马克斯克鲁维酵母FIM1基因组分析  

Genome Analysis of Kluyveromyces marxianus FIM1

作　　者：罗通宇 曾俊源 吕奕琳 周峻岗[1,2] 余垚 吕红[1,2] LUO Tongyu;ZENG Junyuan;LÜYilin;ZHOU Jungang;YU Yao;LÜHong(State Key Laboratory of Genetic Engineering,Fudan University,Shanghai 200438,China;Shanghai Engineering Research Center of Industrial Microorganisms,School of Life Sciences,Fudan University,Shanghai 200438,China)

机构地区：[1]复旦大学遗传工程国家重点实验室,上海200438 [2]复旦大学生命科学学院上海工业菌株工程技术研究中心,上海200438

出　　处：《复旦学报（自然科学版）》2022年第3期303-312,316,共11页Journal of Fudan University：Natural Science

基　　金：国家自然科学基金面上项目(31770094,31970068)。

摘　　要：马克斯克鲁维酵母(Kluyveromyces marxianus)是一种富有潜力的新型细胞工厂宿主菌。K.marxianus FIM1(CGMCC No.10621)基因组组装与注释已于2019年完成并在NCBI上公布(GCA_001854445.2),但在应用该基因组信息时发现其仍不完善。所以本研究使用重测序的DNA-seq数据校验了K.marxianus FIM1的基因组序列,随后补充了K.marxianus FIM1的注释,并使用比较基因组学的方法进一步完善了K.marxianus FIM1的基因组信息。根据重测序比对结果,删除了测序数据无法覆盖的位点61处,共4910bp。K.marxianus FIM1新序列总长为10909543bp,可覆盖酵母目保守基因库中99.5%的基因。同时对K.marxianus FIM1的非编码RNA、次级代谢产物基因簇的也进行了补充注释。进一步,我们使用基因组共线性分析的方法分析了K.marxianus FIM1在物种分化过程中基因排列顺序保守的区域,并将K.marxianus FIM1与NCBI公布的11株K.marxianus进行了种内基因组比较。发现12株K.marxianus早在约180万年前分化为两个亚型,它们共有的同源基因家族有4009个,基因组中核心基因平均占比为79.88%,预测K.marxianus为闭合型泛基因组,核心基因数为3760个,为K.marxianus FIM1遗传学的研究与遗传工程的改造提供了数据支持。Kluyveromyces marxianus is a promising microbial cell factory host.Genome assembly and annotation of K.marxianus FIM1(CGMCC No.10621)was completed and uploaded to NCBI in 2019(GCA_001854445.2),but the genomic information was still not complete.In this study,resequenced DNA-seq data was used to verify the genome sequence of K.marxianus FIM1.The annotations of K.marxianus FIM1 was supplemented and genomic information was refined by comparative genomics analysis.According to the mapping results,61 sites with a total length of 4910 bp that could not be covered by sequencing data were deleted.The new K.marxianus FIM1 genome was composed of 10909543bp and contained 99.5%of genes conserved in the Saccharomyces order.Non-coding RNA and the gene cluster of secondary metabolite in K.marxianus FIM1 were also annotated.Genome collinearity analysis was performed to reveal the regions of K.marxianus FIM1 genes following conserved order during speciation.Intraspecific Comparative genomic analysis of K.marxianus FIM1 with other eleven K.marxianus strains from NCBI showed that 12 of K.marxianus strains differentiated into two subtypes about 1.8 million years ago and 4009 orthologue families were shared by these strains.The average percentage of core genes in the genomes was 79.88%.K.marxianus was predicted to be a closed pan-genome including 3760 core genes.The results facilitate following genetic engineering of this strain.

关 键 词：马克斯克鲁维酵母 基因组校验 基因组注释 比较基因组学 

分 类 号：Q36[生物学—遗传学]