We can't all be supermodels: the value of comparative transcriptomics to the study of non-model insects

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

Meiotic Drive Impacts Expression and Evolution of X-Linked Genes in Stalk-Eyed Flies

(2014) Josephine A. Reinhardt et al.   PLoS Genetics

Developmental Link between Sex and Nutrition; doublesex Regulates Sex-Specific Mandible Growth via Juvenile Hormone Signaling in Stag Beetles

(2014) Hiroki Gotoh et al.   PLoS Genetics

Autophagy in Antarctica

(2013) Nicholas M. Teets et al.   Autophagy

Differential impacts of juvenile hormone, soldier head extract and alternate caste phenotypes on host and symbiont transcriptome composition in the gut of the termite Reticulitermes flavipes

(2013) Ruchira Sen et al.   BMC GENOMICS

The genome- and transcriptome-wide analysis of innate immunity in the brown planthopper, Nilaparvata lugens

(2013) Yan-Yuan Bao et al.   BMC GENOMICS

The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions

(2013) Brian R Johnson et al.   BMC GENOMICS

The Nap family proteins, CG5017/Hanabi and Nap1, are essential forDrosophilaspermiogenesis

(2013) Shuhei Kimura   FEBS LETTERS

Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality

(2013) D. F. Simola et al.   GENOME RESEARCH

Maize toxin degrades peritrophic matrix proteins and stimulates compensatory transcriptome responses in fall armyworm midgut

(2013) Howard W. Fescemyer et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Detoxification activity and energy cost is attenuated in whiteflies feeding onTomato yellow leaf curl China virus-infected tobacco plants

(2013) J.-B. Luan et al.   INSECT MOLECULAR BIOLOGY

Cloning and expression profiling of odorant-binding proteins in the tarnished plant bug,Lygus lineolaris

(2013) J. J. Hull et al.   INSECT MOLECULAR BIOLOGY

Comparative transcriptome analysis of the venom sac and gland of social wasp Vespa tropica and solitary wasp Rhynchium brunneum

(2013) Ji Hyeong Baek et al.   JOURNAL OF ASIA-PACIFIC ENTOMOLOGY

RNA-Seq reveals early distinctions and late convergence of gene expression between diapause and quiescence in the Asian tiger mosquito, Aedes albopictus

(2013) M. F. Poelchau et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Mechanisms of macroevolution: polyphagous plasticity in butterfly larvae revealed by RNA-Seq

(2013) Maria de la Paz Celorio-Mancera et al.   MOLECULAR ECOLOGY

Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial

(2013) Jochen B. W. Wolf   Molecular Ecology Resources

Reversal of an ancient sex chromosome to an autosome in Drosophila

(2013) Beatriz Vicoso et al.   NATURE

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

New genes as drivers of phenotypic evolution

(2013) Sidi Chen et al.   NATURE REVIEWS GENETICS

The evolutionary causes and consequences of sex-biased gene expression

(2013) John Parsch et al.   NATURE REVIEWS GENETICS

Adaptive divergence of a transcriptional enhancer between populations of Drosophila melanogaster

(2013) A. Glaser-Schmitt et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Transcriptome sequencing as a platform to elucidate molecular components of the diapause response in the Asian tiger mosquitoAedes albopictus

(2013) MONICA F. POELCHAU et al.   PHYSIOLOGICAL ENTOMOLOGY

Sex-Biased Gene Expression during Head Development in a Sexually Dimorphic Stalk-Eyed Fly

(2013) Gerald S. Wilkinson et al.   PLoS One

Developmental Gene Discovery in a Hemimetabolous Insect: De Novo Assembly and Annotation of a Transcriptome for the Cricket Gryllus bimaculatus

(2013) Victor Zeng et al.   PLoS One

An Analysis of the Athetis lepigone Transcriptome from Four Developmental Stages

(2013) Li-Tao Li et al.   PLoS One

Global Transcriptome Analysis of Orange Wheat Blossom Midge, Sitodiplosis mosellana (Gehin) (Diptera: Cecidomyiidae) to Identify Candidate Transcripts Regulating Diapause

(2013) Zhong-Jun Gong et al.   PLoS One

Characterizing the Infection-Induced Transcriptome of Nasonia vitripennis Reveals a Preponderance of Taxonomically-Restricted Immune Genes

