Comparative profiling of the transcriptional response to infection in two species of Drosophila by short-read cDNA sequencing.


BACKGROUND:Homology-based comparisons of the genes involved in innate immunity across many insect taxa with fully sequenced genomes has revealed a striking pattern of gene gain and loss, particularly among genes that encode proteins involved in clearing pathogens (effectors). However, limited functional annotation in non-model systems has hindered understanding of evolutionary novelties in the insect innate immune system. RESULTS:We use short read sequencing technology (Illumina/Solexa) to compare the transcriptional response to infection between the well studied model system Drosophila melanogaster and the distantly related drosophilid D. virilis. We first demonstrate that Illumina/Solexa sequencing of cDNA from infected and uninfected D. melanogaster recapitulates previously published microarray studies of the transcriptional response to infection in this species, validating our approach. We then show that patterns of transcription of homologous genes differ considerably between D. melanogaster and D. virilis, and identify potential candidates for novel components of the D. virilis immune system based on transcriptional data. Finally, we use a proteomic approach to characterize the protein constituents of the D. virilis hemolymph and validate our transcriptional data. CONCLUSION:These results suggest that the acquisition of novel components of the immune system, and particularly novel effector proteins, may be a common evolutionary phenomenon.


BMC Genomics


BMC genomics


Sackton TB,Clark AG




Has Abstract


2009-06-07 00:00:00










  • Comparing de novo assemblers for 454 transcriptome data.

    abstract:BACKGROUND:Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base) reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcr...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kumar S,Blaxter ML

    更新日期:2010-10-16 00:00:00

  • Cell population-specific expression analysis of human cerebellum.

    abstract:BACKGROUND:Interpreting gene expression profiles obtained from heterogeneous samples can be difficult because bulk gene expression measures are not resolved to individual cell populations. We have recently devised Population-Specific Expression Analysis (PSEA), a statistical method that identifies individual cell types...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kuhn A,Kumar A,Beilina A,Dillman A,Cookson MR,Singleton AB

    更新日期:2012-11-12 00:00:00

  • Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (Elaeis guineensis Jacq.).

    abstract:BACKGROUND:Oil palm is the second largest source of edible oil which contributes to approximately 20% of the world's production of oils and fats. In order to understand the molecular biology involved in in vitro propagation, flowering, efficient utilization of nitrogen sources and root diseases, we have initiated an ex...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ho CL,Kwan YY,Choi MC,Tee SS,Ng WH,Lim KA,Lee YP,Ooi SE,Lee WW,Tee JM,Tan SH,Kulaveerasingam H,Alwee SS,Abdullah MO

    更新日期:2007-10-22 00:00:00

  • Transcriptome of the floral transition in Rosa chinensis 'Old Blush'.

    abstract:BACKGROUND:The floral transition plays a vital role in the life of ornamental plants. Despite progress in model plants, the molecular mechanisms of flowering regulation remain unknown in perennial plants. Rosa chinensis 'Old Blush' is a unique plant that can flower continuously year-round. In this study, gene expressio...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Guo X,Yu C,Luo L,Wan H,Zhen N,Xu T,Tan J,Pan H,Zhang Q

    更新日期:2017-02-23 00:00:00

  • In silico identification and comparative analysis of differentially expressed genes in human and mouse tissues.

    abstract:BACKGROUND:Screening for differentially expressed genes on the genomic scale and comparative analysis of the expression profiles of orthologous genes between species to study gene function and regulation are becoming increasingly feasible. Expressed sequence tags (ESTs) are an excellent source of data for such studies ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Pao SY,Lin WL,Hwang MJ

    更新日期:2006-04-21 00:00:00

  • First comprehensive analysis of lysine acetylation in Alvinocaris longirostris from the deep-sea hydrothermal vents.

    abstract:BACKGROUND:Deep-sea hydrothermal vents are unique chemoautotrophic ecosystems with harsh conditions. Alvinocaris longirostris is one of the dominant crustacean species inhabiting in these extreme environments. It is significant to clarify mechanisms in their adaptation to the vents. Lysine acetylation has been known to...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Hui M,Cheng J,Sha Z

