ArticleInsect biochemistry and molecular biology2015
Integrated modeling of protein-coding genes in the Manduca sexta genome using RNA-Seq data from the biochemical model insect.
Article in Insect biochemistry and molecular biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Genome-wide identification, classification, and expression profiling of serine esterases and other esterase-related proteins in the tobacco hornworm, Manduca sexta.Insect science · 2023Article
- Cleavage activation and functional comparison of Manduca sexta serine protease homologs SPH1a, SPH1b, SPH4, and SPH101 in conjunction with SPH2.Insect biochemistry and molecular biology · 2022Article
- Changes in composition and levels of hemolymph proteins during metamorphosis of Manduca sexta.Insect biochemistry and molecular biology · 2020Article
- Digestion-related proteins in the tobacco hornworm, Manduca sexta.Insect biochemistry and molecular biology · 2020Article
- Building a platform for predicting functions of serine protease-related proteins in Drosophila melanogaster and other insects.Insect biochemistry and molecular biology · 2018Article
- The Manduca sexta serpinome: Analysis of serpin genes and proteins in the tobacco hornworm.Insect biochemistry and molecular biology · 2018Article
- WaspBase: a genomic resource for the interactions among parasitic wasps, insect hosts and plants.Database : the journal of biological databases and curation · 2018Article
- An analysis of 67 RNA-seq datasets from various tissues at different stages of a model insect, Manduca sexta.BMC genomics · 2017Article
- Serine protease-related proteins in the malaria mosquito, Anopheles gambiae.Insect biochemistry and molecular biology · 2017Article
- Transcriptome Analysis of Male Drosophila melanogaster Exposed to Ethylparaben Using Digital Gene Expression Profiling.Journal of insect science (Online) · 2017Article
- Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community.Database : the journal of biological databases and curation · 2017Article
- Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta.Insect biochemistry and molecular biology · 2016Article
- Changes in the Plasma Proteome of Manduca sexta Larvae in Relation to the Transcriptome Variations after an Immune Challenge: Evidence for High Molecular Weight Immune Complex Formation.Molecular & cellular proteomics : MCP · 2016Article
- A genome-wide analysis of antimicrobial effector genes and their transcription patterns in Manduca sexta.Insect biochemistry and molecular biology · 2015Article
- The immune signaling pathways of Manduca sexta.Insect biochemistry and molecular biology · 2015Article
- Phylogenetic analysis and expression profiling of the pattern recognition receptors: Insights into molecular recognition of invading pathogens in Manduca sexta.Insect biochemistry and molecular biology · 2015Article
- Sequence conservation, phylogenetic relationships, and expression profiles of nondigestive serine proteases and serine protease homologs in Manduca sexta.Insect biochemistry and molecular biology · 2015Article
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2 authors.
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Abstract
The genome sequence of Manduca sexta was recently determined using 454 technology. Cufflinks and MAKER2 were used to establish gene models in the genome assembly based on the RNA-Seq data and other species' sequences. Aided by the extensive RNA-Seq data from 50 tissue samples at various life stages, annotators over the world (including the present authors) have manually confirmed and improved a small percentage of the models after spending months of effort. While such collaborative efforts are highly commendable, many of the predicted genes still have problems which may hamper future research on this insect species. As a biochemical model representing lepidopteran pests, M. sexta has been used extensively to study insect physiological processes for over five decades. In this work, we assembled Manduca datasets Cufflinks 3.0, Trinity 4.0, and Oases 4.0 to assist the manual annotation efforts and development of Official Gene Set (OGS) 2.0. To further improve annotation quality, we developed methods to evaluate gene models in the MAKER2, Cufflinks, Oases and Trinity assemblies and selected the best ones to constitute MCOT 1.0 after thorough crosschecking. MCOT 1.0 has 18,089 genes encoding 31,666 proteins: 32.8% match OGS 2.0 models perfectly or near perfectly, 11,747 differ considerably, and 29.5% are absent in OGS 2.0. Future automation of this process is anticipated to greatly reduce human efforts in generating comprehensive, reliable models of structural genes in other genome projects where extensive RNA-Seq data are available.
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