(2013) Timothy B. Sackton et al.   PLoS One

Gene amplification and microsatellite polymorphism underlie a recent insect host shift

(2013) C. Bass et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Blood meal-induced changes to antennal transcriptome profiles reveal shifts in odor sensitivities in Anopheles gambiae

(2013) D. C. Rinker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Invasive Harlequin Ladybird Carries Biological Weapons Against Native Competitors

(2013) A. Vilcinskas et al.   SCIENCE

RNA-Seq: revelation of the messengers

(2013) Marcel C. Van Verk et al.   TRENDS IN PLANT SCIENCE

Masculinization of the X Chromosome in the Pea Aphid

(2013) Julie Jaquiéry et al.   PLoS Genetics

Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes

(2013) Pedro G Ferreira et al.   GENOME BIOLOGY

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

Cyp15F1: A NOVEL CYTOCHROME P450 GENE LINKED TO JUVENILE HORMONE-DEPENDENT CASTE DIFFERENTION IN THE TERMITE Reticulitermes flavipes

(2012) Matthew R. Tarver et al.   ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY

Newly evolved genes: Moving from comparative genomics to functional studies in model systems

(2012) José M. Ranz et al.   BIOESSAYS

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

The evolution of Dscam genes across the arthropods

(2012) Sophie AO Armitage et al.   BMC EVOLUTIONARY BIOLOGY

Demasculinization of the Anopheles gambiae X chromosome

(2012) Kalle Magnusson et al.   BMC EVOLUTIONARY BIOLOGY

Population and sex differences in Drosophila melanogaster brain gene expression

(2012) Ana Catalán et al.   BMC GENOMICS

Identification of cold-responsive genes in a New Zealand alpine stick insect using RNA-Seq

(2012) Luke T. Dunning et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

A novel function – Thermal protective properties of an antifreeze protein from the summer desert beetle Microdera punctipennis

(2012) Liming Qiu et al.   CRYOBIOLOGY

Deciphering the single-cell omic: innovative application for translational medicine

(2012) Ferdinando Mannello et al.   Expert Review of Proteomics

Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

(2012) Ana Riesgo et al.   Frontiers in Zoology

Behavioral plasticity in honey bees is associated with differences in brain microRNA transcriptome

(2012) J. K. Greenberg et al.   GENES BRAIN AND BEHAVIOR

Patterns of Transcriptome Divergence in the Male Accessory Gland of Two Closely Related Species of Field Crickets

(2012) J. A. Andres et al.   GENETICS

Incomplete Sex Chromosome Dosage Compensation in the Indian Meal Moth, Plodia interpunctella, Based on De Novo Transcriptome Assembly

(2012) Peter W. Harrison et al.   Genome Biology and Evolution

Genes Involved in the Evolution of Herbivory by a Leaf-Mining, Drosophilid Fly

(2012) Noah K. Whiteman et al.   Genome Biology and Evolution

Sex-Biased Transcriptome Evolution in Drosophila

(2012) Raquel Assis et al.   Genome Biology and Evolution

Pyrosequencing-Based Transcriptome Analysis of the Asian Rice Gall Midge Reveals Differential Response during Compatible and Incompatible Interaction

(2012) Deepak Sinha et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Retrogenes Moved Out of the Z Chromosome in the Silkworm

(2012) Jun Wang et al.   JOURNAL OF MOLECULAR EVOLUTION

Sex Chromosomes Evolved from Independent Ancestral Linkage Groups in Winged Insects

(2012) James B. Pease et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population transcriptomics of cactus host shifts inDrosophila mojavensis

(2012) LUCIANO M. MATZKIN   MOLECULAR ECOLOGY

Genomic approaches towards finding cis-regulatory modules in animals

(2012) Ross C. Hardison et al.   NATURE REVIEWS GENETICS

Gene duplication, tissue-specific gene expression and sexual conflict in stalk-eyed flies (Diopsidae)

(2012) R. H. Baker et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Transcriptome of Lutzomyia longipalpis (Diptera: Psychodidae) Male Reproductive Organs

