Wang Yingzhu, Zeng Xianlu, Liu Wenguang
The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Institute of Genetics and Cytology, School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China.
The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Institute of Genetics and Cytology, School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China.
Gene. 2018 Jan 30;641:326-334. doi: 10.1016/j.gene.2017.10.061. Epub 2017 Oct 21.
The fruiting body of Lentinula edodes is a popular edible mushroom, and extracts from the mycelium and the fruiting body of this species have diverse therapeutic potential. To gain insights into the molecular mechanisms underlying the fruiting body growth of L. edodes from the early bud stage (EBS), through the intermediate developing stage (IDS), to the fully developed stage (FDS), we performed de novo transcriptomic analysis using high-throughput Illumina RNA-sequencing. First, we generated three cDNA libraries representative of the three respective stages. We then obtained 38,933,148, 44,594,472, and 37,905,646 high-quality reads from the respective libraries and assembled the reads into 25,104 transcriptional contigs, containing 15,199 unigenes. We found that only 9331 of the unigenes had been annotated in the NCBI non-redundant protein database, and we functionally annotated 4758 of them through Gene Ontology (GO) analysis and 2921 of them through Clusters of Orthologous Groups of proteins (COGs) analysis. We also assigned 3995 unigenes to metabolic pathways by using the Kyoto Encyclopedia of Genes and Genomes (KEGG). We further identified 399 differentially expressed genes (DEGs) between EBS and IDS, 1428 between IDS and FDS, and 1830 between EBS and FDS, uncovering 769 DEGs in multiple metabolic and signaling pathways. Interestingly, there were a limited number of DEGs whose expression was dramatically associated with FDS. Finally, genes, whose expression was either highly up-regulated in FDS or remained at a high level during fruiting body growth, were annotated specifically in the pathways of purine metabolism, unsaturated fatty acid metabolism and meiosis, suggesting that these key molecular events were actively occurring in the fruiting body. Our work is the first high-throughput transcriptome study on the growth of L. edodes fruiting bodies, and the results uncovered candidate genes for future gene identification and utilization of this commercially and medically important mushroom.
香菇的子实体是一种广受欢迎的食用菌，该物种菌丝体和子实体的提取物具有多种治疗潜力。为了深入了解香菇子实体从早期芽阶段（EBS）、经过中间发育阶段（IDS）到完全发育阶段（FDS）生长的分子机制，我们使用高通量Illumina RNA测序进行了从头转录组分析。首先，我们构建了分别代表三个阶段的三个cDNA文库。然后，我们从各个文库中分别获得了38,933,148、44,594,472和37,905,646条高质量 reads，并将这些 reads 组装成25,104个转录重叠群，其中包含15,199个单基因。我们发现，只有9331个单基因在NCBI非冗余蛋白质数据库中得到注释，我们通过基因本体（GO）分析对其中4758个进行了功能注释，通过蛋白质直系同源簇（COG）分析对其中2921个进行了功能注释。我们还使用京都基因与基因组百科全书（KEGG）将3995个单基因分配到代谢途径中。我们进一步鉴定出EBS和IDS之间有399个差异表达基因（DEG），IDS和FDS之间有1428个，EBS和FDS之间有1830个，在多个代谢和信号通路中发现了769个DEG。有趣的是，与FDS显著相关的DEG数量有限。最后，那些在FDS中表达高度上调或在子实体生长过程中保持高水平的基因，在嘌呤代谢、不饱和脂肪酸代谢和减数分裂途径中被特异性注释，表明这些关键分子事件在子实体中活跃发生。我们的工作是关于香菇子实体生长的首次高通量转录组研究，结果揭示了未来用于鉴定和利用这种具有商业和医学重要性的蘑菇的候选基因。
