Mya. Chemoreceptor and mechanoreceptor genes are important in the parasitic behavior. We identified 17 OBPs, 11 CSPs, 4 NPC2s, 88 ORs, 7 GRs, 22 IRs and 13 SNMPs in the genome of A. nilaparvatae, which are associated with the chemosensory function. Strikingly, there are only 1 PPK and 3 TRP genes in the genome that are relevant to the mechanosensory function. Conclusions The small numbers of chemo- and mechano-sensory genes in A. nilaparvatae indicate the species-specific host detection and oviposition behavior of A. nilaparvatae might be regulated by relatively simple molecular pathways.

show abstract

InsectBase 2.0: a comprehensive gene resource for insects

Cited by 103 publications

References 56 publications

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

A high-quality genome assembly and annotation of the European earwig Forficula auricularia

The Genome of Rice Planthopper Egg Parasitoid Wasps Anagrus Nilaparvatae (Hymenoptera: Mymaridae) Casts Light on the Chemo- and Mechano-Sensing in Parasitism

Contact Info

Product

Resources

About