(2012) Renata V. D. M. Azevedo et al.   PLoS One

High-Throughput Sequencing to Reveal Genes Involved in Reproduction and Development in Bactrocera dorsalis (Diptera: Tephritidae)

(2012) Weiwei Zheng et al.   PLoS One

Characterization of Head Transcriptome and Analysis of Gene Expression Involved in Caste Differentiation and Aggression in Odontotermes formosanus (Shiraki)

(2012) Qiuying Huang et al.   PLoS One

Transcriptional Profiles of Mating-Responsive Genes from Testes and Male Accessory Glands of the Mediterranean Fruit Fly, Ceratitis capitata

(2012) Francesca Scolari et al.   PLoS One

A link between host plant adaptation and pesticide resistance in the polyphagous spider mite Tetranychus urticae

(2012) W. Dermauw et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene expression changes governing extreme dehydration tolerance in an Antarctic insect

(2012) N. M. Teets et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Determinants of Scouting Behavior in Honey Bees

(2012) Zhengzheng S. Liang et al.   SCIENCE

A Mechanism of Extreme Growth and Reliable Signaling in Sexually Selected Ornaments and Weapons

(2012) D. J. Emlen et al.   SCIENCE

Gene discovery in the horned beetle Onthophagus taurus

(2011) Jeong-Hyeon Choi et al.   BMC GENOMICS

Somatic sex-specific transcriptome differences in Drosophila revealed by whole transcriptome sequencing

(2011) Peter L Chang et al.   BMC GENOMICS

A comprehensive gene expression atlas of sex- and tissue-specificity in the malaria vector, Anopheles gambiae

(2011) Dean A Baker et al.   BMC GENOMICS

Taxonomically restricted genes are associated with the evolution of sociality in the honey bee

(2011) Brian R Johnson et al.   BMC GENOMICS

The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus

(2011) Ben Ewen-Campen et al.   BMC GENOMICS

Sex chromosome evolution in moths and butterflies

(2011) Ken Sahara et al.   CHROMOSOME RESEARCH

Transcriptome profiling of female alates and egg-laying queens of the Formosan subterranean termite

(2011) Claudia Husseneder et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

Polyphenism in Insects

(2011) Stephen J. Simpson et al.   CURRENT BIOLOGY

DECOUPLING OF RAPID AND ADAPTIVE EVOLUTION AMONG SEMINAL FLUID PROTEINS IN HELICONIUS BUTTERFLIES WITH DIVERGENT MATING SYSTEMS

(2011) James R. Walters et al.   EVOLUTION

Getting a Full Dose? Reconsidering Sex Chromosome Dosage Compensation in the Silkworm, Bombyx mori

(2011) James R. Walters et al.   Genome Biology and Evolution

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Insights into the transcriptomics of polyphagy: Bemisia tabaci adaptability to phenylpropanoids involves coordinated expression of defense and metabolic genes

(2011) Michal Alon et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Social immunity in honeybees (Apis mellifera): transcriptome analysis of varroa-hygienic behaviour

(2011) Y. Le Conte et al.   INSECT MOLECULAR BIOLOGY

Selective Sweep of a cis-Regulatory Sequence in a Non-African Population of Drosophila melanogaster

(2011) S. S. Saminadin-Peter et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nutrition and division of labor: Effects on foraging and brain gene expression in the paper wasp Polistes metricus

(2011) T. H. F. DAUGHERTY et al.   MOLECULAR ECOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

The Fat Body Transcriptomes of the Yellow Fever Mosquito Aedes aegypti, Pre- and Post- Blood Meal

(2011) David P. Price et al.   PLoS One

Microarray-Based Transcriptomic Analysis of Differences between Long-Term Gregarious and Solitarious Desert Locusts

(2011) Liesbeth Badisco et al.   PLoS One

Genes involved in convergent evolution of eusociality in bees

(2011) S. H. Woodard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CSP and Takeout Genes Modulate the Switch between Attraction and Repulsion during Behavioral Phase Change in the Migratory Locust

(2011) Wei Guo et al.   PLoS Genetics

Single-molecule direct RNA sequencing without cDNA synthesis

(2011) Fatih Ozsolak et al.   Wiley Interdisciplinary Reviews-RNA

Evolution of Sexual Dimorphism in the Lepidoptera

(2010) Cerisse E. Allen et al.   Annual Review of Entomology

Evolution of Sex Chromosomes in Insects

(2010) Vera B. Kaiser et al.   Annual Review of Genetics

Function and evolution of sex determination mechanisms, genes and pathways in insects

