| Tetrahymena thermophila, a unicellular eukaryotic model of ciliated Protozoa, has made a series of achievements in the basic biological research. Currently, two versions of genome annotation about this model organism are available, however, there still exist some problems in both of them due to the limited transcriptome data, which also led to the lack of annotations about alternative splicing genes. Therefore, it becomes particularly important and urgent to refine the genome annotation of T. thermophila based on more transcriptome sequencing data.To address these possible problems including inaccurate gene structure annotation, incomplete prediction of gene models in the current versions of genome annotation, twenty-four transcriptome sequencing data of T.thermophila in three different physiological/developmental stages(growth, starvation and conjugation) were analyzed in this study. By using TopHat and related downstream software and T.thermophila SB210 genome sequence as reference, these 24 transcriptome data were aligned, assembled and merged to 30,901 transcripts. Comparing these transcripts with gene models in current genome annotation by using related software directly and correcting manually combined with Gbrowse network graphical method for partial genes, it indicated that in the current genome annotation, 22,656 gene models were supported accurately by transcripts. In addition, 5,206 genes that have errors in structure and/or location information were corrected manually and 234 new genes were identified. Finally, we confirmed 28,096 refined gene models in Tetrahymena thermophila.We further identify and analyze the predicted alternative splicing genes of T.thermophila. Considering the complexity of transcripts brought from vast transcriptome data and the imperfection of transcript assembly, we chose genes with at least one isoform matching the existing gene models exactly. Finally, 464 alternative splicing genes were selected. And it contained four common alternative splicing types in these 464 genes, in which intron retention is the major alternative splicing way. Of the 464 genes, some are expressed specifically in different physiological/developmental stages. The functional classification of these specific expressed genes in different stages is different but generally the major biological process involved is protein phosphorylation, which consists with the fact that there is a large number of protein kinase in T.thermophila.With the accomplishment of genome re-annotation and identification of alternative splicing genes of T. thermophila, the quantity and quality of gene models have increased and improved on the basis of current genome annotation. At the same time, we also increase the information about gene untranslated regions. What's more, this work helps to fill the vacancy about the identification and functional analysis of alternative splicing genes in current genome annotation, which lays a foundation for intensive study of this model organism.Protozoan includes various and widespread species. Stylonychia lemnae is a classic species of the ciliated protozoa, whose complex mating types and special mating mechanisms have long been one of the most important topics in S. lemnae research. S.lemnae has hundreds of mating types, which is different from other ciliates. However, the mechanism of mating type determination in S. lemnae has not been solved for many years. With the development of bioinformatics, this study makes a preliminary attempt and exploration on this issue by using transcriptome sequencing data of seven different mating type of S.lemnae. On the basis of its existing genome sequence, we have preliminarly selected three transcript sequences containing protein function annotation as the candidate mating type genes. And their function still need further verification. |
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