    更新日期:2018-05-10 00:00:00

  • Comparative transcriptomics of early petal development across four diverse species of Aquilegia reveal few genes consistently associated with nectar spur development.

    abstract:BACKGROUND:Petal nectar spurs, which facilitate pollination through animal attraction and pollen placement, represent a key innovation promoting diversification in the genus Aquilegia (Ranunculaceae). Identifying the genetic components that contribute to the development of these three-dimensional structures will inform...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ballerini ES,Kramer EM,Hodges SA

    更新日期:2019-08-22 00:00:00

  • Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis.

    abstract:BACKGROUND:The sequence of the pathogen Mycobacterium tuberculosis (Mtb) strain H37Rv has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other Mtb strains and closely related bacteria present an opportunity to apply the power of comparative genomics to...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: McGuire AM,Weiner B,Park ST,Wapinski I,Raman S,Dolganov G,Peterson M,Riley R,Zucker J,Abeel T,White J,Sisk P,Stolte C,Koehrsen M,Yamamoto RT,Iacobelli-Martinez M,Kidd MJ,Maer AM,Schoolnik GK,Regev A,Galagan J

    更新日期:2012-03-28 00:00:00

  • Limited sex-biased neural gene expression patterns across strains in Zebrafish (Danio rerio).

    abstract:BACKGROUND:Male and female vertebrates typically differ in a range of characteristics, from morphology to physiology to behavior, which are influenced by factors such as the social environment and the internal hormonal and genetic milieu. However, sex differences in gene expression profiles in the brains of vertebrates...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wong RY,McLeod MM,Godwin J

    更新日期:2014-10-17 00:00:00

  • Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple.

    abstract:BACKGROUND:Apple is an economically important fruit crop worldwide. Developing a genetic linkage map is a critical step towards mapping and cloning of genes responsible for important horticultural traits in apple. To facilitate linkage map construction, we surveyed and characterized the distribution and frequency of pe...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhang Q,Ma B,Li H,Chang Y,Han Y,Li J,Wei G,Zhao S,Khan MA,Zhou Y,Gu C,Zhang X,Han Z,Korban SS,Li S,Han Y

    更新日期:2012-10-07 00:00:00

  • A deconvolution method and its application in analyzing the cellular fractions in acute myeloid leukemia samples.

    abstract:BACKGROUND:The identification of cell type-specific genes (markers) is an essential step for the deconvolution of the cellular fractions, primarily, from the gene expression data of a bulk sample. However, the genes with significant changes identified by pair-wise comparisons cannot indeed represent the specificity of ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li H,Sharma A,Ming W,Sun X,Liu H

    更新日期:2020-09-23 00:00:00

  • ProSeeK: a web server for MLPA probe design.

    abstract:BACKGROUND:The technological evolution of platforms for detecting genome-wide copy number imbalances has allowed the discovery of an unexpected amount of human sequence that is variable in copy number among individuals. This type of human variation can make an important contribution to human diversity and disease susce...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Pantano L,Armengol L,Villatoro S,Estivill X

    更新日期:2008-11-28 00:00:00

  • An advanced bioinformatics approach for analyzing RNA-seq data reveals sigma H-dependent regulation of competence genes in Listeria monocytogenes.

    abstract:BACKGROUND:Alternative σ factors are important transcriptional regulators in bacteria. While σ(B) has been shown to control a large regulon and play important roles in stress response and virulence in the pathogen Listeria monocytogenes, the function of σ(H) has not yet been well defined in Listeria, even though σ(H) c...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Liu Y,Orsi RH,Boor KJ,Wiedmann M,Guariglia-Oropeza V

    更新日期:2016-02-16 00:00:00

  • Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array.

    abstract:BACKGROUND:A whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any given Malus progeny. To test the applicability of the array for mapping in diverse Malus genotypes, ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Antanaviciute L,Fernández-Fernández F,Jansen J,Banchi E,Evans KM,Viola R,Velasco R,Dunwell JM,Troggio M,Sargent DJ

    更新日期:2012-05-25 00:00:00

  • Skipper genome sheds light on unique phenotypic traits and phylogeny.

