Bioinformatics Vol. 19 no. 18 2003
pages 2343-2350
© 2003 Oxford University Press
Annotation pattern of ESTs from Spodoptera frugiperda Sf9 cells and analysis of the ribosomal protein genes reveal insect-specific features and unexpectedly low codon usage bias
1 Laboratoire de Pathologie Comparée, INRA—CNRS—Université Montpellier II, UMR 5087, 30380 Saint Christol-les-Alès, France, 2 Laboratory of Insect Genome, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8634, Japan and 3 Laboratory of Insect Genetics and Bioscience, Department Agricultural & Environmental Biology, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
Received on November 28, 2002
; revised on May 2, 2003
; accepted on May 29, 2003
Motivation: A whole set of Expressed Sequence Tags (ESTs) from the Sf9 cell line of Spodoptera frugiperda is presented here for the first time. By this way we want to identify both conserved and specific genes of this pest species. We also expect from this analysis to find a class of protein sequences providing a tool to explore genomic features and phylogeny of Lepidoptera.
Results: The ESTs display both housekeeping as well as developmentally regulated genes, and a high percentage of sequences with unknown function. Among the identified ORFs, almost all ribosomal proteins (RPs) were found with high EST redundancy and hence sequence accuracy. The codon usage found among RP genes is in average surprisingly much less biased in Lepidoptera than in other organisms. Other Spodoptera genes also displayed a low bias, suggesting a general genome expression feature in this Lepidoptera. We also found that the L35A and L36 RP sequences, respectively, display 40 and 10 amino-acid insertions, both being present only in insects. Sequence analysis suggests that they are probably not subjected to a strong selective pressure and may be good phylogenetic markers for Lepidoptera. Most interestingly, the Lepidoptera sequences of 9 RP genes displayed a specific signature different from the canonical one. We conclude that the RP family allows valuable comparative genomics and phylogeny of Lepidoptera.
Availability: All EST sequence data are available from the private ‘Spodo-Base’ upon request.
Contact: devauche{at}ales.inra.fr
* To whom correspondence should be addressed.
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