Biotechnology Bulletin ›› 2021, Vol. 37 ›› Issue (11): 42-56.doi: 10.13560/j.cnki.biotech.bull.1985.2021-1158
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CHEN Ti-qiang1(), XU Xiao-lan2, SHI Lin-chun3, ZHONG Li-Yi4
Received:
2021-09-09
Online:
2021-11-26
Published:
2021-12-03
Contact:
CHEN Ti-qiang
E-mail:chen_tiqiang@189.cn
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.
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 |
Table 1 Statistics of second generation sequencing data(Illumina Nova Seq6000)and filtering results
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* |
Table 2 Statistics of third generation sequencing data and filtering results
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 |
Table 3 Assessment of genome size and heterozygosity(k = 17)
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 |
数据库 Database | *版本或公开时间 Version or publication time |
---|---|
Gene Ontology(GO) | Releases_2017-09-08 |
Kyoto Encyclopedia of Genes and Genomes,KEGG | v_81 |
Cluster of Orthologous Groups of proteins,COG | Releases_2014-11-10 |
Swiss-Pro | Release_2017-07 |
Trembl | Release_2017-09 |
NR | Release_2017-10-10 |
EggNOG | v_4.5 |
Antibiotic Resistance Genes Database,ARDB | v_1.1 |
Pathogen Host Interactions,PHI | v_4.3 |
Fungal Cytochrome P450 Database | v_1.1 |
Carbohydrate-Active enzymes Database,CAZy | Release_2017-09 |
Virulence Factor Database,VFDB | Release_2017-09 |
Type III Secretion System Effector Proteins,T3SS | v_1.0 |
TransportDB | v_2.0 |
Table 4 Protein database for genome annotation
数据库 Database | *版本或公开时间 Version or publication time |
---|---|
Gene Ontology(GO) | Releases_2017-09-08 |
Kyoto Encyclopedia of Genes and Genomes,KEGG | v_81 |
Cluster of Orthologous Groups of proteins,COG | Releases_2014-11-10 |
Swiss-Pro | Release_2017-07 |
Trembl | Release_2017-09 |
NR | Release_2017-10-10 |
EggNOG | v_4.5 |
Antibiotic Resistance Genes Database,ARDB | v_1.1 |
Pathogen Host Interactions,PHI | v_4.3 |
Fungal Cytochrome P450 Database | v_1.1 |
Carbohydrate-Active enzymes Database,CAZy | Release_2017-09 |
Virulence Factor Database,VFDB | Release_2017-09 |
Type III Secretion System Effector Proteins,T3SS | v_1.0 |
TransportDB | v_2.0 |
基因组Genome | 序列类型 Seq type | 数目 Total number | 组装总长度 Total length/bp | 序列N50长度 N50 length/bp | 间隙数 Gap number | 序列GC含量 GC content /% |
---|---|---|---|---|---|---|
核基因组 Nuclear genome | Scaffold | 71 | 56 763 274 | 1 200 238 | 0 | 56.14 |
Contig | 71 | 56 763 274 | 1 200 238 | - | 56.14 | |
线粒体基因组Mitochondrion genome | Scaffold | 1 | 85 353 | 85 353 | 0 | 26.91 |
Contig | 1 | 85 353 | 85 353 | - | 26.91 |
Table 5 Whole genome of Ganoderma sp. strain Zizhi S2* assembled by De novo sequencing
基因组Genome | 序列类型 Seq type | 数目 Total number | 组装总长度 Total length/bp | 序列N50长度 N50 length/bp | 间隙数 Gap number | 序列GC含量 GC content /% |
---|---|---|---|---|---|---|
