Insect genome content phylogeny and functional annotation of core insect genomes

•Gene presence/absence matrices were constructed for 21 insect genomes.•Gene presence/absence matrices were used to reconstruct insect phylogeny.•The role of e-value cutoff in phylogenetic analysis and genome content determination was examined.•Common ancestors of major insect groups experience more gene gain than gene loss.•The functional significance of gene gain/loss is examined in the divergence of major insect groups.

Twenty-one fully sequenced and well annotated insect genomes were examined for genome content in a phylogenetic context. Gene presence/absence matrices and phylogenetic trees were constructed using several phylogenetic criteria. The role of e-value on phylogenetic analysis and genome content characterization is examined using scaled e-value cutoffs and a single linkage clustering approach to orthology determination. Previous studies have focused on the role of gene loss in terminals in the insect tree of life. The present study examines several common ancestral nodes in the insect tree. We suggest that the common ancestors of major insect groups like Diptera, Hymenoptera, Hemiptera and Holometabola experience more gene gain than gene loss. This suggests that as major insect groups arose, their genomic repertoire expanded through gene duplication (segmental duplications), followed by contraction by gene loss in specific terminal lineages. In addition, we examine the functional significance of the loss and gain of genes in the divergence of some of the major insect groups.

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