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

Abstract

All EST sequence data are available from the private 'Spodo-Base' upon request.

A Crassostrea gigas Toll-like receptor and comparative analysis of TLR pathway in invertebrates

“…They were orthologs in selected species but with irregular ENCs as well. In Spodoptera frugiperda and Bombyx mori, highly expressed ribosomal proteins are found to be with high codon usage bias, but not in D. melanogaster [51], which indicating that the expression level, codon usage bias pattern and sequence identity are not absolutely identical. Such doubt can also be explained by remote genetic distance of analyzed species for limitation of sequence information of mollusk.…”

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

“…Nucleotide sequences for target genes in fall armyworm (Table 1; Supplemental Tables 1e3) were obtained from a closely related species, H. armigera, and used in a tBLASTx search against expressed sequence tags (ESTs) in SPODOBASE (Landais et al, 2003;Negre et al, 2006; http://bioweb.ensam.inra.fr/spodobase) to find the corresponding sequence in fall armyworm based on those having the highest bit score. A similar approach was used for European corn borer except that target genes from H. armigera were used in a tBLASTx search against only ESTs from European corn borer in GenBank.…”

“…The 138911 Sanger ESTs in SPODOBASE (Landais et al, 2003;Negre et al, 2006) were assembled into a reference transcriptome using SeqMan Pro version 8.0.2 (DNASTAR Lasergene Ò , Madison, WI) and default parameters as recommended by the manufacturer for Sanger sequences. Preassembly involved a medium end trim, a vector scan and contaminant sequence screen that used a minimum of 5 mismatches; vector and contaminant sequence catalogs were those provided by the software.…”

Expressed sequence tags analysis of Blattella germanica

“…This protein gene was expected to be used to repair 8-oxoguanine in man (Cappelli et al, 2003). In addition, the ribosomal protein family provides valuable comparative genomic and phylogenic data on insecta (Landais et al, 2003).…”