紫芝栽培品种‘武芝2号’（‘紫芝S2’）全基因组测序及分析

doi:10.13560/j.cnki.biotech.bull.1985.2021-1158

摘要/Abstract

摘要：

采用 PacBio SMART技术并基于三代和二代数据（3+2策略）完成紫芝栽培品种‘武芝2号’（原名:S2）（通称‘紫芝S2’）基因组De novo测序、组装,完整地获得紫芝栽培品种‘武芝2号’（原名:S2）全基因组,序列总长度56.849 Mb,包括核基因组和线粒体基因组共72条Scaffolds。其中,核基因组16 681个基因,完成其中13 161个基因的注释,约占总数的78.89%;预测分析到4组串联重复的rRNA簇、405个非编码RNA 和3 305个启动子,并找到rpb2、beta-tubulin和18S,28S rRNA（SSU,LSU）等基因序列以及漆酶同工酶基因,鲨烯合酶、羊毛甾醇合酶基因与麦角甾醇合成代谢相关基因及其分布位置,为今后紫芝栽培品种（系）分子鉴定与菌株鉴别、功能基因的挖掘与利用提供可靠信息,同时也为其后续开展中国栽培灵芝种类的比较基因组学分析积累科学数据。

关键词: 紫芝, 栽培品种, 全基因组测序, 基因组组分, 基因功能注释

Abstract:

The cultivar ‘Wuzhi No. 2（original name:S2）’ has been applied and extended in south China（Fujian,Guangdong and Guangxi province,etc.）,known as Ganoderma sp. strain Zizhi S2 that belongs to Ganoderma sinense complex. Whole genome of the Zizhi S2 was completed after genomic sequencing and assembly using the PacBio SMRT technology and based on the third-generation and second-generation data（3 + 2 strategy）,the total length of the sequence was 56.849 Mb,totally 72 scaffolds including nuclear genome and mitochondrial genome. There were 16 681 genes in the nuclear genome,and 13 161 genes were annotated and accounting for 78.89% of the total. Four groups of tandem repeat rRNA clusters,405 non-coding RNAs and 3 305 promoters were predicted and analyzed. The gene sequences of rpb2,beta-tubulin and 18S,28S rRNA（SSU,LSU）,laccase isoenzyme genes,squalene synthase and lanosterol synthesis genes,ergo-sterol synthesis and metabolism related genes and their distribution positions were revealed. This finding not only provides reliable information for the molecular identification and strain identification of cultivated varieties（lines）of Zizhi,but also for further mining and utilization of functional genes. Furthermore,this also accumulates scientific data for the subsequent comparative genomic analysis of cultivated Ganoderma spp. complex species in China.

Key words: Zizhi(Ganoderma sinense complex), cultivar, whole genome sequencing, genomic components, gene functional annotation

陈体强, 徐晓兰, 石林春, 钟礼义. 紫芝栽培品种‘武芝2号’（‘紫芝S2’）全基因组测序及分析[J]. 生物技术通报, 2021, 37(11): 42-56.

CHEN Ti-qiang, XU Xiao-lan, SHI Lin-chun, ZHONG Li-Yi. Sequencing and Analysis of the Whole Genome of Zizhi Cultivar ‘Wuzhi No.2’（Ganoderma sp. strain Zizhi S2）[J]. Biotechnology Bulletin, 2021, 37(11): 42-56.

图/表 18

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数据Data	Read总条数 Total number of reads	碱基总数目 Total base/bp	Reads长度 Reads length/bp	GC%	Q20*	Q30**
Raw data	61 457 184	9 218 577 600	150∶150	54.37	97.49	93.09
Clean data	55 973 534	8 396 030 100	150∶150	54.36	97.33	92.81

数据Data	Read总条数 Total number of reads	碱基总数目 Total base/bp	Reads长度 Reads length/bp	GC%	Q20*	Q30**
Raw data	61 457 184	9 218 577 600	150∶150	54.37	97.49	93.09
Clean data	55 973 534	8 396 030 100	150∶150	54.36	97.33	92.81

项目 Item		数据 Data
下机的碱基数目	Polymerase read total bases（bp）	11 049 130 528
下机的reads数目	Number of polymerase reads	531 175
下机的read平均长度	Post-filter mean read length	20 801
下机的read的N50长度	Polymerase read N50	35 250
去掉接头后的碱基数目	Subreads total bases（bp）	11 029 483 296
去掉接头后的 Subread数目	Number of subreads	970 426
去掉接头后的 Subread 平均长度	Mean subread length（bp）	11 365.61
去掉接头后的 Subread N50长度	Subreads N50 length	15 985
过滤无效数据后Subreads总长度	Subreads total bases（bp）	10 997 790 898
过滤无效数据后Subreads数目	Number of subreads	908 820
过滤无效数据后Subreads平均长度*	Subreads mean length（bp）*	12 101
过滤无效数据后Subreads N50长度	Subreads N50 length（bp）	16 018*

项目 Item		数据 Data
下机的碱基数目	Polymerase read total bases（bp）	11 049 130 528
下机的reads数目	Number of polymerase reads	531 175
下机的read平均长度	Post-filter mean read length	20 801
下机的read的N50长度	Polymerase read N50	35 250
去掉接头后的碱基数目	Subreads total bases（bp）	11 029 483 296
去掉接头后的 Subread数目	Number of subreads	970 426
去掉接头后的 Subread 平均长度	Mean subread length（bp）	11 365.61
去掉接头后的 Subread N50长度	Subreads N50 length	15 985
过滤无效数据后Subreads总长度	Subreads total bases（bp）	10 997 790 898
过滤无效数据后Subreads数目	Number of subreads	908 820
过滤无效数据后Subreads平均长度*	Subreads mean length（bp）*	12 101
过滤无效数据后Subreads N50长度	Subreads N50 length（bp）	16 018*

Property	Min	Max	Min	Max	Min	Max
Heterozygosity/%	1.965 62	2.008 05	1.955 13	1.973 2	1.958 25	1.984 25
Genome haploid length/ bp	46 347 904	46 440 807	50 222 379	50 301 292	48 878 189	48 958 199
Genome repeat length/ bp	4 637 105	4 646 400	8 024 318	8 036 926	6 841 040	6 852 239
Sequences repeat rate/%	10.005	10.005	15.977	15.977	13.996	13.996
Genome unique length/ bp	41 710 799	41 794 407	42 198 061	42 264 366	42 037 149	42 105 960
Model fit/%	95.5952	NA	96.9219	98.2063	96.2289	96.9645
Read error rate/%	0.253032	0.253032	0.229964	0.229964	0.238092	0.238092