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Vol. 52, 2013
Transcriptional profiling of adult Drosophila antennae by high-throughput
sequencing
Meng-Shin
Shiao1,2, Wen-Lang Fan1,2,
Shu Fang1, Mei-Yeh Jade Lu1, Rumi Kondo3
and Wen-Hsiung Li1,4*
1Biodiversity
Research Center, Academia Sinica, Taipei 11529, Taiwan
2Genomics Research Center, Academia Sinica, Taipei
11529, Taiwan
3Graduate School of Humanities and Sciences,
Ochanomizu University, Tokyo 112-8610, Japan
4Department of Ecology and Evolution, University of
Chicago, Chicago, IL 60637, USA
Abstract
Background: Antennae of fruit flies
are the major organs responsible for detecting environmental volatiles,
e.g., egg-laying substrates. An adult antenna contains many sensilla
full of olfactory sensory neurons, where olfactory receptor (Or) genes
are expressed. Each sensory neuron only expresses up to three
receptors, making it difficult to estimate expression levels by
conventional methods. In this study, we applied Illumina RNA sequencing
(RNA-seq) to study the expression levels of Or and other genes in fly
antennae.
Results: RNA from approximately 1,200 pairs of
adult antennae from each sex of Drosophila
melanogaster was used to
obtain the antennal transcriptome of each sex. We detected
approximately 12,000 genes expressed in antennae of either sex. The
most highly expressed genes included pheromone-binding genes,
transmembrane transporter genes, and sensory reception genes. Among the
61 annotated Or genes, we observed 53 and 54 genes (approximately 90%)
expressed (fragments per kilobase of exon per million fragments mapped
(FPKM) > 0.05) in male and female antennae, respectively;
approximately 25 genes were expressed with FPKM > 15. Compared to
previous studies, which extracted RNA from the whole body or head and
used microarrays, antenna-specific transcriptomes obtained by RNA-seq
provided more reliable estimates of gene expression levels and revealed
many lowly expressed genes. Ninty-one genes, including one
odorant-binding protein (Obp) gene and four Or genes, were
differentially expressed between male and female antennae. These
sexually biased genes were enriched on the X chromosome and showed
enrichment in different gene ontology categories for male and female
flies. The present and previous data together suggest that a gene
family with putative immune response functions is related to pheromone
detection and involved in the courtship behavior of male flies.
Conclusions: Tissue-specific
RNA-seq is powerful for detecting lowly expressed genes. Our study
provides new insight into the expression of olfactory-related genes in
Drosophila antennae.
Key words: Transcriptome; RNA-seq; Olfactory
receptors; Odorant-binding proteins; Sexual bias.
*Correspondence: E-mail: whli@sinica.edu.tw
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