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. 2019 Dec 12;10:2819. doi: 10.3389/fmicb.2019.02819

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Copyright © 2019 Pan, Chen, Hou, Zhang, Qu, Warren and Miao.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Comparative genomic analysis of Chilodontopsis depressa and phyllopharyngean and nassophorean ciliates. (A) Bubble plot showing comparison of genes controlling biological process among nassophorean (Furgasonia blochmanni, Pseudomicrothorax dubius) (1–2), synhymenian (C. depressa) (3), and phyllopharyngean (Chilodochona sp., Dysteria derouxi, Hartmannula sinica, Trithigmostoma cucullulus, Trochilia petrani, and Trochilia sp.) (4–9) ciliates based on Gene Ontology analysis by R package ggplot2. The upper and lower panels show the pathways in which up-regulated and down-regulated genes are enriched, respectively. The color bar and dot size measure the p-values of the gene enrichment and the percentage of covered genes in the corresponding pathways, respectively. (B) Bar chart showing the bias of stop codon usage among C. depressa, phyllopharyngeans, nassophoreans, and other well-annotated ciliates.