title: Protein domain evolution is associated with reproductive diversification and adaptive radiation in the genus Eucalyptus.
abstract: Eucalyptus is a pivotal genus within the rosid order Myrtales with distinct geographic history and adaptations. Comparative analysis of protein domain evolution in the newly sequenced Eucalyptus grandis genome and other rosid lineages sheds light on the adaptive mechanisms integral to the success of this genus of woody perennials. We reconstructed the ancestral domain content to elucidate the gain, loss and expansion of protein domains and domain arrangements in Eucalyptus in the context of rosid phylogeny. We used functional gene ontology (GO) annotation of genes to investigate the possible biological and evolutionary consequences of protein domain expansion. We found that protein modulation within the angiosperms occurred primarily on the level of expansion of certain domains and arrangements. Using RNA-Seq data from E. grandis, we showed that domain expansions have contributed to tissue-specific expression of tandemly duplicated genes. Our results indicate that tandem duplication of genes, a key feature of the Eucalyptus genome, has played an important role in the expansion of domains, particularly in proteins related to the specialization of reproduction and biotic and abiotic interactions affecting root and floral biology, and that tissue-specific expression of proteins with expanded domains has facilitated subfunctionalization in domain families.
authors.affiliation: Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany.|Bioinformatics Group, Institute for Computer Science, Heinrich-Heine-University, Duesseldorf, Germany.
authors.forename: Anna R
authors.initials: AR
authors.lastname: Kersting
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
authors.forename: Eshchar
authors.initials: E
authors.lastname: Mizrachi
authors.affiliation: Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany.
authors.forename: Erich
authors.initials: E
authors.lastname: Bornberg-Bauer
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Myburg
mesh_terms: D016000:Cluster Analysis; D005052:Eucalyptus / Q000235:genetics*; D019143:Evolution, Molecular; D020440:Gene Duplication; D017343:Genes, Plant; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry* / Q000235:genetics*; D017434:Protein Structure, Tertiary; D020543:Proteome / Q000378:metabolism; D012098:Reproduction
chemical_list: D010940:Plant Proteins; D020543:Proteome
keywords: Eucalyptus; expansion; flower; gene expression; protein domains; root; rosids