State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China.
Appl Microbiol Biotechnol. 2013 Jun;97(11):4977-89. doi: 10.1007/s00253-013-4832-y. Epub 2013 Apr 28.
High-throughput Illumina RNA-seq was used for deep sequencing analysis of the transcriptome of poly(A)+ RNA from mycelium grown under three different conditions: 30 days darkness (sample 118), 80 days darkness (313W), and 30 days darkness followed by 50 days in the light (313C), in order to gain insight into the molecular mechanisms underlying the process of light-induced brown film (BF) formation in the edible mushroom, Lentinula edodes. Of the three growth conditions, BF formation occurred in 313C samples only. Approximately 159.23 million reads were obtained, trimmed, and de novo assembled into 31,511 contigs with an average length of 1,746 bp and an N 50 of 2,480 bp. Based on sequence orientations determined by a BLASTX search against the NR, Swiss-Prot, COG, and KEGG databases, 24,246 (76.9 %) contigs were assigned putative descriptions. Comparison of 313C/118 and 313C/313W expression profiles revealed 3,958 and 5,651 significantly differentially expressed contigs (DECs), respectively. Annotation using the COG database revealed that candidate genes for light-induced BF formation encoded proteins linked to light reception (e.g., WC-1, WC-2, phytochrome), light signal transduction pathways (e.g., two-component phosphorelay system, mitogen-activated protein kinase pathway), and pigment formation (e.g., polyketide synthase, O-methyltransferase, laccase, P450 monooxygenase, oxidoreductase). Several DECs were validated using quantitative real-time polymerase chain reaction. Our report is the first to identify genes associated with light-induced BF formation in L. edodes and represents a valuable resource for future genomic studies on this commercially important mushroom.
采用高通量 Illumina RNA-seq 对在三种不同条件下生长的菌丝体 Poly(A)+ RNA 的转录组进行深度测序分析：30 天黑暗（样品 118）、80 天黑暗（313W）和 30 天黑暗后 50 天光照（313C），以深入了解香菇（Lentinula edodes）光诱导棕膜（BF）形成过程中的分子机制。在这三种生长条件中，只有 313C 样品中形成了 BF。获得了约 159.23 百万个读数，经过修剪和从头组装成 31511 个 contigs，平均长度为 1746bp，N50 为 2480bp。基于与 NR、Swiss-Prot、COG 和 KEGG 数据库的 BLASTX 搜索确定的序列方向，24246（76.9%）个 contigs被赋予了可能的描述。313C/118 和 313C/313W 表达谱的比较显示，分别有 3958 和 5651 个显著差异表达的 contigs（DECs）。使用 COG 数据库注释表明，光诱导 BF 形成的候选基因编码与光接收（如 WC-1、WC-2、光敏色素）、光信号转导途径（如双组分磷酸传递系统、丝裂原激活蛋白激酶途径）和色素形成（如聚酮合酶、O-甲基转移酶、漆酶、P450 单加氧酶、氧化还原酶）相关的蛋白质。使用定量实时聚合酶链反应验证了几个 DECs。本报告首次鉴定了与香菇光诱导 BF 形成相关的基因，为该商业上重要蘑菇的未来基因组研究提供了有价值的资源。
