title: Evolutionary dynamics of triosephosphate isomerase gene intron location pattern in Metazoa: A new perspective on intron evolution in animals.
abstract: Intron evolution, including its dynamics in the evolutionary transitions and diversification of eukaryotes, remains elusive. Inadequate taxon sampling due to data shortage, unclear phylogenetic framework, and inappropriate outgroup application might be among the causes. Besides, the integrity of all the introns within a gene was often neglected previously. Taking advantage of the ancient conserved triosephosphate isomerase gene (tim), the relatively robust phylogeny of Metazoa, and choanoflagellates as outgroup, the evolutionary dynamics of tim intron location pattern (ILP) in Metazoa was investigated. From 133 representative species of ten phyla, 30 types of ILPs were identified. A most common one, which harbors the maximum six intron positions, is deduced to be the common ancestral tim ILP of Metazoa, which almost had formed in their protozoan ancestor and was surprisingly retained and passed down till to each ancestors of metazoan phyla. In the subsequent animal diversification, it underwent different evolutionary trajectories: within Deuterostomia, it was almost completely retained only with changes in a few species with relatively recently fast-evolving histories, while within the rapidly radiating Protostomia, besides few but remarkable retention, it usually displayed extensive intron losses and a few gains. Therefore, a common ancestral exon-intron arrangement pattern of an animal gene is definitely discovered; besides the 'intron-rich view' of early animal genes being confirmed, the novel insight that high exon-intron re-arrangements of genes seem to be associated with the relatively recently rapid evolution of lineages/species/genomes but have no correlation with the ancient major evolutionary transitions in animal evolution, is revealed.
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. Electronic address: chenbing@mail.kiz.ac.cn.
authors.forename: Bing
authors.initials: B
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. Electronic address: shaojr@mail.kiz.ac.cn.
authors.forename: Jingru
authors.initials: J
authors.lastname: Shao
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. Electronic address: zhuanghuifu@mail.kib.ac.cn.
authors.forename: Huifu
authors.initials: H
authors.lastname: Zhuang
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. Electronic address: wenjf@mail.kiz.ac.cn.
authors.forename: Jianfan
authors.initials: J
authors.lastname: Wen
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D056897:Choanoflagellata / Q000201:enzymology / Q000235:genetics; D017124:Conserved Sequence; D019143:Evolution, Molecular; D006801:Humans; D007438:Introns; D010802:Phylogeny; D016415:Sequence Alignment; D014305:Triose-Phosphate Isomerase / Q000235:genetics*
chemical_list: D014305:Triose-Phosphate Isomerase
keywords: Exon-intron arrangement; Intron evolution; Intron location pattern (ILP); Metazoan divergence; Triosephosphate isomerase gene (tim)