真菌基因组de novo测序组装的方法与实践  

Methods and Practice for Fungal Genome de novo Sequencing and Assembly

作　　者：李丽翠 曲积彬[2] 曾昭清 Tom Hsiang 余知和[1] Li Licui;Qu Jibin;Zeng Zhaoqing;Hsiang Tom;Yu Zhihe(College of Life Science,Yangtze University,Jingzhou,434025;Institute of Agricultural Resources and Regional Planning,Beijing,100081;State Key Laboratory of Mycology,Institute of Microbiology,Chinese Academy of Science,Beijing,100101;School of Environmental Sciences,Universi-ty of Guelph,Guelph,Canada,NIG 2W1)

机构地区：[1]长江大学生命科学学院,荆州434025 [2]中国农业科学院农业资源与农业区划研究所,北京100081 [3]中国科学院微生物研究所真菌学国家重点实验室,北京100101 [4]圭尔夫大学环境科学学院,加拿大圭尔夫NIG 2W1

出　　处：《基因组学与应用生物学》2020年第1期173-180,共8页Genomics and Applied Biology

基　　金：国家自然科学基金面上项目(31570022)资助。

摘　　要：真菌基因组较其他真核生物基因组结构简单,长度短,易于测序、组装与注释,因此真菌基因组是研究真核生物基因组的模型。为研究真菌基因组组装策略,本研究基于Illumina HiSeq测序平台对烟曲霉菌株An16007基因组测序,分别使用5种de novo组装软件ABySS、SOAP-denovo、Velvet、MaSuRCA和IDBA-UD组装基因组,然后通过Augustus软件进行基因预测,BUSCO软件评估组装结果。研究发现,5种组装软件对基因组组装结果不同,ABySS组装的基因组较其他4种组装软件具有更高的完整性和准确性,且预测的基因数量较高,因此,ABySS更适合本研究基因组的组装。本研究提供了真菌de novo测序、组装及组装质量评估的技术流程,为基因组<100 Mb的真菌或其他生物基因组的研究提供参考。Fungal genomes,compared with other eukaryotic genomes,have much simpler structure particularly a much smaller size,and hence are more convenient for sequencing,assembly and subsequent attempts at annotation.Because of their reduced complexity,fungal genomes are efficient models for the study of eukaryotic genomes.In order to study fungal genome assembly strategies,this work assembled a genome of Aspergillusfumigates An16007 using next generation sequencing data from the IlluminaHiseq platform.We used five different de novo assemblers,specifically ABy SS,SOAP-denovo,Velvet,Ma Su RCA and IDBA-UD,and then predicted genes by Augustus,and evaluated assembly quality using BUSCO.The results showed that the performance of five assemblers were different.The genome assembled by ABySS performed higher integrity and accuracy than other four assemblers and predicted more genes.So the assembler ABy SS was more suitable for genome assembly in this study.This work offer a guide to de novo genome sequencing,assembly and evaluation of assembly quality,particularly for researchers working with fungi or other organisms whose genomes are generally less than 100 Mb in size.

关 键 词：基因组 N50 K-mer 生物信息学软件 UBUNTU LINUX 组装 

分 类 号：Q933[生物学—微生物学]