Best Practices in Insect Genome Sequencing: What Works and What Doesn't.

No abstract is available for this paper.

• Publication year

  2015

• Venue

  Current Opinion in Insect Science

• Publication date

  2015-02-01

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1016/J.COIS.2015.02.013PMID 26085980PMCID PMC4465116
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• DBG2OLC: Efficient Assembly of Large Genomes Using the Compressed Overlap Graph

  2015cited by this paper
• A maturing understanding of the composition of the insect gene repertoire.

  2015cited by this paper
• Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

  2015cited by this paper
• The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima

  2014cited by this paper
• Comprehensive variation discovery in single human genomes

  2014cited by this paper
• Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements

  2014cited by this paper
• Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

  2014cited by this paper
• Comparative validation of the D. melanogaster modENCODE transcriptome annotation

  2014cited by this paper
• On the middle ground between open source and commercial software - the case of the Newbler program

  2014cited by this paper
• Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

  2014cited by this paper
• The genome sequence of the colonial chordate, Botryllus schlosseri

  2013cited by this paper
• The MaSuRCA genome assembler

  2013cited by this paper
• Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

  2013cited by this paper
• Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

  2013cited by this paper
• Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

  2012cited by this paper
• Hybrid error correction and de novo assembly of single-molecule sequencing reads

  2012cited by this paper
• Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

  2012cited by this paper
• Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

  2012cited by this paper
• A flexible and efficient template format for circular consensus sequencing and SNP detection

  2010cited by this paper
• Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements

  2010cited by this paper
• High-quality draft assemblies of mammalian genomes from massively parallel sequence data

  2010cited by this paper
• Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

  2008cited by this paper
• SOAP: short oligonucleotide alignment program

  2008cited by this paper
• ALLPATHS: de novo assembly of whole-genome shotgun microreads.

  2008cited by this paper
• Aggressive assembly of pyrosequencing reads with mates

  2008cited by this paper
• Evolution of genes and genomes on the Drosophila phylogeny

  2007cited by this paper
• Genome sequencing in microfabricated high-density picolitre reactors

  2005cited by this paper
• A whole-genome assembly of Drosophila.

  2000cited by this paper
• The genome sequence of Drosophila melanogaster.

  2000cited by this paper
• Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping.

  1993cited by this paper

• Omics in mini-livestock: a genomic perspective on the future of sustainable food systems

  2026cites this paper
• Fusarium Genome Sequencing and Assembly.

  2025cites this paper
• Proteomic insights into Novel Food Insects: Homology-based proteome characterization and allergenicity considerations for EU-regulated insect species

  2025cites this paper
• Genomic Monitoring of a Reintroduced Butterfly Uncovers Contrasting Founder Lineage Survival

  2025cites this paper
• Telomere-to-telomere genome assembly of the Dipteran Bactrocera dorsalis from a single individual

  2025cites this paper
• Unsupervised AI reveals insect species-specific genome signatures

  2024cites this paper
• The genome of the soybean gall midge (Resseliella maxima)

  2023cites this paper
• Genome-Wide Analyses of Tea Plant Stress-Associated Proteins (SAPs) Reveal the Role of CsSAP12 in Increased Drought Tolerance in Transgenic Tomatoes

  2022cites this paper
• Validation of reference-assisted assembly using existing and novel Heliothine genomes.

  2022cites this paper
• Genomic insights into evolution and control of Wohlfahrtia magnifica, a widely distributed myiasis‐causing fly of warm‐blooded vertebrates

  2022cites this paper
• The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research

  2021cites this paper
• Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce’s disease

  2021cites this paper
• Chronological Incongruences between Mitochondrial and Nuclear Phylogenies of Aedes Mosquitoes

  2021cites this paper
• Perspectives in Triatomine Biology Studies: “OMICS”-Based Approaches

  2021cites this paper
• Genome assembly, annotation, and comparative analysis of the cattail Typha latifolia

  2021cites this paper
• Characterization of Mariner transposons in seven species of Rhus gall aphids

  2021cites this paper
• A haploid diamondback moth (Plutella xylostella L.) genome assembly resolves 31 chromosomes and identifies a diamide resistance mutation.

  2021cites this paper
• Development and characterization of genomic resources for a non-model marine teleost, the red snapper (Lutjanus campechanus, Lutjanidae): Construction of a high-density linkage map, anchoring of genome contigs and comparative genomic analysis

  2020cites this paper
• Jekyll or Hyde? The genome (and more) of Nesidiocoris tenuis, a zoophytophagous predatory bug that is both a biological control agent and a pest

  2020cites this paper
• Highly conserved genes expressed in aphid saliva are candidates for host plant adaptation in Aphis gossypii

  2020cites this paper
• Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis

  2020cites this paper
• High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus

  2020cites this paper
• Next‐generation biological control: the need for integrating genetics and genomics

  2020cites this paper
• A high-quality de novo genome assembly from a single parasitoid wasp

  2020cites this paper
• De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly

  2020cites this paper
• Diaci v3.0: Chromosome-level assembly, de novo transcriptome and manual annotation of Diaphorina citri, insect vector of Huanglongbing

  2019cites this paper
• Two Lys-vasopressin-like peptides, EFLamide, and other phasmid neuropeptides.

