Table I
Summary of mRNA sequencing reads from BS and CO in M. acridum.
| Treatment | Raw reads | Clean reads | Clean bases | Q30 (%) | GC (%) | Mapped reads |
|---|---|---|---|---|---|---|
| BS1 | 98,843,641 | 95,572,956 | 14.02G | 94.06% | 47.09% | 67,073,032 (70.18%) |
| BS2 | 98,842,417 | 95,807,416 | 14.02G | 94.30% | 46.33% | 63,815,312 (66.61%) |
| BS3 | 98,841,869 | 95,719,538 | 13.98G | 94.28% | 45.60% | 62,158,068 (64.94%) |
| CO1 | 91,944,126 | 90,288,984 | 13.30G | 95.74% | 48.16% | 68,087,397 (75.41%) |
| CO2 | 98,843,196 | 97,087,780 | 14.31G | 95.79% | 47.56% | 71,191,515 (73.33%) |
| CO3 | 94,432,568 | 92,631,328 | 13.62G | 95.68% | 46.99% | 666,88,341 (71.99%) |
Fig. 1
Overview of mRNA expression profiles and DEGs in BS and CO.
A) The gene expression distribution. B) The DEGs in BS and CO, significantly downregulated genes, and upregulated genes are identified with |log2FC| ≥ 1 and p-values ≤ 0.05.
Fig. 1
Overview of mRNA expression profiles and DEGs in BS and CO.
C) Heatmap of Pearson correlations of the expression levels among samples.
Fig. 2
Functional analysis of the DEGs.
A) Gene ontology analysis.
Table II
Summary of small RNA sequencing and annotation from BS and CO in M. acridum.
| BS1 | BS2 | BS3 | CO1 | CO2 | CO3 | |
|---|---|---|---|---|---|---|
| Raw reads | 13,988,897 | 11,502,145 | 12,788,571 | 14,441,950 | 14,456,831 | 14,449,135 |
| Clean reads | 11,994,110 | 10,092,323 | 10,846,886 | 10,825,978 | 12232,894 | 11,080,402 |
| Mapped sRNA reads | 5,691,210 | 4,397,198 | 4,929,924 | 5,365,353 | 5,761,415 | 5,133,510 |
| Known milRNA numbers | 828 | 825 | 765 | 1,441 | 1,479 | 798 |
| Novel milRNA numbers | 23 | 16 | 19 | 12 | 14 | 14 |
| rRNA numbers | 8,775 | 9,271 | 5,949 | 9,275 | 5,224 | 7,396 |
| tRNA numbers | 1,584 | 1,515 | 1,325 | 1,739 | 977 | 1,180 |
| snRNA numbers | 24,078 | 17,117 | 20,740 | 25,581 | 10,368 | 1,5410 |
| Cis-reg numbers | 6,425 | 3,662 | 4,141 | 6,507 | 5,228 | 4,408 |
| Other Rfam RNA numbers | 8,846 | 8,065 | 11,414 | 12,470 | 8,706 | 8,757 |
| Unannotation reads | 10,495,519 | 9,025,652 | 9,407,612 | 9096,962 | 11,074,942 | 9,625,519 |
Fig. 2
Functional analysis of the DEGs.
KEGG pathway classification of DEGs in BS and CO.
Fig. 2
Functional analysis of the DEGs.
KEGG pathway enrichment analysis of DEGs in BS and CO. The abscissa represented the enrichment score. A more significant enrichment score indicates a greater degree of enrichment. The p-value indicates the significantly enriched, and the size of the circle indicates the number of the target genes.
Fig. 3
Overview of the differentially expressed milRNAs (DEMs) in BS and CO.
A) and B) The DEMs distribution.
Fig. 3
Overview of the differentially expressed milRNAs (DEMs) in BS and CO.
C) The length distribution of milRNAs in six libraries.
Fig. 4
GO classification analysis of the target genes of milRNAs between BS and CO in M. acridum.
Fig. 5
KEGG enrichment analysis of the target genes of milRNAs between BS and CO in M. acridum. The abscissa represented the enrichment score. A more significant enrichment score indicates a greater degree of enrichment. The p-value indicates the significantly enriched, and the size of the circle indicates the number of the target genes.
Fig. 6
The relations of the differentially expressed milRNAs and target genes. The color indicated a differentially expressed levels in BS vs. CO for milRNAs and target genes: red indicates upregulated and blue indicates downregulated.
Fig. 7
Real-time PCR validation of several DEMs and DEGs.