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
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
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DOI：
10.1093/bioinformatics/btg324
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发表时间：
2003-12-12
期刊：
影响因子：
5.8
通讯作者：
Devauchelle, G
中科院分区：
文献类型：
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作者：
Landais, I;Ogliastro, M;Devauchelle, G
目的：首次从草地贪夜蛾Sf9细胞系中获得了一整套表达序列标签（EST）。通过这种方法，我们希望确定该害虫物种的保守和特异基因。我们还希望通过分析发现一类蛋白质序列，为探讨鳞翅目昆虫的基因组特征和进化提供工具。结果：EST既显示了管家基因，也显示了发育调控基因，并且有很高比例的序列功能未知。在已鉴定的ORF中，几乎所有的核糖体蛋白（RP）都具有较高的EST冗余度，因此序列准确性较高。在RP基因中发现的密码子使用在鳞翅目中比在其他生物中平均令人惊讶地少得多的偏见。其他的夜蛾基因也显示出较低的偏好性，表明该鳞翅目昆虫具有普遍的基因组表达特征。我们还发现，L35 A和L36 RP序列，分别显示40和10个氨基酸的插入，都是只存在于昆虫。序列分析表明，它们可能不会受到很强的选择压力，可能是很好的系统发育标记。最有趣的是，9个RP基因的鳞翅目序列显示出不同于典型的一个特定的签名。我们的结论是RP家庭允许有价值的比较基因组学和鳞翅目昆虫的进化。
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.