  2019cites this paper
• DNA Sequencing and the Evolution of the “-Omics”

  2019cites this paper
• Molecular Tools Used in Medical and Veterinary Entomology

  2019cites this paper
• The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations

  2019cites this paper
• Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies

  2019cites this paper
• Insect genomes: progress and challenges

  2019cites this paper
• Circadian and Seasonal Timing of Insect Olfactory Systems

  2019cites this paper
• Evolutionary history and classification of Micropia retroelements in Drosophilidae species

  2019cites this paper
• Evolutionary genetics in insect phenotypic radiations: the value of a comparative genomic approach.

  2019cites this paper
• Next Generation Biological Control: The Need for Integrating Genetics and Evolution

  2019cites this paper
• Moving On from the Insect Apocalypse Narrative: Engaging with Evidence-Based Insect Conservation

  2019cites this paper
• Whole genome resequencing of a laboratory-adapted Drosophila melanogaster

  2019cites this paper
• Long Range Sequencing and Validation of Insect Genome Assemblies.

  2018cites this paper
• Biosurveillance of forest insects: part I—integration and application of genomic tools to the surveillance of non-native forest insects

  2018cites this paper
• Chapter 2 Whole-Genome Sequencing Recommendations

  2018cites this paper
• Using BUSCO to Assess Insect Genomic Resources.

  2018cites this paper
• Open access genomic resources for terrestrial arthropods.

  2018cites this paper
• Cytomolecular analysis of the male sex chromosome of Tropidacris cristata grandis (Thunberg, 1824) (Orthoptera: Romaleidae)

  2018cites this paper
• Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices, common challenges, and experimental design for genomic studies

  2018cites this paper
• Genomes of the Hymenoptera.

  2018cites this paper
• De novo genome assembly of the olive fruit fly (Bactrocera oleae) developed through a combination of linked-reads and long-read technologies

  2018cites this paper
• Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction

  2017cites this paper
• Junk DNA Contribution to Evolutionary Capacitance Can Drive Species Dynamics

  2017cites this paper
• Temporal Expression of the Clock Genes in the Water Flea Daphnia pulex (Crustacea: Cladocera).

  2016cites this paper
• Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art

  2016cites this paper
• Avirulence gene mapping in the Hessian fly (Mayetiola destructor) reveals a protein phosphatase 2C effector gene family.

  2016cites this paper
• Chapter 6. Comparative genomic approaches to investigate molecular traits specific to social insects.

  2016cites this paper
• Similarities between decapod and insect neuropeptidomes

  2016cites this paper
• Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample

  2016cites this paper
• Neuropeptide Evolution: Chelicerate Neurohormone and Neuropeptide Genes may reflect one or more whole genome duplications.

  2016cites this paper
• Agricultural applications of insect ecological genomics.

  2016cites this paper
• The life cycle of a genome project: perspectives and guidelines inspired by insect genome projects

  2016cites this paper
• Neuropeptide evolution: Chelicerate neurohormone and neuropeptide genes may reflect one or more whole genome duplications.

  2016cites this paper
• Whole-Genome Sequencing Recommendations

  2016cites this paper
• DEVELOPMENT OF GENOMIC RESOURCES FOR THE EVALUATION OF RED SNAPPER, AN EMERGING SPECIES CANDIDATE FOR MARINE AQUACULTURE AND STOCK ENHANCEMENT

  2016cites this paper
• Karyotyping and in silico characterisation of the chromosomes of Diuraphis noxia (Hemiptera: Aphididae)

  2016cites this paper
• Whole genome resequencing of a laboratory-adapted population sample Drosophila melanogaster

  2016cites this paper
• Open Peer Review

  2016cites this paper
• Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly

  2016cites this paper
• The power of next-generation sequencing as illustrated by the neuropeptidome of the crayfish Procambarus clarkii.

  2015cites this paper
• Contact genomics: scaffolding and phasing (meta)genomes using chromosome 3D physical signatures

  2015cites this paper
• Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution

  2015influential citation
• The Genome and Methylome of a Beetle with Complex Social Behavior, Nicrophorus vespilloides (Coleoptera: Silphidae)

  2015cites this paper
• 1 The Nicrophorus vespilloides genome and methylome , a beetle with complex social behavior 1 2

  2015cites this paper
• The Nicrophorus vespilloides genome and methylome, a beetle with complex social behavior

  2015cites this paper
• Neuroanatomy of pars intercerebralis neurons with special reference to their connections with neurons immunoreactive for pigment-dispersing factor in the blow fly Protophormia terraenovae

  2015cites this paper