2013;11(1):e1001473. Library. 2, Academia Road, Nankang, Taipei, 115, Taiwan, Yu-Hsuan Cheng, Chien-Fu Jeff Liu, Yen-Hsin Yu, Yu-Ting Jhou & Jun-Yi Leu, Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8512, Japan, You can also search for this author in 1. Anatomy: P. bursaria is 80-150 μm long, with a wide oral groove, two contractile vacuoles, and a single micronucleus as well as a single macronucleus. Total genomic DNA of the aposymbiotic DK1 strain was labeled with Digoxigenin (DIG) by using DIG-High Prime (Cat. Nat Methods. 2004;14(6):1188–90. A two-proportional test was used to test the orthogroups with a significantly different gene number in the three species, with a p value threshold equal to or less than 0.05 after Benjamini-Hochberg adjustment. 2017;14(6):587–9. 1990;63(4):763–72. Duret L, Cohen J, Jubin C, Dessen P, Gout JF, Mousset S, et al. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. Versatile and open software for comparing large genomes. Kreutz M, Stoeck T, Foissner W. Morphological and molecular characterization of Paramecium (Viridoparamecium nov. Gene. The copy number of each gene was also calculated by normalizing gene length and read depth to the whole genome coverage derived from the SAMtools bedcov module. 2013;64:47–70. If the regions with highly divergent alleles are assigned as two alternate contigs, the assembled genome will become fragmented and bigger than the real genome. Forney JD, Blackburn EH. Hurowitz EH, Brown PO. The conserved blocks from the multiple sequence alignment of each orthogroup were selected using Gblocks v0.91b  and concatenated. The outermost cuticular membrane of the Paramoecium is cuticular membrane of the Paramoecium is pellicle which secreted by ectoplasm. To examine the orthologs specifically duplicated in P. bursaria, we categorized the genes in P. bursaria, P. caudatum, and P. tetraurelia into orthogroups depending on the protein similarity using OrthoFinder v2.0.0  with default settings. Protist. Origins and functional impact of copy number variation in the human genome. Basic Anatomy Macro nucleus- preforms normal functions (eating, moving, etc.) Genome Biol Evol. Genome Res. 2007;24(8):1586–91. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. 2018;34(22):3921–3. Nucleic Acids Res. Both DK1 and DK2 cells showed a period of sexual immaturity after conjugation, which is consistent with the phenotype of true cross-fertilized clones. Green paramecia consume less oxygen in darkness than colourless organisms but more than the isolated algae. Eisen JA, Coyne RS, Wu M, Wu DY, Thiagarajan M, Wortman JR, et al. Yao MC. Nucleotide diversity analysis highlights functionally important genomic regions. Mol Ecol Resour. Proc Natl Acad Sci U S A. To calculate the evolutionary rates of individual genes, pairwise Ka/Ks was calculated for all alleles in the functional allele subgroup (Fig. After the F1 cells started propagating, we used PCR followed by Sanger sequencing to check the genotype of specific regions in the progeny. Volpe M, Miralto M, Gustincich S, Sanges R. ClusterScan: simple and generalistic identification of genomic clusters. A comparative study on the electron microscopic enzymo-cytochemistry of Paramecium bursaria from light and dark cultures. Heyse G, Jonsson F, Chang WJ, Lipps HJ. Mol Cell. Sometimes zoochlorellae are digested by the host. Schoeberl UE, Mochizuki K. Keeping the soma free of transposons: programmed DNA elimination in ciliates. If the genotype was a combination of both parents, then the cells were used for further analyses. Developmentally controlled telomere addition in wild-type and mutant paramecia. Detection of large-scale variation in the human genome. Enriched GO terms for P. bursaria specific genes (p-value ≤0.05 after the Benjamini-Hochberg correction). BMC Cell Biol. Conservation of sequences adjacent to the telomeric C4A2 repeats of ciliate macronuclear ribosomal-RNA gene molecules. Bioinformatics. Bioinformatics. "oblong") is a genus of the unicellular Eukaryotic ciliate protozoan.It is one of the most widely studied protozoan as a representative of the ciliate group and as a model organism for biological processes. We used MUMMER v3.23  to generate the haploid genome and manually joined the overlapping contigs. 1995;57(1):289–300. Protist. Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Farslow JC, Lipinski KJ, Packard LB, Edgley ML, Taylor J, Flibotte S, et al. Visualization was performed after staining with ethidium bromide. Genome Res. Cheng, YH., Liu, CF.J., Yu, YH. Isme J. Proc Natl Acad Sci U S A. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. Les unités symbiotiques persistent aussi à travers la conjugaison et la réorganisation subséquente de l'hôte. The correlation matrix (Spearman’s correlation coefficient ρ) of the gene copy number between genetically divergent strains. The cells were starved for 2 days and several hundred cells were mixed. 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