On molecular biology of ciliated protozoa: Frontier areas and progresses

Abstract

Ciliated protists are important organisms which play significant roles in studies on cell biology, genetics, biodiversity, biogeography and ecology, environmental biology etc. In last decade, molecular investigations on phylogeny, barcoding, epigenetics, genomics, and gene evolution have been performed by the authors' groups and the main results can be summarized as follows: (i) Phylogenetic relationships within over 50 classes/orders are analyzed, and two new classes, six new orders/suborders are established by the authors' groups, based on more than 2000 new sequences. Additionally, theoretical researches focusing on gene marker selection and topological optimization are also performed, in order to provide theoretical guidance for future study. We suggested that unidentified environmental sequences, and secondary structures of rRNA gene could be used for inferring phylogenetic relationships of ciliates, at least on some taxon level. And we also discussed the impact of missing data present in concatenated analyses, and paralogs of protein-coding genes on phylogenetic analyses. (ii) Transcriptome/genome genome of six representative ciliates (Strombidium sulcatum, Uronema marinum, Metanophrys similis, Euplotes vannus, Uroleptopsis citrina, Paramecium caudatum) were sequenced and analyzed, which will help to find out the evolutionary position of key species, the relationship between expression of the functional gene family and morphological characteristics, and to understand the association between genetic information and phenotype; Also, we compared mitochondrial genome of the genus Euplotes species, thus found the gene order and transcriptional directions were the same among three species, but 3 split protein coding genes (nad9, nad2 and rpl16) were predicted only in mt-genome of E. vannus. (iii) Knockout of histone methyltransferase TXR1 (Tetrahymena Trithorax related 1), specific for H3 lysine 27 mono-methylation (H3K27me1), leads to severe replication stress in the model organism Tetrahymena thermophila. Consequently, cells mobilize the DNA damage response, indicating that perturbation of epigenetic information can directly affect replication elongation. (iv) Alternative processing is extensive among gene families in Chilodonella uncinata which are likely to be C. uncinata specific; and the processing patterns are different among gene families which is more complex than previously believed. We propose a new model whereby gene scrambling evolves by gene duplication followed by partial and reciprocal degradation of the duplicate sequences. In this model, alternative processing represents an intermediate step in the evolution of scrambled genes and yields important insights into the mechanism for speciation in ciliates. (v) Four gene markers, viz. COI, ITS1, ITS2, D2 region of 28SrRNA gene, are evaluated as promising candidate barcoding markers, by comparing 8 gene makers on the same organisms for the first time. DNA barcoding sequences of 83 species covering subclass Peniculia, Oligotrichia and Euplotia are firstly sequenced. And sampling information, morphological characters and pictures of these species are also recorded for constructing DNA barcoding database of ciliates.