Gubaev R F, Gorshkov V Y, Gapa L M, Gogoleva N E, Vetchinkina E P, Gogolev Y V
Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of RAS", Kazan, 420111 Russia.
Kazan (Volga Region) Federal University, Kazan, 420008 Russia.
Mol Biol (Mosk). 2018 Jul-Aug;52(4):576-590. doi: 10.1134/S0026898418040079.
Modern techniques of next-generation sequencing (NGS) allow obtaining expression profile of all genes and provide an essential basis for characterizing metabolism in the organism of interest on a broad scale. An important condition for obtaining a demonstrative physiological picture using high throughput sequencing data is the availability of the genome sequence and its sufficient annotation for the target organism. However, a list of species with properly annotated genomes is limited. Transcriptome profiling is often performed in the so-called non-model organisms, which are those with unknown or poorly assembled and/or annotated genome sequences. The transcriptomes of non-model organisms are possible to investigate using algorithms of de novo assembly of the transcripts from sequences obtained as the result of RNA sequencing. A physiological interpretation of the data is difficult in this case because of the absence of annotation of the assembled transcripts and their classification by metabolic pathway and functional category. An algorithm for transcriptome profiling in non-model organisms was developed, and a transcriptome analysis was performed for the basidiomycete Lentinus edodes. The algorithm includes open access software and custom scripts and encompasses a complete analysis pipeline from the selection of cDNA reads to the functional classification of differentially expressed genes and the visualization of the results. Based on this algorithm, a comparative transcriptome analysis of the nonpigmented mycelium and brown mycelial mat was performed in L. edodes. The comparison revealed physiological differences between the two morphogenetic stages, including an induction of cell wall biogenesis, intercellular communication, ion transport, and melanization in the brown mycelial mat.
现代的新一代测序（NGS）技术能够获取所有基因的表达谱，并为大规模表征目标生物体的代谢提供重要依据。利用高通量测序数据获得具有说服力的生理图景的一个重要条件是目标生物体的基因组序列及其足够的注释信息。然而，具有正确注释基因组的物种列表是有限的。转录组分析通常在所谓的非模式生物中进行，即那些基因组序列未知、组装不佳或注释不充分的生物。对于非模式生物的转录组，可以使用从RNA测序结果获得的序列进行转录本从头组装的算法来进行研究。由于组装的转录本缺乏注释以及它们按代谢途径和功能类别分类，在这种情况下对数据进行生理解释很困难。开发了一种用于非模式生物转录组分析的算法，并对担子菌香菇进行了转录组分析。该算法包括开源软件和自定义脚本，涵盖了从cDNA读数选择到差异表达基因的功能分类以及结果可视化的完整分析流程。基于该算法，对香菇的无色素菌丝体和褐色菌丝体垫进行了比较转录组分析。比较揭示了两个形态发生阶段之间的生理差异，包括褐色菌丝体垫中细胞壁生物合成、细胞间通讯、离子运输和黑色素生成的诱导。