核基因组 Nuclear genome | Scaffold | 71 | 56 763 274 | 1 200 238 | 0 | 56.14 |
Contig | 71 | 56 763 274 | 1 200 238 | - | 56.14 | |
线粒体基因组Mitochondrion genome | Scaffold | 1 | 85 353 | 85 353 | 0 | 26.91 |
Contig | 1 | 85 353 | 85 353 | - | 26.91 |
Assembly length/bp | Coverage(#) | Coverage rate/% | Depth(#) | Reads usage percent/% |
---|---|---|---|---|
56 848 627 | 56 499 028 | 99.39 | 177 | 83.45 |
Table 6 Genome sequencing depth and coverage
Assembly length/bp | Coverage(#) | Coverage rate/% | Depth(#) | Reads usage percent/% |
---|---|---|---|---|
56 848 627 | 56 499 028 | 99.39 | 177 | 83.45 |
基因组 Genome | 类型 Type | 数目 Total number | 序列总长度 Total length/bp | 平均长度 Average length/bp | 占基因组总长的比例 Percentage in total length /% |
---|---|---|---|---|---|
核基因组 Nuclear genome | Gene | 16 681 | 32 438 896 | 1 944.66 | 57.15 |
Exons | 95 839 | 23 930 217 | 249.69 | 42.16 | |
CDS | 16 681 | 23 930 217 | 1 434.58 | 42.16 | |
Introne | 79 158 | 8 508 679 | 107.49 | 14.99 | |
线粒体基因组 Mitochondrion genome | Gene | 56 | 77 918 | 1 391.39 | 91.29 |
Exons | 78 | 46 571 | 597.06 | 54.56 | |
CDS | 56 | 46 571 | 831.62 | 54.56 | |
Introne | 22 | 29 854 | 1 357.00 | 34.98 |
Table 7 Statistics of gene composition of the genome
基因组 Genome | 类型 Type | 数目 Total number | 序列总长度 Total length/bp | 平均长度 Average length/bp | 占基因组总长的比例 Percentage in total length /% |
---|---|---|---|---|---|
核基因组 Nuclear genome | Gene | 16 681 | 32 438 896 | 1 944.66 | 57.15 |
Exons | 95 839 | 23 930 217 | 249.69 | 42.16 | |
CDS | 16 681 | 23 930 217 | 1 434.58 | 42.16 | |
Introne | 79 158 | 8 508 679 | 107.49 | 14.99 | |
线粒体基因组 Mitochondrion genome | Gene | 56 | 77 918 | 1 391.39 | 91.29 |
Exons | 78 | 46 571 | 597.06 | 54.56 | |
CDS | 56 | 46 571 | 831.62 | 54.56 | |
Introne | 22 | 29 854 | 1 357.00 | 34.98 |
Fig. 2 Gene length distribution in nuclear genome and mitochondrial genome The abscissa is gene length,and the ordinate is the number of genes corresponding to the gene length
Seq_name | Seq_length | Gene number | Seq_name | Seq_length | Gene number | Seq_name | Seq_length | Gene number |
---|---|---|---|---|---|---|---|---|
Scaffold_1 | 4469875 | 1393 | Scaffold_31 | 666660 | 203 | Scaffold_53 | 207498 | 52 |
Scaffold_10 | 1494552 | 424 | Scaffold_32 | 647059 | 167 | Scaffold_54 | 183478 | 51 |
Scaffold_11 | 1421539 | 426 | Scaffold_33 | 627493 | 161 | Scaffold_55 | 176875 | 41 |
Scaffold_12 | 1200238 | 334 | Scaffold_34 | 621976 | 186 | Scaffold_56 | 174271 | 58 |
Scaffold_13 | 1081736 | 337 | Scaffold_35 | 614529 | 155 | Scaffold_57 | 167193 | 47 |
Scaffold_14 | 1072049 | 347 | Scaffold_36 | 532656 | 153 | Scaffold_58 | 161880 | 47 |
Scaffold_15 | 1050642 | 314 | Scaffold_37 | 511480 | 126 | Scaffold_59 | 161526 | 43 |
Scaffold_16 | 1046259 | 337 | Scaffold_38 | 506477 | 122 | Scaffold_6 | 2277588 | 668 |
