41株戈登菌的系统发育学分析及其基因组功能的挖掘

Phylogenetic analysis and genomic function mining of 41 strains of genus Gordonia

目的探讨41株戈登菌的系统发育学及其基因组中含碳水化合物活性酶、次级代谢产物生物合成基因簇的种类及多样性。方法以公开发表的41株戈登菌全基因组数据为研究对象,利用原核生物泛基因组学分析的自动化软件对泛基因组特征进行分析,结合直系同源蛋白分组对数据库、碳水化合物活性酶数据库和基因组次级代谢产物分析工具对基因组进行预测;提取19株戈登菌基因组DNA,采用16S小亚基核糖体RNA(16S rRNA)通用引物进行PCR扩增,并构建系统发育树。结果戈登菌基因组平均大小为4941636.42 bp,预测的基因数均数4370.46,G+C平均含量为67.25%,蛋白质编码区平均为4445.60;平均核苷酸多态性、DNA-DNA杂交值和16S rRNA基因序列分析表明戈登菌分类地位明确;戈登菌具有开放型泛基因组,核心基因组基因数目会稳定在1036个左右;所有菌株基因序列中含有丰富的糖基转移酶和糖苷水解酶;聚酮合酶、非核糖体肽合成酶和萜烯类生物合成基因簇在戈登菌属中占比较高,且土壤来源的菌株含生物合成基因簇最长。结论戈登菌基因组具有多样性,含丰富的碳水化合物活性酶,能产生多种抗菌和抗肿瘤的次级代谢产物。

Objective To explore the phylogeny of 41 strains of genus Gordonia,types and diversity of gene clusters carrying carbohydrate active enzymes(CAZymes)and secondary metabolite biosynthesis in their genomes.Methods Publically published whole genome data of 41 strains of genus Gordonia were taken as the research subject.Automatic software of Prokaryote pan-genome analysis pipeline was applied to analyze the characteristics of pan-genome.Their genomes were predicted by combining evolutionary genealogy of genes:non-supervised orthologous groups(eggnog),CAZymes database,and antibiotics and secondary metabolite analysis shell(antiSMASH).Genomic DNAs were extracted from 19 strains of genus Gordonia.16S ribosomal RNA(16S rRNA)was amplified by polymerase chain reaction using 16S rRNA universal primers to construct phylogenetic trees.Results The average genome size of Gordonia was 4941636.42 bp,and the average number of predicted genes was 4370.46.The average content of G+C was 67.25%,and the average protein-coding region was 4445.60.The analyses of average nucleotide polymorphism,DNA-DNA hybridization value and 16S rRNA gene sequences showed that the taxonomic status of Gordonia was clearly classified.Gordonia had an open pan-genome,and the number of core genome genes remained stable at around 1036.The gene sequences of all strains revealed that there were abundant in glycosyltransferase and glycoside hydrolase.Gene clusters of polyketide synthase,non-ribosome peptide synthase,and terpene biosynthesis accounted for a relatively high proportion in the genus Gordonia,and soil-derived strains contained the longest gene cluster of biosynthesis.Conclusion The genomes of genus Gordonia are diverse and abundant in carbohydrate active enzymes,which can produce a variety of secondary metabolite of antibacterial and anti-tumor activities.