Dataset Information

InsectBase 2.0: a comprehensive gene resource for insects.

ABSTRACT: Insects are the largest group of animals on the planet and have a huge impact on human life by providing resources, transmitting diseases, and damaging agricultural crop production. Recently, a large amount of insect genome and gene data has been generated. A comprehensive database is highly desirable for managing, sharing, and mining these resources. Here, we present an updated database, InsectBase 2.0 (http://v2.insect-genome.com/), covering 815 insect genomes, 25 805 transcriptomes and >16 million genes, including 15 045 111 coding sequences, 3 436 022 3'UTRs, 4 345 664 5'UTRs, 112 162 miRNAs and 1 293 430 lncRNAs. In addition, we used an in-house standard pipeline to annotate 1 434 653 genes belonging to 164 gene families; 215 986 potential horizontally transferred genes; and 419 KEGG pathways. Web services such as BLAST, JBrowse2 and Synteny Viewer are provided for searching and visualization. InsectBase 2.0 serves as a valuable platform for entomologists and researchers in the related communities of animal evolution and invertebrate comparative genomics.

SUBMITTER: Mei Y

PROVIDER: S-EPMC8728184 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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InsectBase 2.0: a comprehensive gene resource for insects.

Mei Yang Y Jing Dong D Tang Shenyang S Chen Xi X Chen Hao H Duanmu Haonan H Cong Yuyang Y Chen Mengyao M Ye Xinhai X Zhou Hang H He Kang K Li Fei F

Nucleic acids research 20220101 D1

Insects are the largest group of animals on the planet and have a huge impact on human life by providing resources, transmitting diseases, and damaging agricultural crop production. Recently, a large amount of insect genome and gene data has been generated. A comprehensive database is highly desirable for managing, sharing, and mining these resources. Here, we present an updated database, InsectBase 2.0 (http://v2.insect-genome.com/), covering 815 insect genomes, 25 805 transcriptomes and >16 mi ...[more]

PMID: 34792158

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Project description:BackgroundThe cell suicide pathway of apoptosis is a necessary event in the life of multicellular organisms. It is involved in many biological processes ranging from development to the immune response. Evolutionarily conserved proteases, called caspases, play a central role in regulating apoptosis. Reception of death stimuli triggers the activation of initiator caspases, which in turn activate the effector caspases. In Lepidoptera, apoptosis is crucial in processes such as metamorphosis or defending against baculovirus infection. The discovery of p35, a baculovirus protein inhibiting caspase activity, has led to the characterization of the first lepidopteran caspase, Sf-Caspase-1. Studies on Sf-Caspase-1 mode of activation suggested that apoptosis in Lepidoptera requires a cascade of caspase activation, as demonstrated in many other species.ResultsIn order to get insights into this gene family in Lepidoptera, we performed an extensive survey of lepidopteran-derived EST datasets. We identified 66 sequences distributed among 27 species encoding putative caspases. Phylogenetic analyses showed that Lepidoptera possess at least 5 caspases, for which we propose a unified nomenclature. According to homology to their Drosophila counterparts and their primary structure, we determined that Lep-Caspase-1, -2 and -3 are putative effector caspases, whereas Lep-Caspase-5 and -6 are putative initiators. The likely function of Lep-Caspase-4 remains unclear. Lep-Caspase-2 is absent from the silkworm genome and appears to be noctuid-specific, and to have arisen from a tandem duplication of the Caspase-1 gene. In the tobacco hawkmoth, 3 distinct transcripts encoding putative Caspase-4 were identified, suggesting at least 2 duplication events in this species.ConclusionsThe basic repertoire of five major types of caspases shared among Lepidoptera seems to be smaller than for most other groups studied to date, but gene duplication still plays a role in lineage-specific increases in diversity, just as in Diptera and mammals.

Dataset Information

InsectBase 2.0: a comprehensive gene resource for insects.

Publications

InsectBase 2.0: a comprehensive gene resource for insects.

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