Scaffold_17 | 1019206 | 303 | Scaffold_39 | 493120 | 139 | Scaffold_60 | 146901 | 39 |
Scaffold_18 | 950046 | 247 | Scaffold_4 | 3153885 | 1014 | Scaffold_61 | 115424 | 31 |
Scaffold_19 | 926904 | 298 | Scaffold_40 | 428051 | 134 | Scaffold_62 | 114060 | 27 |
Scaffold_2 | 3484778 | 1149 | Scaffold_41 | 415410 | 111 | Scaffold_63 | 103079 | 35 |
Scaffold_20 | 895893 | 264 | Scaffold_42 | 375402 | 111 | Scaffold_64 | 95381 | 24 |
Scaffold_21 | 879786 | 257 | Scaffold_43 | 333682 | 104 | Scaffold_65 | 86665 | 14 |
Scaffold_22 | 879764 | 234 | Scaffold_44 | 331534 | 85 | Scaffold_66 | 83587 | 23 |
Scaffold_23 | 848793 | 236 | Scaffold_45 | 319851 | 90 | Scaffold_67 | 78814 | 27 |
Scaffold_24 | 842024 | 258 | Scaffold_46 | 311630 | 87 | Scaffold_68 | 66934 | 13 |
Scaffold_25 | 790967 | 201 | Scaffold_47 | 282820 | 90 | Scaffold_69 | 59421 | 15 |
Scaffold_26 | 790090 | 218 | Scaffold_48 | 257692 | 74 | Scaffold_7 | 2147372 | 600 |
Scaffold_27 | 747333 | 216 | Scaffold_49 | 248,648 | 51 | Scaffold_70 | 58166 | 16 |
Scaffold_28 | 714016 | 198 | Scaffold_5 | 2522070 | 731 | Scaffold_71 | 33177 | 15 |
Scaffold_29 | 692498 | 211 | Scaffold_50 | 232229 | 58 | Scaffold_72 | 85353 | 56 |
Scaffold_3 | 3315994 | 946 | Scaffold_51 | 226670 | 86 | Scaffold_8 | 2100477 | 654 |
Scaffold_30 | 691292 | 185 | Scaffold_52 | 212908 | 70 | Scaffold_9 | 1783301 | 500 |
Table 8 Statistics on the total sequence length and genes’ number on each scaffold
Seq_name | Seq_length | Gene number | Seq_name | Seq_length | Gene number | Seq_name | Seq_length | Gene number |
---|---|---|---|---|---|---|---|---|
Scaffold_1 | 4469875 | 1393 | Scaffold_31 | 666660 | 203 | Scaffold_53 | 207498 | 52 |
Scaffold_10 | 1494552 | 424 | Scaffold_32 | 647059 | 167 | Scaffold_54 | 183478 | 51 |
Scaffold_11 | 1421539 | 426 | Scaffold_33 | 627493 | 161 | Scaffold_55 | 176875 | 41 |
Scaffold_12 | 1200238 | 334 | Scaffold_34 | 621976 | 186 | Scaffold_56 | 174271 | 58 |
Scaffold_13 | 1081736 | 337 | Scaffold_35 | 614529 | 155 | Scaffold_57 | 167193 | 47 |
Scaffold_14 | 1072049 | 347 | Scaffold_36 | 532656 | 153 | Scaffold_58 | 161880 | 47 |
Scaffold_15 | 1050642 | 314 | Scaffold_37 | 511480 | 126 | Scaffold_59 | 161526 | 43 |
Scaffold_16 | 1046259 | 337 | Scaffold_38 | 506477 | 122 | Scaffold_6 | 2277588 | 668 |
Scaffold_17 | 1019206 | 303 | Scaffold_39 | 493120 | 139 | Scaffold_60 | 146901 | 39 |
Scaffold_18 | 950046 | 247 | Scaffold_4 | 3153885 | 1014 | Scaffold_61 | 115424 | 31 |
Scaffold_19 | 926904 | 298 | Scaffold_40 | 428051 | 134 | Scaffold_62 | 114060 | 27 |
Scaffold_2 | 3484778 | 1149 | Scaffold_41 | 415410 | 111 | Scaffold_63 | 103079 | 35 |
Scaffold_20 | 895893 | 264 | Scaffold_42 | 375402 | 111 | Scaffold_64 | 95381 | 24 |
Scaffold_21 | 879786 | 257 | Scaffold_43 | 333682 | 104 | Scaffold_65 | 86665 | 14 |
Scaffold_22 | 879764 | 234 | Scaffold_44 | 331534 | 85 | Scaffold_66 | 83587 | 23 |
