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

Novel genomic resources for shelled pteropods: a draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance

(2020) Le Qin Choo et al.   BMC GENOMICS

Diamide resistance: 10 years of lessons from lepidopteran pests

(2020) Ewan B. Richardson et al.   JOURNAL OF PEST SCIENCE

Variation among 532 genomes unveils the origin and evolutionary history of a global insect herbivore

(2020) Minsheng You et al.   Nature Communications

Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle

(2020) Wai Yee Low et al.   Nature Communications

CRISPR/Cas9 mediated ryanodine receptor I4790M knockin confers unequal resistance to diamides in Plutella xylostella

(2020) Xingliang Wang et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Genome-wide analysis of diamondback moth, Plutella xylostella L., from Brassica crops and wild host plants reveals no genetic structure in Australia

(2020) Kym D. Perry et al.   Scientific Reports

Resistance to Bacillus thuringiensis Cry1Ac toxin requires mutations in two Plutella xylostella ATP-binding cassette transporter paralogs

(2020) Zhaoxia Liu et al.   PLoS Pathogens

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

(2020) Sergey Nurk et al.   GENOME RESEARCH

TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads

(2020) Mengyang Xu et al.   GigaScience

A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

(2020) Eugenie C Yen et al.   GigaScience

Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects

(2019) Malte Petersen et al.   BMC EVOLUTIONARY BIOLOGY

A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing

(2019) Sarah Kingan et al.   Genes

High-quality genome assembly of the silkworm, Bombyx mori

(2019) Munetaka Kawamoto et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Insect genomes: progress and challenges

(2019) Fei Li et al.   INSECT MOLECULAR BIOLOGY

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

A chromosome-level genome assembly of Cydia pomonella provides insights into chemical ecology and insecticide resistance

(2019) Fanghao Wan et al.   Nature Communications

Patterns of Genome-Wide Variation, Population Differentiation and SNP Discovery of the Red Banded Stink Bug (Piezodorus guildinii)

(2019) Maria I. Zucchi et al.   Scientific Reports

Chromosomal-level reference genome of Chinese peacock butterfly (Papilio bianor) based on third-generation DNA sequencing and Hi-C analysis

(2019) Sihan Lu et al.   GigaScience

ngsReports: a Bioconductor package for managing FastQC reports and other NGS related log files

(2019) Christopher M Ward et al.   BIOINFORMATICS

Ryanodine receptor mutations (G4946E and I4790K) differentially responsible for diamide insecticide resistance in diamondback moth, Plutella xylostella L.

(2019) Akiya Jouraku et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Identification and characterization of a Masculinizer homologue in the diamondback moth, Plutella xylostella

(2019) T. Harvey‐Samuel et al.   INSECT MOLECULAR BIOLOGY

Cryptic Plutella species show deep divergence despite the capacity to hybridize

(2018) Kym D. Perry et al.   BMC EVOLUTIONARY BIOLOGY

Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly

(2018) Sagar Patel et al.   BMC GENOMICS

Multiple large-scale gene and genome duplications during the evolution of hexapods

(2018) Zheng Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

De novo assembly of haplotype-resolved genomes with trio binning

(2018) Sergey Koren et al.   NATURE BIOTECHNOLOGY

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Ryanodine receptor point mutations confer diamide insecticide resistance in tomato leafminer, Tuta absoluta (Lepidoptera: Gelechiidae)

(2017) Emmanouil Roditakis et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Investigation of the contribution of RyR target-site mutations in diamide resistance by CRISPR/Cas9 genome modification in Drosophila

(2017) Vassilis Douris et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Rapid selection for resistance to diamide insecticides in Plutella xylostella via specific amino acid polymorphisms in the ryanodine receptor

(2017) Bartlomiej J. Troczka et al.   NEUROTOXICOLOGY

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Spread and global population structure of the diamondback moth Plutella xylostella (Lepidoptera: Plutellidae) and its larval parasitoids Diadegma semiclausum and Diadegma fenestrale (Hymenoptera: Ichneumonidae) based on mtDNA

(2016) I. Juric et al.   BULLETIN OF ENTOMOLOGICAL RESEARCH

A Thousand Fly Genomes: An ExpandedDrosophilaGenome Nexus

(2016) Justin B. Lack et al.   MOLECULAR BIOLOGY AND EVOLUTION

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

(2016) Evgeny M. Zdobnov et al.   NUCLEIC ACIDS RESEARCH

Genome Sizes of Nine Insect Species Determined by Flow Cytometry and k-mer Analysis

(2016) Kang He et al.   Frontiers in Physiology

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Characterization and expression profiling of glutathione S-transferases in the diamondback moth, Plutella xylostella (L.)

