Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China.
Sci Rep. 2017 Jul 18;7(1):5711. doi: 10.1038/s41598-017-04303-6.
Ganoderma lucidum is a white-rot fungus best-known for its medicinal and ligninolytic activities. To discover the underlying genes responsible for these activities, we identified and characterized the natural antisense transcripts (NATs) using strand-specific (ss) RNA-seq data obtained from the mycelia, primordia and fruiting bodies. NATs were identified using a custom pipeline and then subjected to functional enrichment and differential expression analyses. A total of 1613 cis- and 244 trans- sense and antisense transcripts were identified. Mapping to GO terms and KEGG pathways revealed that NATs were frequently associated with genes of particular functional categories in particular stages. ssRT-qPCR experiments showed that the expression profiles of 30 of 50 (60%) transcripts were highly correlated with those of the RNA-seq results (r ≥ 0.9). Expression profiles of 22 of 25 (88%) pairs of NATs and STs were highly correlated (p ≤ 0.01), with 15 having r ≥ 0.8 and 4 having r ≤ -0.8. Six lignin-modifying genes and their NATs were analyzed in detail. Diverse patterns of differential expression among different stages and positive and negative correlations were observed. These results suggested that NATs were implicated in gene expression regulation in a function-group and developmental-stage specific manner through complex mechanisms.
灵芝是一种白腐真菌，以其药用和木质素降解活性而闻名。为了发现这些活性的潜在基因，我们使用从菌丝体、原基和子实体获得的链特异性 (ss) RNA-seq 数据，鉴定和表征了天然反义转录本 (NAT)。使用自定义管道鉴定 NAT，然后对其进行功能富集和差异表达分析。共鉴定到 1613 个顺式和 244 个反式 sense 和 antisense 转录本。GO 术语和 KEGG 途径的映射表明，NAT 经常与特定功能类别的基因在特定阶段相关。ssRT-qPCR 实验表明，50 个 (60%) 转录本中有 30 个的表达谱与 RNA-seq 结果高度相关（r≥0.9）。25 对 NATs 和 STs 中有 22 对 (88%) 的表达谱高度相关（p≤0.01），其中 15 对 r≥0.8，4 对 r≤-0.8。对 6 个木质素修饰基因及其 NATs 进行了详细分析。观察到不同阶段之间的差异表达模式多样，存在正相关和负相关。这些结果表明，NAT 通过复杂的机制以功能组和发育阶段特异性的方式参与基因表达调控。