Scaffold_23 | 848793 | 236 | Scaffold_45 | 319851 | 90 | Scaffold_67 | 78814 | 27 |
Scaffold_24 | 842024 | 258 | Scaffold_46 | 311630 | 87 | Scaffold_68 | 66934 | 13 |
Scaffold_25 | 790967 | 201 | Scaffold_47 | 282820 | 90 | Scaffold_69 | 59421 | 15 |
Scaffold_26 | 790090 | 218 | Scaffold_48 | 257692 | 74 | Scaffold_7 | 2147372 | 600 |
Scaffold_27 | 747333 | 216 | Scaffold_49 | 248,648 | 51 | Scaffold_70 | 58166 | 16 |
Scaffold_28 | 714016 | 198 | Scaffold_5 | 2522070 | 731 | Scaffold_71 | 33177 | 15 |
Scaffold_29 | 692498 | 211 | Scaffold_50 | 232229 | 58 | Scaffold_72 | 85353 | 56 |
Scaffold_3 | 3315994 | 946 | Scaffold_51 | 226670 | 86 | Scaffold_8 | 2100477 | 654 |
Scaffold_30 | 691292 | 185 | Scaffold_52 | 212908 | 70 | Scaffold_9 | 1783301 | 500 |
基因组 Genome | 类型 Type | 拷贝数目 Number of copies | 平均长度 Average length/bp | 总长度 Total length/bp | 占基因组百分比 Percentage in genome/% |
---|---|---|---|---|---|
核基因组 Nuclear genome | tRNA | 226 | 81.04 | 18 316 | 0.0323 |
rRNA(by De novo prediction)* | 12 | 2 883.08 | 34 597 | 0.0609 | |
sRNA | 64 | 62.23 | 3 983 | 0.007 | |
snRNA | 29 | 102.79 | 2 981 | 0.0053 | |
miRNA | 74 | 59.91 | 4 434 | 0.0078 | |
线粒体基因组 Mitochondrion genome | tRNA | 20 | 72.9 | 1 458 | 1.7082 |
rRNA(by De novo prediction)** | 0 | 0 | 0 | 0 | |
sRNA | 1 | 90 | 90 | 0.1054 | |
snRNA | 1 | 38 | 38 | 0.0445 | |
miRNA | 1 | 88 | 88 | 0.1031 |
Table 9 Statistics of non-coding RNA
基因组 Genome | 类型 Type | 拷贝数目 Number of copies | 平均长度 Average length/bp | 总长度 Total length/bp | 占基因组百分比 Percentage in genome/% |
---|---|---|---|---|---|
核基因组 Nuclear genome | tRNA | 226 | 81.04 | 18 316 | 0.0323 |
rRNA(by De novo prediction)* | 12 | 2 883.08 | 34 597 | 0.0609 | |
sRNA | 64 | 62.23 | 3 983 | 0.007 | |
snRNA | 29 | 102.79 | 2 981 | 0.0053 | |
miRNA | 74 | 59.91 | 4 434 | 0.0078 | |
线粒体基因组 Mitochondrion genome | tRNA | 20 | 72.9 | 1 458 | 1.7082 |
rRNA(by De novo prediction)** | 0 | 0 | 0 | 0 | |
sRNA | 1 | 90 | 90 | 0.1054 | |
snRNA | 1 | 38 | 38 | 0.0445 | |
miRNA | 1 | 88 | 88 | 0.1031 |
Genome | Method | Repeat size/bp | Percentage in genome/% |
---|---|---|---|
核基因组 Nuclear genome | Repbase | 1 307 464 | 2.3034 |
ProMask | 1 973 669 | 3.477 | |
De novo | 6 991 719 | 12.3173 | |
TRF | 326 000 | 0.5743 | |
Total | 7 954 327 | 14.0132 | |
线粒体基因组 Mitochondrion genome | Repbase | 128 | 0.15 |
ProMask | 1 005 | 1.1775 | |
De novo | 0 | ||
TRF | 320 | 0.3749 | |
Total | 1 453 | 1.7023 |
Table 10 Statistics of repeat sequences in the genome
Genome | Method | Repeat size/bp | Percentage in genome/% |
---|---|---|---|
核基因组 Nuclear genome | Repbase | 1 307 464 | 2.3034 |
ProMask | 1 973 669 | 3.477 | |
De novo | 6 991 719 | 12.3173 | |
TRF | 326 000 | 0.5743 | |
Total | 7 954 327 | 14.0132 | |
线粒体基因组 Mitochondrion genome | Repbase | 128 | 0.15 |
ProMask | 1 005 | 1.1775 | |
De novo | 0 | ||
TRF | 320 | 0.3749 | |
Total | 1 453 | 1.7023 |