(2015) Yanchun You et al.   BMC GENOMICS

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts

(2015) Alison C Testa et al.   BMC GENOMICS

High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep

(2015) S V Song et al.   HEREDITY

Geographic spread, genetics and functional characteristics of ryanodine receptor based target-site resistance to diamide insecticides in diamondback moth, Plutella xylostella

(2015) Denise Steinbach et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Stable expression and functional characterisation of the diamondback moth ryanodine receptor G4946E variant conferring resistance to diamide insecticides

(2015) Bartlomiej J. Troczka et al.   Scientific Reports

Genome-wide characterization and expression profiling of immune genes in the diamondback moth, Plutella xylostella (L.)

(2015) Xiaofeng Xia et al.   Scientific Reports

Characterization and expression of the cytochrome P450 gene family in diamondback moth, Plutella xylostella (L.)

(2015) Liying Yu et al.   Scientific Reports

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Best practices in insect genome sequencing: what works and what doesn’t

(2015) Stephen Richards et al.   Current Opinion in Insect Science

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution

(2014) Zhen Yan et al.   NATURE

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

(2014) Virpi Ahola et al.   Nature Communications

DBM-DB: the diamondback moth genome database

(2014) W. Tang et al.   Database-The Journal of Biological Databases and Curation

Novel mutations and mutation combinations of ryanodine receptor in a chlorantraniliprole resistant population of Plutella xylostella (L.)

(2014) Lei Guo et al.   Scientific Reports

KONAGAbase: a genomic and transcriptomic database for the diamondback moth, Plutella xylostella

(2013) Akiya Jouraku et al.   BMC GENOMICS

A heterozygous moth genome provides insights into herbivory and detoxification

(2013) Minsheng You et al.   NATURE GENETICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Species differences in chlorantraniliprole and flubendiamide insecticide binding sites in the ryanodine receptor

(2013) Suzhen Qi et al.   PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY

Plutella australiana (Lepidoptera, Plutellidae), an overlooked diamondback moth revealed by DNA barcodes

(2013) Jean-Francois Landry et al.   ZooKeys

Insect Ryanodine Receptor: Distinct but Coupled Insecticide Binding Sites for [N-C3H3]Chlorantraniliprole, Flubendiamide, and [3H]Ryanodine

(2012) André K. Isaacs et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Resistance to diamide insecticides in diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae) is associated with a mutation in the membrane-spanning domain of the ryanodine receptor

(2012) Bartek Troczka et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Estimating the Economic Cost of One of the World's Major Insect Pests, Plutella xylostella (Lepidoptera: Plutellidae): Just How Long Is a Piece of String?

(2012) Myron P. Zalucki et al.   JOURNAL OF ECONOMIC ENTOMOLOGY

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

The Monarch Butterfly Genome Yields Insights into Long-Distance Migration

(2011) Shuai Zhan et al.   CELL

A guided tour of large genome size in animals: what we know and where we are heading

(2011) France Dufresne et al.   CHROMOSOME RESEARCH

SyMAP v3.4: a turnkey synteny system with application to plant genomes

(2011) Carol Soderlund et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Linkage Mapping and Comparative Genomics Using Next-Generation RAD Sequencing of a Non-Model Organism

(2011) Simon W. Baxter et al.   PLoS One

Susceptibility of four field populations of the diamondback moth Plutella xylostella L. (Lepidoptera: Yponomeutidae) to six insecticides in the Sydney region, New South Wales, Australia

(2010) Vincent Y Eziah et al.   AUSTRALIAN JOURNAL OF ENTOMOLOGY

Induction and Transmission of Tolerance to the Synthetic Pesticide Emamectin Benzoate in Field and Laboratory Populations of Diamondback Moth

(2010) M. M. Rahman et al.   JOURNAL OF ECONOMIC ENTOMOLOGY

A new repeat-masking method enables specific detection of homologous sequences

(2010) Martin C. Frith   NUCLEIC ACIDS RESEARCH

Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements

(2010) E. d'Alençon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ecology of diamondback moth in Australian canola: landscape perspectives and the implications for management

(2008) Michael J. Furlong et al.   Australian journal of experimental agriculture

Genome size diversity in the family Drosophilidae

(2008) T R Gregory et al.   HEREDITY

Genome size evolution: Within-species variation in genome size

(2008) C Biémont   HEREDITY

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY