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Chemosensory adaptations of the mountain fly Drosophila nigrosparsa (Insecta: Diptera) through genomics’ and structural biology’s lenses

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Identification of geosmin as a volatile metabolite ofAnabaena sp.
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Elements of Olfactory Reception in Adult Drosophila melanogaster
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Protein Structure Modeling with MODELLER
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Protein Structure Modeling with MODELLER
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ProtTest-HPC: Fast Selection of Best-Fit Models of Protein Evolution
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Flying the Fly: Long-range Flight Behavior of Drosophila melanogaster to Attractive Odors
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Microbial Volatile Emissions as Insect Semiochemicals
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The four cysteine residues in the second extracellular loop of the human adenosine A2B receptor: Role in ligand binding and receptor function
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Coding of Odors by a Receptor Repertoire
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Variant Ionotropic Glutamate Receptors as Chemosensory Receptors in Drosophila
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Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing
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A Conserved Dedicated Olfactory Circuit for Detecting Harmful Microbes in Drosophila
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Structure and Dynamics of AMPA Receptor GluA2 in Resting, Pre-Open, and Desensitized States
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The chemical ecology of the fly
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Drosophila odorant receptors are novel seven transmembrane domain proteins that can signal independently of heterotrimeric G proteins
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Insights into subunit interactions within the insect olfactory receptor complex using FRET
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Ionotropic Receptors (IRs): Chemosensory ionotropic glutamate receptors in Drosophila and beyond
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Or83b Encodes a Broadly Expressed Odorant Receptor Essential for Drosophila Olfaction
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Two Gr Genes Underlie Sugar Reception in Drosophila
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Evolution of Insect Olfaction
inferredcites →https://doi.org/10.1016/j.tig.2014.11.001openalex-snapshot
On the meaning of the word ‘epimutation’: a comment
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Drosophila Chemoreceptors: A Molecular Interface Between the Chemical World and the Brain
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Orthology, paralogy and proposed classification for paralog subtypes
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Mechanisms for Activation and Antagonism of an AMPA-Sensitive Glutamate Receptor
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LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery
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HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
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Junk DNA as an evolutionary force
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Crystal structure and association behaviour of the GluR2 amino‐terminal domain
inferredcites →https://doi.org/10.1038/hdy.2009.55openalex-snapshot
Molecular evolution of the major chemosensory gene families in insects
inferredcites →https://doi.org/10.1038/nature06341openalex-snapshot
Evolution of genes and genomes on the Drosophila phylogeny
inferredcites →https://doi.org/10.1038/nature06861openalex-snapshot
Drosophila odorant receptors are both ligand-gated and cyclic-nucleotide-activated cation channels
inferredcites →https://doi.org/10.1038/nature10428openalex-snapshot
An olfactory receptor for food-derived odours promotes male courtship in Drosophila
inferredcites →https://doi.org/10.1038/nature11896openalex-snapshot
Molecular signatures of G-protein-coupled receptors
inferredcites →https://doi.org/10.1038/nature13430openalex-snapshot
Visualization of arrestin recruitment by a G-protein-coupled receptor
inferredcites →https://doi.org/10.1038/nature13603openalex-snapshot
Structural mechanism of glutamate receptor activation and desensitization
inferredcites →https://doi.org/10.1038/ncomms5401openalex-snapshot
The bacterial metabolite 2-aminoacetophenone promotes association of pathogenic bacteria with flies
inferredcites →https://doi.org/10.1038/ncomms7077openalex-snapshot
Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors
inferredcites →https://doi.org/10.1038/nn.2944openalex-snapshot
Evolutionary differences in food preference rely on Gr64e, a receptor for glycerol
inferredcites →https://doi.org/10.1038/nprot.2012.016openalex-snapshot
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
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Structural diversity of G protein-coupled receptors and significance for drug discovery
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Causes of evolutionary rate variation among protein sites
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Volatile codes: Correlation of olfactory signals and reception in Drosophila-yeast chemical communication
inferredcites →https://doi.org/10.1038/srep21841openalex-snapshot
DoOR 2.0 - Comprehensive Mapping of Drosophila melanogaster Odorant Responses
inferredcites →https://doi.org/10.1038/srep28722openalex-snapshot
Correction: Corrigendum: The changing shape of vaccination: improving immune responses through geometrical variations of a microdevice for immunization
inferredcites →https://doi.org/10.1073/pnas.1017351108openalex-snapshot
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
inferredcites →https://doi.org/10.1073/pnas.1311724111openalex-snapshot
Detection of sweet tastants by a conserved group of insect gustatory receptors
inferredcites →https://doi.org/10.1073/pnas.1424656112openalex-snapshot
Evolution of herbivory in Drosophilidae linked to loss of behaviors, antennal responses, odorant receptors, and ancestral diet
inferredcites →https://doi.org/10.1073/pnas.1513771112openalex-snapshot
Glycine activated ion channel subunits encoded by ctenophore glutamate receptor genes
inferredcites →https://doi.org/10.1073/pnas.2335847100openalex-snapshot
Molecular evolution of the insect chemoreceptor gene superfamily in Drosophila melanogaster
inferredcites →https://doi.org/10.1073/pnas.261432998openalex-snapshot
Candidate odorant receptors from the malaria vector mosquito Anopheles gambiae and evidence of down-regulation in response to blood feeding
inferredcites →https://doi.org/10.1074/jbc.m113.505289openalex-snapshot
Crystal and Solution Studies of the “Plus-C” Odorant-binding Protein 48 from Anopheles gambiae
inferredcites →https://doi.org/10.1074/jbc.m114.603993openalex-snapshot
Mutational Analysis of Cysteine Residues of the Insect Odorant Co-receptor (Orco) from Drosophila melanogaster Reveals Differential Effects on Agonist- and Odorant-tuning Receptor-dependent Activation
inferredcites →https://doi.org/10.1093/bib/bbq072openalex-snapshot
PHAST and RPHAST: phylogenetic analysis with space/time models
inferredcites →https://doi.org/10.1093/bioinformatics/17.9.849openalex-snapshot
The HMMTOP transmembrane topology prediction server
inferredcites →https://doi.org/10.1093/bioinformatics/bti079openalex-snapshot
HyPhy: hypothesis testing using phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btl461openalex-snapshot
Bio3d: an R package for the comparative analysis of protein structures
inferredcites →https://doi.org/10.1093/bioinformatics/btm404openalex-snapshot
Clustal W and Clustal X version 2.0
inferredcites →https://doi.org/10.1093/bioinformatics/btq600openalex-snapshot
A variable selection method for genome-wide association studies
inferredcites →https://doi.org/10.1093/bioinformatics/btr088openalex-snapshot
ProtTest 3: fast selection of best-fit models of protein evolution
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btt607openalex-snapshot
Protter: interactive protein feature visualization and integration with experimental proteomic data
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
inferredcites →https://doi.org/10.1093/bioinformatics/btv661openalex-snapshot
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS
inferredcites →https://doi.org/10.1093/chemse/bjq042openalex-snapshot
Integrating Heterogeneous Odor Response Data into a Common Response Model: A DoOR to the Complete Olfactome
inferredcites →https://doi.org/10.1093/gbe/evr033openalex-snapshot
Comparative Genomics of the Odorant-Binding and Chemosensory Protein Gene Families across the Arthropoda: Origin and Evolutionary History of the Chemosensory System
inferredcites →https://doi.org/10.1093/gbe/evu130openalex-snapshot
Family Size Evolution in Drosophila Chemosensory Gene Families: A Comparative Analysis with a Critical Appraisal of Methods
inferredcites →https://doi.org/10.1093/molbev/msu339openalex-snapshot
MBE Citation Classics (2015 Edition)
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RELAX: Detecting Relaxed Selection in a Phylogenetic Framework
inferredcites →https://doi.org/10.1093/molbev/msv022openalex-snapshot
Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection
inferredcites →https://doi.org/10.1093/nar/gkg169openalex-snapshot
Identification of pseudogenes in the Drosophila melanogaster genome
inferredcites →https://doi.org/10.1093/nar/gki408openalex-snapshot
The HHpred interactive server for protein homology detection and structure prediction
inferredcites →https://doi.org/10.1093/nar/gkq395openalex-snapshot
3V: cavity, channel and cleft volume calculator and extractor
inferredcites →https://doi.org/10.1093/nar/gku1203openalex-snapshot
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic
inferredcites →https://doi.org/10.1093/nar/gkv485openalex-snapshot
The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides
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The Biology of Alpine Habitats
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025883openalex-snapshot
Pseudogene Evolution in Drosophila Suggests a High Rate of DNA Loss
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
inferredcites →https://doi.org/10.1098/rsbl.2016.0407openalex-snapshot
Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies
inferredcites →https://doi.org/10.1101/gr.3715005openalex-snapshot
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
inferredcites →https://doi.org/10.1111/1755-0998.12340openalex-snapshot
Genomic Resources Notes Accepted 1 August 2014–30 September 2014
inferredcites →https://doi.org/10.1111/j.1365-2435.2008.01457.xopenalex-snapshot
Reproductive ecology of Drosophila
inferredcites →https://doi.org/10.1111/j.1476-5381.2011.01629.xopenalex-snapshot
Lifting the lid on GPCRs: the role of extracellular loops
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The Long‐Term Effects of Feeding Honey Compared with Sucrose and a Sugar‐Free Diet on Weight Gain, Lipid Profiles, and DEXA Measurements in Rats
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Study of the Biosynthesis of 1‐Octen‐3‐ol Using a Crude Homogenate of Agaricus bisporus in a Bioreactor
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Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
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Structure of an agonist-bound ionotropic glutamate receptor
inferredcites →https://doi.org/10.1128/aem.02250-06openalex-snapshot
Biochemical and Ecological Control of Geosmin and 2-Methylisoborneol in Source Waters
inferredcites →https://doi.org/10.1128/am.13.6.935-938.1965openalex-snapshot
Geosmin, an Earthy-Smelling Substance Isolated from Actinomycetes
inferredcites →https://doi.org/10.1146/annurev-ento-120811-153635openalex-snapshot
Odorant Reception in Insects: Roles of Receptors, Binding Proteins, and Degrading Enzymes
inferredcites →https://doi.org/10.1146/annurev.neuro.30.051606.094306openalex-snapshot
Molecular Architecture of Smell and Taste in Drosophila
inferredcites →https://doi.org/10.1186/1471-2105-7-62openalex-snapshot
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
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SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
inferredcites →https://doi.org/10.1186/gb-2011-12-1-r9openalex-snapshot
Coding potential of the products of alternative splicing in human
inferredcites →https://doi.org/10.1186/gb-2013-14-4-r36openalex-snapshot
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
inferredcites →https://doi.org/10.1186/s12864-016-2983-9openalex-snapshot
The making of a pest: Insights from the evolution of chemosensory receptor families in a pestiferous and invasive fly, Drosophila suzukii
inferredcites →https://doi.org/10.1371/journal.pbio.0040020openalex-snapshot
Atypical Membrane Topology and Heteromeric Function of Drosophila Odorant Receptors In Vivo
inferredcites →https://doi.org/10.1371/journal.pbio.0050007openalex-snapshot
Drug Export Pathway of Multidrug Exporter AcrB Revealed by DARPin Inhibitors
inferredcites →https://doi.org/10.1371/journal.pbio.0050106openalex-snapshot
Peptides Encoded by Short ORFs Control Development and Define a New Eukaryotic Gene Family
inferredcites →https://doi.org/10.1371/journal.pgen.1001064openalex-snapshot
Ancient Protostome Origin of Chemosensory Ionotropic Glutamate Receptors and the Evolution of Insect Taste and Olfaction
inferredcites →https://doi.org/10.1371/journal.pgen.1002764openalex-snapshot
Detecting Individual Sites Subject to Episodic Diversifying Selection
inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
inferredcites →https://doi.org/10.1371/journal.pone.0022594openalex-snapshot
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
inferredcites →https://doi.org/10.1371/journal.pone.0050698openalex-snapshot
Anatomical Brain Images Alone Can Accurately Diagnose Chronic Neuropsychiatric Illnesses
inferredcites →https://doi.org/10.1371/journal.pone.0052249openalex-snapshot
FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads
inferredcites →https://doi.org/10.1371/journal.pone.0165743openalex-snapshot
Oviposition Substrate of the Mountain Fly Drosophila nigrosparsa (Diptera: Drosophilidae)
inferredcites →https://doi.org/10.3389/fevo.2015.00041openalex-snapshot
Chemicals and chemoreceptors: ecologically relevant signals driving behavior in Drosophila
inferredcites →https://doi.org/10.3389/fgene.2013.00237openalex-snapshot
Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots
inferredcites →https://doi.org/10.3389/fncel.2010.00020openalex-snapshot
Molecular and cellular designs of insect taste receptor system
inferredcites →https://doi.org/10.3389/fphys.2014.00320openalex-snapshot
Soluble proteins of chemical communication: an overview across arthropods
inferredcites →https://doi.org/10.3389/fphys.2014.00337openalex-snapshot
Toward panoramic in situ mapping of action potential propagation in transgenic hearts to investigate initiation and therapeutic control of arrhythmias
inferredcites →https://doi.org/10.4161/fly.4.3.11627openalex-snapshot
Tuning the chemosensory window
inferredcites →https://doi.org/10.5281/zenodo.10738508openalex-snapshot
The Ecology of Drosophila breeding sites.

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/ece3.6212openalex-snapshot
Wolbachia affect behavior and possibly reproductive compatibility but not thermoresistance, fecundity, and morphology in a novel transinfected host, Drosophila nigrosparsa
inferred← citeshttps://doi.org/10.1002/ece3.6410openalex-snapshot
Transcriptome analysis of Drosophila melanogaster laboratory strains of different geographical origin after long‐term laboratory maintenance
inferred← citeshttps://doi.org/10.1002/mbo3.1291openalex-snapshot
Analyses of locomotion, wing morphology, and microbiome in Drosophila nigrosparsa after recovery from antibiotics
inferred← citeshttps://doi.org/10.1007/s00441-020-03363-xopenalex-snapshot
Functional properties of insect olfactory receptors: ionotropic receptors and odorant receptors
inferred← citeshttps://doi.org/10.1016/j.cbd.2018.03.003openalex-snapshot
Identification and evolution of olfactory genes in the small poplar longhorn beetle Saperda populnea
inferred← citeshttps://doi.org/10.1016/j.cois.2018.01.007openalex-snapshot
Genomes of Diptera
inferred← citeshttps://doi.org/10.1016/j.gecco.2019.e00638openalex-snapshot
Is temperature preference in the laboratory ecologically relevant for the field? The case of Drosophila nigrosparsa
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2019.133753openalex-snapshot
Major range loss predicted from lack of heat adaptability in an alpine Drosophila species
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.04.023openalex-snapshot
Positive diversifying selection is a pervasive adaptive force throughout the Drosophila radiation
inferred← citeshttps://doi.org/10.1038/s41467-023-41412-5openalex-snapshot
Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies
inferred← citeshttps://doi.org/10.1038/s41598-021-90857-5openalex-snapshot
Differential gene expression in Drosophila melanogaster and D. nigrosparsa infected with the same Wolbachia strain
inferred← citeshttps://doi.org/10.1080/19336934.2017.1396400openalex-snapshot
Identifying the minimum number of microsatellite loci needed to assess population genetic structure: A case study in fly culturing
inferred← citeshttps://doi.org/10.1093/jeb/voaf114openalex-snapshot
Evolution of the olfactory system during the radiation of Heliconiini butterflies
inferred← citeshttps://doi.org/10.1093/molbev/msaa076openalex-snapshot
Genomic Signature of Shifts in Selection in a Subalpine Ant and Its Physiological Adaptations
inferred← citeshttps://doi.org/10.1101/2022.08.12.503723openalex-snapshot
Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies
inferred← citeshttps://doi.org/10.1186/s12864-024-10180-xopenalex-snapshot
De novo assembly and annotation of Popillia japonica’s genome with initial clues to its potential as an invasive pest
inferred← citeshttps://doi.org/10.21203/rs.3.rs-2203028/v1openalex-snapshot
Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies
inferred← citeshttps://doi.org/10.32657/10356/73444openalex-snapshot
Deep learning neural network approaches for one-dimensional structure prediction from protein sequences
inferred← citeshttps://doi.org/10.3389/fnmol.2020.638839openalex-snapshot
The Structure and Function of Ionotropic Receptors in Drosophila
inferred← citeshttps://doi.org/10.3389/fphys.2017.00734openalex-snapshot
Distinct Subfamilies of Odorant Binding Proteins in Locust (Orthoptera, Acrididae): Molecular Evolution, Structural Variation, and Sensilla-Specific Expression
inferred← citeshttps://doi.org/10.3390/biom16020330openalex-snapshot
Adaptive Evolution of Odorant-Binding and Chemosensory Protein Gene Families in Genus Drosophila Fallén, 1823 (Diptera, Drosophilidae)
inferred← citeshttps://doi.org/10.6084/m9.figshare.26692588openalex-snapshot
Additional file 1 of De novo assembly and annotation of Popillia japonica’s genome with initial clues to its potential as an invasive pest
inferred← citeshttps://doi.org/10.6084/m9.figshare.26692591openalex-snapshot
Additional file 2 of De novo assembly and annotation of Popillia japonica’s genome with initial clues to its potential as an invasive pest
inferred← citeshttps://doi.org/10.6084/m9.figshare.26692594openalex-snapshot
Additional file 3 of De novo assembly and annotation of Popillia japonica’s genome with initial clues to its potential as an invasive pest
inferred← citeshttps://doi.org/10.6084/m9.figshare.26692597openalex-snapshot
Additional file 4 of De novo assembly and annotation of Popillia japonica’s genome with initial clues to its potential as an invasive pest
inferred← citeshttps://doi.org/10.6084/m9.figshare.26692600openalex-snapshot
Additional file 5 of De novo assembly and annotation of Popillia japonica’s genome with initial clues to its potential as an invasive pest
inferred← citeshttps://doi.org/10.6084/m9.figshare.26692603openalex-snapshot
Additional file 6 of De novo assembly and annotation of Popillia japonica’s genome with initial clues to its potential as an invasive pest
inferred← citeshttps://doi.org/10.6084/m9.figshare.26692606openalex-snapshot
Additional file 7 of De novo assembly and annotation of Popillia japonica’s genome with initial clues to its potential as an invasive pest
inferred← citeshttps://doi.org/10.6084/m9.figshare.26692609openalex-snapshot
Additional file 8 of De novo assembly and annotation of Popillia japonica’s genome with initial clues to its potential as an invasive pest
inferred← citeshttps://doi.org/10.6084/m9.figshare.26692612openalex-snapshot
Additional file 9 of De novo assembly and annotation of Popillia japonica’s genome with initial clues to its potential as an invasive pest
inferred← citeshttps://doi.org/10.6084/m9.figshare.26692615openalex-snapshot
Additional file 10 of De novo assembly and annotation of Popillia japonica’s genome with initial clues to its potential as an invasive pest
inferred← citeshttps://doi.org/10.70675/465a2e38zeb5cz4afaz98fcz9fc34af19af9openalex-snapshot
Evolution of sweet taste perception in Drosophila suzukii egg-laying behavior
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