    abstract:BACKGROUND:Butterflies and moths are emerging as model organisms in genetics and evolutionary studies. The family Hesperiidae (skippers) was traditionally viewed as a sister to other butterflies based on its moth-like morphology and darting flight habits with fast wing beats. However, DNA studies suggest that the famil...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Cong Q,Borek D,Otwinowski Z,Grishin NV

    更新日期:2015-08-27 00:00:00

  • Phylogenetic patterns of gene rearrangements in four mitochondrial genomes from the green algal family Hydrodictyaceae (Sphaeropleales, Chlorophyceae).

    abstract:BACKGROUND:The variability in gene organization and architecture of green algal mitochondrial genomes is only recently being studied on a finer taxonomic scale. Sequenced mt genomes from the chlorophycean orders Volvocales and Sphaeropleales exhibit considerable variation in size, content, and structure, even among clo...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Farwagi AA,Fučíková K,McManus HA

    更新日期:2015-10-21 00:00:00

  • Stress-mediated convergence of splicing landscapes in male and female rock doves.

    abstract:BACKGROUND:The process of alternative splicing provides a unique mechanism by which eukaryotes are able to produce numerous protein products from the same gene. Heightened variability in the proteome has been thought to potentiate increased behavioral complexity and response flexibility to environmental stimuli, thus c...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Lang AS,Austin SH,Harris RM,Calisi RM,MacManes MD

    更新日期:2020-03-23 00:00:00

  • The complete mitochondrial genomes for three Toxocara species of human and animal health significance.

    abstract:BACKGROUND:Studying mitochondrial (mt) genomics has important implications for various fundamental areas, including mt biochemistry, physiology and molecular biology. In addition, mt genome sequences have provided useful markers for investigating population genetic structures, systematics and phylogenetics of organisms...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li MW,Lin RQ,Song HQ,Wu XY,Zhu XQ

    更新日期:2008-05-16 00:00:00

  • Comparison between two amplicon-based sequencing panels of different scales in the detection of somatic mutations associated with gastric cancer.

    abstract:BACKGROUND:Sequencing data from The Cancer Genome Atlas (TGCA), the International Cancer Genome Consortium and other research institutes have revealed the presence of genetic alterations in several tumor types, including gastric cancer. These data have been combined into a catalog of significantly mutated genes for eac...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Hirotsu Y,Kojima Y,Okimoto K,Amemiya K,Mochizuki H,Omata M

    更新日期:2016-10-26 00:00:00

  • Exclusivity offers a sound yet practical species criterion for bacteria despite abundant gene flow.

    abstract:BACKGROUND:The question of whether bacterial species objectively exist has long divided microbiologists. A major source of contention stems from the fact that bacteria regularly engage in horizontal gene transfer (HGT), making it difficult to ascertain relatedness and draw boundaries between taxa. A natural way to defi...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wright ES,Baum DA

    更新日期:2018-10-03 00:00:00

  • The complete mitochondrial genome of the early flowering plant Nymphaea colorata is highly repetitive with low recombination.

    abstract:BACKGROUND:Mitochondrial genomes of flowering plants (angiosperms) are highly dynamic in genome structure. The mitogenome of the earliest angiosperm Amborella is remarkable in carrying rampant foreign DNAs, in contrast to Liriodendron, the other only known early angiosperm mitogenome that is described as 'fossilized'. ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Dong S,Zhao C,Chen F,Liu Y,Zhang S,Wu H,Zhang L,Liu Y

    更新日期:2018-08-14 00:00:00

  • Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa.

    abstract:BACKGROUND:Winter-ulcer Moritella viscosa infections continue to be a significant burden in Atlantic salmon (Salmo salar L.) farming. M. viscosa comprises two main clusters that differ in genetic variation and phenotypes including virulence. Horizontal gene transfer through acquisition and loss of mobile genetic elemen...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Karlsen C,Hjerde E,Klemetsen T,Willassen NP

    更新日期:2017-04-20 00:00:00

  • Identification of transcription factors potential related to brown planthopper resistance in rice via microarray expression profiling.

    abstract:BACKGROUND:Brown planthopper (BPH), Nilaparvata lugens Stål, is one of the most destructive insect pests of rice. The molecular responses of plants to sucking insects resemble responses to pathogen infection. However, the molecular mechanism of BPH-resistance in rice remains unclear. Transcription factors (TF) are up-s...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wang Y,Guo H,Li H,Zhang H,Miao X

