A5011424994- Insect behavior and control techniques
- Insect symbiosis and bacterial influences
- Insect Resistance and Genetics
- CRISPR and Genetic Engineering
- Insect-Plant Interactions and Control
- Genomics and Phylogenetic Studies
- Entomopathogenic Microorganisms in Pest Control
- Chromosomal and Genetic Variations
- Plant Diversity and Evolution
- Plant and animal studies
- Genomic variations and chromosomal abnormalities
- RNA modifications and cancer
- Insect and Pesticide Research
- Protist diversity and phylogeny
- Plant and Fungal Species Descriptions
- Hymenoptera taxonomy and phylogeny
- Forest Insect Ecology and Management
Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center
2017-2025
United States Department of Agriculture
2023-2024
Agricultural Research Service
2023
Abstract High‐throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic commonly contain 50‐ to 100‐fold more loci than those generated using traditional Sanger sequencing‐based approaches. Here, we demonstrate a new approach for building single‐tube, highly multiplexed amplicon sequencing, which name Hi MAP (highly amplicon‐based phylogenomics) present bioinformatic pipelines locus selection based on genomic transcriptomic resources...
Tephritid fruit flies are destructive agricultural pests that the targets of expensive population eradication and suppression efforts. Genetic pest management is one strategies for reducing or eliminating tephritid populations, relying upon genetic manipulation insects to render them sterile capable transmitting deleterious traits through gene drive. Currently, radiation, chemical mutagenesis, transgenic techniques employed generate agents management, but new methods must be explored...
DNA sequencing technology has undergone substantial improvements in recent years, to the extent that Third Generation Sequencing platforms are capable of massively generating long-reads. Amplicon been among most popular techniques due its wide application diverse fields biological sciences. However, there is a lack software specifically designed analyse intra-individual genetic variation using amplicon long-read data. Here, we present CCS-consensuser, an end-to-end pipeline generates...
Abstract Anthurium amnicola is in the monocot family Araceae, subfamily Pothoideae and a contributing species Hawaii floriculture industry hybrids. To support future genetic improvements to this commodity, we sequenced assembled A. genome chromosome-scale using PacBio HiFi short-read Hi-C sequencing. A total of 98.51% 4.79 Gb anchored into 15 chromosomes, with 99.2% gene completeness high LTR assembly index (LAI) score 21.73, indicative complete, high-quality assembly. Annotation reveals...
Abstract Tephritid fruit flies are among the most invasive and destructive agricultural pests worldwide. Over recent years, many studies have implemented CRISPR/Cas9 genome-editing technology to dissect gene functions in tephritids create new strains facilitate their genetics, management, control. This growing literature allows us compare diverse strategies for delivering components into tephritid embryos, optimize procedures, advance systems outside thoroughly studied species within family....
The West Indian fruit fly, Anastrepha obliqua, is a major pest of mango in Central and South America attacks more than 60 species host fruits. To support current genetic genomic research on A. we sequenced the genome using high-fidelity long-read sequencing. This resulted highly contiguous contig assembly with 90% 10 contigs. was placed chromosomal context synteny closely related species, ludens, as both are members fraterculus group. resulting represents five autosomes X chromosome which...
Abstract The remarkable diversity of insect pigmentation offers a captivating avenue for exploring evolution and genetics. In tephritid fruit flies, decoding the molecular pathways underlying traits also plays central role in applied entomology. Mutant phenotypes like black pupae (bp) have long been used as component genetic sexing strains, allowing male-only release sterile technique applications. However, basis bp remains largely unknown. Here, we present independent evidence from...
Parasitoid wasps are one of the most species-rich groups animals on Earth, due to their ability successfully develop as parasites nearly all types insects. Unlike known parasitoid that specialize towards or a few host species, Diachasmimorpha longicaudata is generalist can survive within multiple genera tephritid fruit fly hosts, including many globally important pest species. has therefore been widely released suppress populations part biological control efforts in tropical and subtropical...
Abstract The Mexican fruit fly, Anastrepha ludens, is a polyphagous true fly (Diptera: Tephritidae) considered one of the most serious insect pests in Central and North America to various economically relevant fruits. Despite its agricultural relevance, high-quality genome assembly has not been reported. Here, we described generation chromosome-level for A. ludens using combination PacBio high fidelity long-reads chromatin conformation capture sequencing data. final consisted 140 scaffolds...
ABSTRACT High-throughput sequencing has fundamentally changed how molecular phylogenetic datasets are assembled, and phylogenomic commonly contain 50-100-fold more loci than those generated using traditional Sanger-based approaches. Here, we demonstrate a new approach for building single tube, highly multiplexed amplicon sequencing, which name HiMAP (Highly Multiplexed Amplicon-based Phylogenomics), present bioinformatic pipelines locus selection based on genomic transcriptomic data...
The implementation of a new genomic assembly pipeline named only the best (otb) has effectively addressed various challenges associated with data management during development and storage genome assemblies. otb, which incorporates comprehensive involving setup layer, quality checks, templating, integration Nextflow Singularity. primary objective otb is to streamline process creating HiFi/HiC genome, aiming minimize manual intervention required in process. 2-lined spittlebug, (Prosapia...
Abstract The West Indian fruit fly, Anastrepha obliqua , is a major pest of mango in Central and South America attacks more than 60 species host fruits. To support current genetic genomic research on A. we sequenced the genome using high-fidelity (HiFi) long-read sequencing. This resulted highly contiguous contig assembly with 90% 10 contigs. was placed chromosomal context synteny closely related species, ludens as both are members fraterculus group. resulting represents five autosomes X...
The implementation of a new genomic assembly pipeline named Only Best (otb) has effectively addressed various challenges associated with data management during the development and storage genome assemblies. otb, which incorporates comprehensive involving setup layer, quality checks, templating, integration Nextflow Singularity. primary objective otb is to streamline process creating HiFi/HiC genome, aiming minimize manual intervention required in process. Two-lined spittlebug Prosapia...