Genome | Method | Type | DNA | LINE | LTR | SINE | Other | Unknown | Total |
---|---|---|---|---|---|---|---|---|---|
核基因组Nuclear genome | Repbase TEs | Length(bp) | 95 474 | 66 559 | 1 146 867 | 2 711 | 165 | 1 360 | 1 307 464 |
% in Genome | 0.1682 | 0.1173 | 2.0204 | 0.0048 | 0.0003 | 0.0024 | 2.3034 | ||
ProteinMask TEs | Length(bp) | 316 367 | 100 469 | 1 558 079 | 0 | 0 | 0 | 1 973 669 | |
% in Genome | 0.5573 | 0.177 | 2.7449 | 0 | 0 | 0 | 3.477 | ||
De novo TEs | Length(bp) | 594 332 | 431 488 | 2 449 588 | 4 081 | 0 | 3 592 915 | 6 991 719 | |
% in Genome | 1.047 | 0.7602 | 4.3154 | 0.0072 | 0 | 6.3296 | 12.3173 | ||
Combined TEs | Length(bp) | 924 792 | 515 460 | 2 849 776 | 5 828 | 165 | 3 594 275 | 7 718 181 | |
% in Genome | 1.6292 | 0.9081 | 5.0205 | 0.0103 | 0.0003 | 6.332 | 13.5971 | ||
线粒体基因组 Mitochondrion genome | Repbase TEs | Length(bp) | 0 | 0 | 128 | 0 | 0 | 0 | 128 |
% in Genome | 0 | 0 | 0.15 | 0 | 0 | 0 | 0.15 | ||
ProteinMask TEs | Length(bp) | 0 | 1 005 | 0 | 0 | 0 | 0 | 1 005 | |
% in Genome | 0 | 1.1775 | 0 | 0 | 0 | 0 | 1.1775 | ||
De novo TEs | Length(bp) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
% in Genome | - | - | - | - | - | - | - | ||
Combined TEs | Length(bp) | 0 | 1 005 | 128 | 0 | 0 | 0 | 1 133 | |
% in Genome | 0 | 1.1775 | 0.15 | 0 | 0 | 0 | 1.3274 |
Table 11 Statistics of transposable factors
Genome | Method | Type | DNA | LINE | LTR | SINE | Other | Unknown | Total |
---|---|---|---|---|---|---|---|---|---|
核基因组Nuclear genome | Repbase TEs | Length(bp) | 95 474 | 66 559 | 1 146 867 | 2 711 | 165 | 1 360 | 1 307 464 |
% in Genome | 0.1682 | 0.1173 | 2.0204 | 0.0048 | 0.0003 | 0.0024 | 2.3034 | ||
ProteinMask TEs | Length(bp) | 316 367 | 100 469 | 1 558 079 | 0 | 0 | 0 | 1 973 669 | |
% in Genome | 0.5573 | 0.177 | 2.7449 | 0 | 0 | 0 | 3.477 | ||
De novo TEs | Length(bp) | 594 332 | 431 488 | 2 449 588 | 4 081 | 0 | 3 592 915 | 6 991 719 | |
% in Genome | 1.047 | 0.7602 | 4.3154 | 0.0072 | 0 | 6.3296 | 12.3173 | ||
Combined TEs | Length(bp) | 924 792 | 515 460 | 2 849 776 | 5 828 | 165 | 3 594 275 | 7 718 181 | |
% in Genome | 1.6292 | 0.9081 | 5.0205 | 0.0103 | 0.0003 | 6.332 | 13.5971 | ||
线粒体基因组 Mitochondrion genome | Repbase TEs | Length(bp) | 0 | 0 | 128 | 0 | 0 | 0 | 128 |
% in Genome | 0 | 0 | 0.15 | 0 | 0 | 0 | 0.15 | ||
ProteinMask TEs | Length(bp) | 0 | 1 005 | 0 | 0 | 0 | 0 | 1 005 | |
% in Genome | 0 | 1.1775 | 0 | 0 | 0 | 0 | 1.1775 | ||
De novo TEs | Length(bp) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
% in Genome | - | - | - | - | - | - | - | ||
Combined TEs | Length(bp) | 0 | 1 005 | 128 | 0 | 0 | 0 | 1 133 | |
% in Genome | 0 | 1.1775 | 0.15 | 0 | 0 | 0 | 1.3274 |
数据库 | Total | P450 | TF | CAZY | PHI | IPR |
---|---|---|---|---|---|---|
Nuclear genome | 16 681 | 1 261(7.55%) | 588(3.52%) | 278(1.66%) | 570(3.41%) | 10 296(61.72%) |
