紫芝基因组rDNA序列特征及ITS2二级结构比较

紫芝栽培品种‘紫芝S2’(武芝2号)的ITS序列与NCBI数据库中5个紫芝菌株/分离株相似度高达99.79%-100%，在系统进化树上相聚成一类。本研究预测‘紫芝S2’基因组与参考基因组中的rRNA基因簇，分析rDNA结构及各构件序列间的多态性。从高质量‘紫芝S2’基因组中挖掘得到完整rDNA，序列全长40.377 kb，由4组串联重复的(18S、5.8S、28S、5S) rRNA基因簇组成，并含有完整的基因内间隔区(ITS1、ITS2)和基因间间隔区(IGS1、IGS2)。在紫芝S2的rDNA中，高度保守的28S rRNA基因间出现3个SNP和2个插入(1 bp，10 bp)位点;虽然第4条ITS2中有1个SNP位点，但紫芝S2的4条ITS2在二级结构上的分子形态高度一致，与ITS2数据库中其他紫芝菌株仅存在螺旋区间夹角的微小差异。由‘紫芝S2’基因组rDNA的ITS2生成的DNA条形码与二维码，可以作为该栽培品种鉴定与同源物种其他菌株鉴别的分子标记。

Sequence characteristics of genomic rDNA and comparison of ITS2 secondary structure of Ganoderma sinense

The similarity level of ITS sequence of cultivar Ganoderma sp. Zizhi S2 (Wuzhi No.2) was 99.79% to 100% to that of five known strains or voucher specimens of G. sinense registered in the NCBI database, and they were clustered together in the phylogenetic tree. In this study, the rRNA gene clusters in Zizhi S2 genome and the reference genomes were predicted, and the rDNA structure and the polymorphism of each component sequence were analyzed. A contiguous rDNA sequence with total length of 40.377 kb was extracted from the high-quality genome of Zizhi S2 for the first time, which was composed of four groups of tandem repeats (18S, 5.8S, 28S, 5S) rRNA gene clusters, and also contained complete gene internal septal regions (ITS1, ITS2) and intergenic septal regions (IGS1, IGS2). There were three SNPs and two insertion (1 bp, 10 bp) sites between the highly conserved 28S rRNA genes in the rDNA of Zizhi S2. There was also one SNP site in the fourth ITS2 region, but molecular morphology of the four ITS2 regions was highly consistent in secondary structure, and there was only a slight difference in the angle of helix interval with other strains of G. sinense in the ITS2 database. The DNA barcode and two-dimensional code generated by ITS2 of genomic rDNA of Zizhi S2, which reveal all information including ITS2 sequence and SNP site, can be used as molecular markers for identification of the cultivar and other strains of homologous species.