title: Actin evolution in ciliates (Protist, Alveolata) is characterized by high diversity and three duplication events.
abstract: Ciliates possess two distinct nuclear genomes and unique genomic features, including highly fragmented chromosomes and extensive chromosomal rearrangements. Recent transcriptomic surveys have revealed that ciliates have several multi-copy genes providing an ideal template to study gene family evolution. Nonetheless, this process remains little studied in ciliated protozoa and consequently, the evolutionary patterns that govern it are not well understood. In this study, we focused on obtaining fine-scale information relative to ciliate species divergence for the first time. A total of 230 actin gene sequences were derived from this study, among which 217 were from four closely related Pseudokeronopsis species and 13 from other hypotrichous ciliates. Our investigation shows that: (1) At least three duplication events occurred in ciliates: diversification of three actin genes (Actin I, II, III) happened after the divergence of ciliate classes but before that of subclasses. And several recent and genus-specific duplications were followed within Actin I (Sterkiella, Oxytricha, Uroleptus, etc.), Actin II (Sterkiella), respectively. (2) Within the genus Pseudokeronopsis, Actin I gene duplication events happened after P. carnea and P. erythrina diverged. In contrast, in the morphologically similar species P. flava and P. rubra, the duplication event preceded diversification of the two species. The Actin II gene duplication events preceded divergence of the genus Pseudokeronopsis. (3) Phylogenetic analyses revealed that actin is suitable for resolving ciliate classes, but may not be used to infer lower taxon relationships.
authors.affiliation: Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Science, South China Normal University, Guangzhou 510631, China. Electronic address: zyi@scnu.edu.cn.
authors.forename: Zhenzhen
authors.initials: Z
authors.lastname: Yi
authors.affiliation: Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Science, South China Normal University, Guangzhou 510631, China.
authors.forename: Lijuan
authors.initials: L
authors.lastname: Huang
authors.affiliation: Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Science, South China Normal University, Guangzhou 510631, China.
authors.forename: Ran
authors.initials: R
authors.lastname: Yang
authors.affiliation: Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Science, South China Normal University, Guangzhou 510631, China. Electronic address: xlin@scnu.edu.cn.
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Lin
authors.affiliation: Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
authors.forename: Weibo
authors.initials: W
authors.lastname: Song
mesh_terms: D000199:Actins / Q000235:genetics*; D016798:Ciliophora / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D020440:Gene Duplication / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D005810:Multigene Family / Q000235:genetics; D010802:Phylogeny
chemical_list: D000199:Actins
keywords: Actin; Ciliates; Gene duplication; Gene evolution; Phylogeny