(2010) Tanja Gempe et al.   BIOESSAYS

Transcriptome analysis of the sex pheromone gland of the noctuid moth Heliothis virescens

(2010) Heiko Vogel et al.   BMC GENOMICS

Hyperexpression of the X Chromosome in Both Sexes Results in Extensive Female Bias of X-Linked Genes in the Flour Beetle

(2010) Eldon G. Prince et al.   Genome Biology and Evolution

Male Sex Drive and the Maintenance of Sex: Evidence from Drosophila

(2010) R. S. Singh et al.   JOURNAL OF HEREDITY

Viral infection of tobacco plants improves performance of Bemisia tabaci but more so for an invasive than for an indigenous biotype of the whitefly

(2010) Jian Liu et al.   Journal of Zhejiang University-SCIENCE B

Combined EST and Proteomic Analysis Identifies Rapidly Evolving Seminal Fluid Proteins in Heliconius Butterflies

(2010) J. R. Walters et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of Gene Expression in Fire Ants: The Effects of Developmental Stage, Caste, and Species

(2010) L. Ometto et al.   MOLECULAR BIOLOGY AND EVOLUTION

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

De Novo Analysis of Transcriptome Dynamics in the Migratory Locust during the Development of Phase Traits

(2010) Shuang Chen et al.   PLoS One

Brain transcriptomic analysis in paper wasps identifies genes associated with behaviour across social insect lineages

(2010) A. L. Toth et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Deconstructing the Superorganism: Social Physiology, Groundplans, and Sociogenomics

(2010) Brian R. Johnson et al.   QUARTERLY REVIEW OF BIOLOGY

Comparative Genomic Hybridization (CGH) Reveals a Neo-X Chromosome and Biased Gene Movement in Stalk-Eyed Flies (Genus Teleopsis)

(2010) Richard H. Baker et al.   PLoS Genetics

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

Genomic analysis of a sexually-selected character: EST sequencing and microarray analysis of eye-antennal imaginal discs in the stalk-eyed fly Teleopsis dalmanni (Diopsidae)

(2009) Richard H Baker et al.   BMC GENOMICS

GENES WITH SOCIAL EFFECTS ARE EXPECTED TO HARBOR MORE SEQUENCE VARIATION WITHIN AND BETWEEN SPECIES

(2009) Timothy A. Linksvayer et al.   EVOLUTION

The Silkworm Z Chromosome Is Enriched in Testis-Specific Genes

(2009) K. P. Arunkumar et al.   GENETICS

Sugar sweet springtails: on the transcriptional response ofFolsomia candida(Collembola) to desiccation stress

(2009) M. J. T. N. Timmermans et al.   INSECT MOLECULAR BIOLOGY

The Deficit of Male-Biased Genes on the D. melanogaster X Chromosome Is Expression-Dependent: A Consequence of Dosage Compensation?

(2009) Beatriz Vicoso et al.   JOURNAL OF MOLECULAR EVOLUTION

Lifetime monogamy and the evolution of eusociality

(2009) J. J. Boomsma   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Molecular mechanisms of gene regulation during Drosophila spermatogenesis

(2009) Helen White-Cooper   REPRODUCTION

A Gene Necessary for Reproductive Suppression in Termites

(2009) J. Korb et al.   SCIENCE

Intralocus sexual conflict

(2009) Russell Bonduriansky et al.   TRENDS IN ECOLOGY & EVOLUTION

The Evolution of Animal Weapons

(2008) Douglas J. Emlen   Annual Review of Ecology Evolution and Systematics

Dosage analysis of Z chromosome genes using microarray in silkworm, Bombyx mori

(2008) Xingfu Zha et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Cowpea bruchid midgut transcriptome response to a soybean cystatin - costs and benefits of counter-defence

(2008) Y. H. Chi et al.   INSECT MOLECULAR BIOLOGY

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Genetic and genomic analyses of the division of labour in insect societies

(2008) Chris R. Smith et al.   NATURE REVIEWS GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS