Toxoplasma, Nicolle & Manceaux, 1909

Xie, Shi-Chen, Zhou, Chun-Xue, Zhai, Bin-Tao, Zheng, Wen-Bin, Liu, Guo-Hua & Zhu, Xing-Quan, 2022, A combined miRNA-piRNA signature in the serum and urine of rabbits infected with ToxoplaSMa gondii oocysts, Parasites & Vectors (490) 15 (1), pp. 1-12 : 3

Expression of small RNAs in serum from both Toxoplasma -infected and normal rabbits

To explore small RNA profiles in serum and urine during toxoplasmosis progression, RNA sequencing was used to analyze sRNA expression in serum and urine from oocysts-infected and non-infected rabbits. After removing low-quality reads,> 19.78 million high-quality clean reads were obtained. Te read quality is shown in Additional file 1: Table S 1. Of the filtered clean reads, 76.50–91.50% detected in serum were mapped to the reference Oryctolagus cuniculus genome. Te first residue at the 5 ′ terminus of the 20–26 nt known miRNAs is predominantly uridine (U) ( Fig. 2a ), while the first residue at the 5 ′ terminus of the predicted miRNAs is predominantly cytosine (C) ( Fig. 2b ). As shown in Fig. 2c , the first residue at the 5 ′ terminus of the 18–45 nt predicted piRNAs is predominantly cytosine (C). To explore the similarity of serum samples, we performed Pearson correlation analysis, principal component analysis ( PCA) and hierarchical clustering analysis. As shown in Fig. 3a, a Pearson correlation matrix separated the AI samples from the other samples, as illustrated by the heatmap correlation matrices (Spearman correlations [r] = 0.898 –0.968), showing a high level of correlation within Con samples ([r] = 0.934 –0.972). As shown in Fig. 3b , PCA score plots did not clearly differentiate chronically infected rabbits from uninfected control rabbits. However, hierarchical clustering displayed that the sRNA expression pattern in acutely infected rabbits was distinguishable compared to that of chronically infected rabbits and uninfected control rabbits ( Fig. 3c ).

Figures

Fig. 2 First nucleotide bias of obtained small RNA in serum samples of rabbits.a First nucleotide bias of known miRNAs in rabbit serum. b First nucleotide bias of predicted miRNAs in rabbit serum.c First nucleotide bias of predicted piRNAs in rabbit serum

Fig. 3 Global view of temporal sRNA expression profiles in rabbit serum during T.gondii infection. a The sRNA correlation heatmap of sample clustering.b Principal component analysis of all identified serum sRNA. c Unsupervised hierarchical clustering of sRNA profiling data. sRNA intensity is normalized so that blue represents low intensity and yellow represents high intensity. Columns are hierarchically clustered based on a complete linkage using Pearson correlation coefficients as the distance measure. Sample groups including acutely infected rabbits, chronically infected rabbits and uninfected control rabbits are labeled as AI, CI and Con,respectively