Gs2019.10.465 7of14 DEO class (correlation coefficient:0.46 versus 0.19).Meanwhile,genes related to essential biological processes such as reproduction and oxidation reduction or are transcription factor and CAZYs were also chosen for correlation analysis.Except for genes related oxidation reduction,the remaining genes howed similar patterns to all orthologs. nam ly,expression change was more divergent in phase h n in phase 1 (Figure S3).Conversely,in both phases,genes related to oxid ation reduction showe hese ge n spe when ody C psy Copia LTR cther LINE 10 04 0.50 025 ortion of different cla s of TEs.(C)Number of TEs in each class PR and FB stages.Percentages above th (E(D)an on le developmental stages.wherein different letters denote statistical significance.Only tes with a tpm value 0 are shown in (E).(F)Negative correlation between mCGs and expression of TEs.Only TEs with a TPM value 0 are tabulated.Very similar profiles were obtained for Pe,shown in Figure S TEs(including their derivatives forming other types of repeats)showed substantially higher mCC evels than genic regions in both species during inall three developmental stages ( 0.52 in Pt and Pe,r vely)(Figure 3A;Figure notea tha the two mus oms sr h stages d it wasb: est in ruit body.followed by and ny te of thes Genes 2019, 10, 465 7 of 14 DE0 class (correlation coefficient: 0.46 versus 0.19). Meanwhile, genes related to essential biological processes such as reproduction and oxidation reduction or are transcription factor and CAZYs were also chosen for correlation analysis. Except for genes related oxidation reduction, the remaining genes showed similar patterns to all orthologs, namely, expression change was more divergent in phase 2 than in phase 1 (Figure S3). Conversely, in both phases, genes related to oxidation reduction showed high divergence of expression changes, indicating these genes were diverged at earlier developmental stages between Pt and Pe. These results suggest the extent of expression divergence between the two mushroom species is magnified when formatting fruit body. Genes 2019, 10, x FOR PEER REVIEW 7 of 14 Meanwhile, genes related to essential biological processes such as reproduction and oxidation reduction or are transcription factor and CAZYs were also chosen for correlation analysis. Except for genes related oxidation reduction, the remaining genes showed similar patterns to all orthologs, namely, expression change was more divergent in phase 2 than in phase 1 (Figure S3). Conversely, in both phases, genes related to oxidation reduction showed high divergence of expression changes, indicating these genes were diverged at earlier developmental stages between Pt and Pe. These results suggest the extent of expression divergence between the two mushroom species is magnified when formatting fruit body. Figure 3. mCG and expression levels in transposable elements (TEs) of Pleurotus tuoliensis (Pt). (A) Meta-plots of mycelium (MY, red), primordium (PR, blue) and fruit body (FB, green) mCG levels in TEs. (B) Distribution and relative proportion of different classes of TEs. (C) Number of TEs in each class (grey bars) and number of expressed TEs (TPM > 1) in the MY, PR and FB stages. Percentages above the bars showing proportions of expressed TEs in each class. (D,E) mCG levels (D) and expression levels (E) for each class of TEs in the M, P and F stages. The dashed line in (E) indicates the static expression trend. The letters above the boxes denote results of Post Hoc Multiple Comparisons among the different developmental stages, wherein different letters denote statistical significance. Only TEs with a TPM value > 0 are shown in (E). (F) Negative correlation between mCGs and expression of TEs. Only TEs with a TPM value > 0 are tabulated. Very similar profiles were obtained for Pe, shown in Figure S4. 3.3. Correlation Between CG Methylation and Expression of TEs During Development in the Two Mushrooms Species TEs (including their derivatives forming other types of repeats) showed substantially higher mCG levels than genic regions in both species during in all three developmental stages (on average 0.55 and 0.52 in Pt and Pe, respectively) (Figure 3A; Figure S4A). We noted that the two mushrooms showed some differences in the changing trends of mCG levels in TEs across the developmental stages. In Pt, methylation profile in TEs was highest in mycelium, followed by fruit body, and lowest in primordium; whereas in Pe, it was highest in fruit body, followed by primordium and mycelium. Figure 3. mCG and expression levels in transposable elements (TEs) of Pleurotus tuoliensis (Pt). (A) Meta-plots of mycelium (MY, red), primordium (PR, blue) and fruit body (FB, green) mCG levels in TEs. (B) Distribution and relative proportion of different classes of TEs. (C) Number of TEs in each class (grey bars) and number of expressed TEs (TPM > 1) in the MY, PR and FB stages. Percentages above the bars showing proportions of expressed TEs in each class. (D,E) mCG levels (D) and expression levels (E) for each class of TEs in the M, P and F stages. The dashed line in (E) indicates the static expression trend. The letters above the boxes denote results of Post Hoc Multiple Comparisons among the different developmental stages, wherein different letters denote statistical significance. Only TEs with a TPM value > 0 are shown in (E). (F) Negative correlation between mCGs and expression of TEs. Only TEs with a TPM value > 0 are tabulated. Very similar profiles were obtained for Pe, shown in Figure S4. 3.3. Correlation Between CG Methylation and Expression of TEs during Development in the Two Mushroom Species TEs (including their derivatives forming other types of repeats) showed substantially higher mCG levels than genic regions in both species during in all three developmental stages (on average 0.55 and 0.52 in Pt and Pe, respectively) (Figure 3A; Figure S4A). We noted that the two mushrooms showed some differences in the changing trends of mCG levels in TEs across the developmental stages. In Pt, methylation profile in TEs was highest in mycelium, followed by fruit body, and lowest in primordium; whereas in Pe, it was highest in fruit body, followed by primordium and mycelium. In spite of these