title: Evolution of eukaryotic genome architecture: Insights from the study of a rapidly evolving metazoan, Oikopleura dioica: Non-adaptive forces such as elevated mutation rates may influence the evolution of genome architecture.
abstract: Recent sequencing of the metazoan Oikopleura dioica genome has provided important insights, which challenges the current understanding of eukaryotic genome evolution. Many genomic features of O. dioica show deviation from the commonly observed trends in other eukaryotic genomes. For instance, O. dioica has a rapidly evolving, highly compact genome with a divergent intron-exon organization. Additionally, O. dioica lacks the minor spliceosome and key DNA repair pathway genes. Even with a compact genome, O. dioica contains tandem repeats, comparable to other eukaryotes, and shows lineage-specific expansion of certain protein domains. Here, we review its genomic features in the context of current knowledge, discuss implications for contemporary biology and identify areas for further research. Analysis of the O. dioica genome suggests that non-adaptive forces such as elevated mutation rates might influence the evolution of genome architecture. The knowledge of unique genomic features and splicing mechanisms in O. dioica may be exploited for synthetic biology applications, such as generation of orthogonal splicing systems.
authors.affiliation: MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK. schavali@mrc-lmb.cam.ac.uk
authors.forename: Sreenivas
authors.initials: S
authors.lastname: Chavali
authors.forename: David A de Lima
authors.initials: DA
authors.lastname: Morais
authors.forename: Julian
authors.initials: J
authors.lastname: Gough
authors.forename: M Madan
authors.initials: MM
authors.lastname: Babu
mesh_terms: D000818:Animals; D004251:DNA Transposable Elements; D019143:Evolution, Molecular; D020440:Gene Duplication; D023061:Gene Order; D007438:Introns; D009154:Mutation; D010802:Phylogeny; D012326:RNA Splicing; D022661:RNA, Untranslated / Q000235:genetics / Q000378:metabolism; D017381:Spliceosomes / Q000235:genetics / Q000378:metabolism; D020080:Tandem Repeat Sequences; D014158:Transcription, Genetic; D014561:Urochordata / Q000145:classification / Q000235:genetics* / Q000378:metabolism
chemical_list: D004251:DNA Transposable Elements; D022661:RNA, Untranslated