Mitochondrial genome | 56 | 0(0%) | 0(0%) | 0(0%) | 1(1.78%) | 47(83.92%) |
数据库 | SWISSPROT | COG | GO | KEGG | NR | Over All |
Nuclear genome | 2 708(16.23%) | 1 244(7.45%) | 7 373(44.19%) | 4 346(26.05%) | 12 161(72.9%) | 13 161(78.89%) |
Mitochondrial genome | 24(42.85%) | 10(17.85%) | 44(78.57%) | 16(28.57%) | 46(82.14%) | 51(91.07%) |
Table 12 Statistics of gene set annotation results
数据库 | Total | P450 | TF | CAZY | PHI | IPR |
---|---|---|---|---|---|---|
Nuclear genome | 16 681 | 1 261(7.55%) | 588(3.52%) | 278(1.66%) | 570(3.41%) | 10 296(61.72%) |
Mitochondrial genome | 56 | 0(0%) | 0(0%) | 0(0%) | 1(1.78%) | 47(83.92%) |
数据库 | SWISSPROT | COG | GO | KEGG | NR | Over All |
Nuclear genome | 2 708(16.23%) | 1 244(7.45%) | 7 373(44.19%) | 4 346(26.05%) | 12 161(72.9%) | 13 161(78.89%) |
Mitochondrial genome | 24(42.85%) | 10(17.85%) | 44(78.57%) | 16(28.57%) | 46(82.14%) | 51(91.07%) |
Species and strain name | G. sp. Zizhi S2 | G. lucidum G.260125-1 | G. sinense ZZ0214-1 |
---|---|---|---|
Chromosomes | NA* | 13 | 12 |
Number of scaffolds | 71 | 82 | 69 |
Length of genome assembly(bp) | 56 763 274 | 43 292 570 | 48 955 697 |
GC content(%) | 56.14 | 56.16 | 56.17 |
Number of protein-coding genes | 16 681 | 16 495 | 15 688 |
Average gene length(bp) | 1 944.66 | 1 569.02 | 1 668.82 |
GC content of protein-coding genes(%) | 59.62 | 59.33 | 59.53 |
Average number of exons per gene | 5.74 | 4.58 | 5.34 |
Average exon size(bp) | 249.69 | 259 | 245.67 |
Average coding sequence size(bp) | 1 434.57 | 1 188.79 | 1 313.03 |
Average intron size(bp) | 107.24 | 94.12 | 81.71 |
Average size of intergenic regions(bp) | 1 452.02 | 1 050.52 | 1 487.12 |
Repeat sequences(%) | 14.01 | 8.15 | 8.53 |
Sequencing platform | PacBio Sequel & Illumina HiSeq | Roche 450 & Illumina | Roche 454 & Illumina HiSeq |
Table 13 Information comparison of 3 nuclear genomes of Ganoderma spp.
Species and strain name | G. sp. Zizhi S2 | G. lucidum G.260125-1 | G. sinense ZZ0214-1 |
---|---|---|---|
Chromosomes | NA* | 13 | 12 |
Number of scaffolds | 71 | 82 | 69 |
Length of genome assembly(bp) | 56 763 274 | 43 292 570 | 48 955 697 |
GC content(%) | 56.14 | 56.16 | 56.17 |
Number of protein-coding genes | 16 681 | 16 495 | 15 688 |
Average gene length(bp) | 1 944.66 | 1 569.02 | 1 668.82 |
GC content of protein-coding genes(%) | 59.62 | 59.33 | 59.53 |
Average number of exons per gene | 5.74 | 4.58 | 5.34 |
Average exon size(bp) | 249.69 | 259 | 245.67 |
Average coding sequence size(bp) | 1 434.57 | 1 188.79 | 1 313.03 |
Average intron size(bp) | 107.24 | 94.12 | 81.71 |
Average size of intergenic regions(bp) | 1 452.02 | 1 050.52 | 1 487.12 |
Repeat sequences(%) | 14.01 | 8.15 | 8.53 |
Sequencing platform | PacBio Sequel & Illumina HiSeq | Roche 450 & Illumina | Roche 454 & Illumina HiSeq |
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