    更新日期:2012-12-10 00:00:00

  • Dual species transcript profiling during the interaction between banana (Musa acuminata) and the fungal pathogen Fusarium oxysporum f. sp. cubense.

    abstract:BACKGROUND:Banana wilt disease, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), is one of the most devastating diseases in banana (Musa spp.). Foc is a soil borne pathogen that causes rot of the roots or wilt of leaves by colonizing the xylem vessels. The dual RNA sequencing is used to simultaneo...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li W,Wang X,Li C,Sun J,Li S,Peng M

    更新日期:2019-06-24 00:00:00

  • EPAS1 gene variants are associated with sprint/power athletic performance in two cohorts of European athletes.

    abstract:BACKGROUND:The endothelial PAS domain protein 1 (EPAS1) activates genes that are involved in erythropoiesis and angiogenesis, thus favoring a better delivery of oxygen to the tissues and is a plausible candidate to influence athletic performance. Using innovative statistical methods we compared genotype distributions a...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Voisin S,Cieszczyk P,Pushkarev VP,Dyatlov DA,Vashlyayev BF,Shumaylov VA,Maciejewska-Karlowska A,Sawczuk M,Skuza L,Jastrzebski Z,Bishop DJ,Eynon N

    更新日期:2014-05-18 00:00:00

  • Histological and global gene expression analysis of the 'lactating' pigeon crop.

    abstract:BACKGROUND:Both male and female pigeons have the ability to produce a nutrient solution in their crop for the nourishment of their young. The production of the nutrient solution has been likened to lactation in mammals, and hence the product has been called pigeon 'milk'. It has been shown that pigeon 'milk' is essenti...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Gillespie MJ,Haring VR,McColl KA,Monaghan P,Donald JA,Nicholas KR,Moore RJ,Crowley TM

    更新日期:2011-09-19 00:00:00

  • Comparative miRNAome analysis revealed different miRNA expression profiles in bovine sera and exosomes.

    abstract:BACKGROUND:Extra-cellular components, such as serum and exosome, have drawn great attention as a readily accessible source of biomarkers for mammalian health. However, the contribution of different blood components to the signature of respective microRNAs (miRNAs) remains unknown, especially in cattle. In this study we...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhao K,Liang G,Sun X,Guan le L

    更新日期:2016-08-12 00:00:00

  • An updated explanation of ancestral karyotype changes and reconstruction of evolutionary trajectories to form Camelina sativa chromosomes.

    abstract:BACKGROUND:Belonging to lineage I of Brassicaceae, Camelina sativa is formed by two hybridizations of three species (three sub-genomes). The three sub-genomes were diverged from a common ancestor, likely derived from lineage I (Ancestral Crucifer karyotype, ACK). The karyotype evolutionary trajectories of the C. sativa...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhang Z,Meng F,Sun P,Yuan J,Gong K,Liu C,Wang W,Wang X

    更新日期:2020-10-12 00:00:00

  • Development of simple sequence repeat (SSR) markers from a genome survey of Chinese bayberry (Myrica rubra).

    abstract:BACKGROUND:Chinese bayberry (Myrica rubra Sieb. and Zucc.) is a subtropical evergreen tree originating in China. It has been cultivated in southern China for several thousand years, and annual production has reached 1.1 million tons. The taste and high level of health promoting characters identified in the fruit in rec...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Jiao Y,Jia HM,Li XW,Chai ML,Jia HJ,Chen Z,Wang GY,Chai CY,van de Weg E,Gao ZS

    更新日期:2012-05-23 00:00:00

  • A novel analytical method, Birth Date Selection Mapping, detects response of the Angus (Bos taurus) genome to selection on complex traits.

    abstract:BACKGROUND:Several methods have recently been developed to identify regions of the genome that have been exposed to strong selection. However, recent theoretical and empirical work suggests that polygenic models are required to identify the genomic regions that are more moderately responding to ongoing selection on com...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Decker JE,Vasco DA,McKay SD,McClure MC,Rolf MM,Kim J,Northcutt SL,Bauck S,Woodward BW,Schnabel RD,Taylor JF

    更新日期:2012-11-09 00:00:00