title: Insect genome content phylogeny and functional annotation of core insect genomes.
abstract: 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.
authors.affiliation: Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA; Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA. Electronic address: jeffrey.rosenfeld@gmail.com.
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Rosenfeld
authors.affiliation: Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA; Richard Gilder Graduate School, American Museum of Natural History, USA. Electronic address: jfoox@amnh.org.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Foox
authors.affiliation: Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA. Electronic address: desalle@amnh.org.
authors.forename: Rob
authors.initials: R
authors.lastname: DeSalle
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D020440:Gene Duplication / Q000235:genetics; D049750:Genome, Insect / Q000235:genetics*; D023281:Genomics; D007313:Insecta / Q000145:classification* / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010802:Phylogeny
keywords: Dollo parsimony; Function; Genome; Insect; Phylogeny