PDF(1014 KB)
Establishment of molecular markers in the whole genome of Ganoderma lingzhi elite varieties
LIU Yiting, JIANG Xiaohan, YANG Chunyan, CHEN Jianhui, WANG Chezhao, LÜ Xiaomeng, YANG Zhikang, DENG Youjin, WU Xiaoping
Mycosystema ›› 2025, Vol. 44 ›› Issue (3) : 240141.
PDF(1014 KB)
PDF(1014 KB)
Establishment of molecular markers in the whole genome of Ganoderma lingzhi elite varieties
,
({{custom_author.role_en}})
,
{{javascript:window.custom_author_en_index++;}}
Ganoderma lingzhi 13 is an excellent cultivated variety with superior agronomic character. The mononucleate strain, G. lingzhi 13-5, as assembled into a complete genome by three-generation HiFi sequencing and Hi-C sequencing, and five replicated bi-nucleate strains were subjected to high throughput sequencing by Illumina, and then the genome of G. lingzhi 13-5 was used as a reference for SNP calling to establish the molecular markers based on the whole genome of G. lingzhi 13. The genome contains 13 chromosomes with a total of 45.73 Mb. After the SNP calling of five replicate strains were de-emphasized and merged, 319 074 shared heterokaryotic allelic difference sites were obtained as a molecular marker library for the identification of G. lingzhi 13 strains. Seven post-fruiting strains were randomly selected from the strain library. It was found that the percentage of allelic difference sites of the post-fruiting strains shared with G. lingzhi 13 ranged from 22.20% to 45.18%, being far inferior to threshold value, indicating that these strains were different from G. lingzhi 13 and they were not the same strains. In this study, molecular markers based on the whole genome of G. lingzhi 13 and its heterokaryotic allelic differentiation sites were established, which can accurately differentiate G. lingzhi 13, a superior cultivated variety.
three generations of HiFi sequencing / SNP calling / variety identification / variety protection {{custom_keyword}} /
Table 1 Genomic information of Ganoderma lingzhi 13-5表1 灵芝13-5基因组信息 |
| 拼接后的 序列 Contig | 大小 Size (Mb) | 5ʹ端端粒 Telomere at 5ʹ end | 3ʹ端端粒 Telomere at 3ʹ end | 完整染色体 Complete chromosome | 注释 Notes |
|---|---|---|---|---|---|
| tig01 | 4.76 | + | + | + | |
| tig02 | 3.34 | + | + | + | |
| tig03 | 4.14 | + | + | + | |
| tig04 | 3.14 | + | + | + | |
| tig05 | 4.55 | + | + | + | |
| tig06 | 3.41 | + | + | + | |
| tig07 | 2.60 | + | + | + | |
| tig08 | 3.19 | + | + | + | |
| tig09 | 3.39 | + | + | + | |
| tig10 | 2.53 | + | 在另一端有连接的rDNA区域 Linked rDNA region on the other end | ||
| tig11 | 5.31 | + | + | + | |
| tig12 | 2.50 | + | + | + | |
| tig13 | 3.32 | + | |||
| tig14 | 0.30 | + | |||
| Others | 32.67 | 共775个小序列，114个属于rDNA区域，500个属于 线粒体基因组 Small contigs totaled 775, including 114 belonging to rDNA region and 500 belonging to mitochondrial genome |
| 注：+表示有端粒，是完整的染色体 | |
| Note: + indicates the presence of telomeres and is the complete chromosome. |
Fig. 1 Evaluation results of genome completeness and accuracy of Ganoderma lingzhi 13-5. A: Heatmap of the Hi-C crosslinking. The color in the figure increases with the intensity of interaction; The coordinate and ordinate indicate the N * bin position on the genome; B: Results of the BUSCO assessment. C: Intact orthologous genes; S: Single copy orthologous genes; D: Multiple copy ortholog genes; F: Fragmented genes; M: Missing genes.图1 灵芝13-5基因组完整性和准确性评估结果 A：Hi-C交联热图；图中颜色从浅到深表示互作程度的增加，颜色越深互作越强；横坐标及纵坐标表示其在基因组上的N * bin位置；B：BUSCO评估结果；C：完整同源基因；S：单拷贝同源基因；D：多拷贝同源基因；F：片段基因；M：缺失的基因 |
Table 2 Centromere characteristics of each chromosome in the genome表2 基因组各条染色体着丝粒特征 |
| 重复序列家族 The family of repeat sequences | 1号 染色 体 C01 | 2号 染色 体 C02 | 3号 染色 体 C03 | 4号 染色 体 C04 | 5号 染色 体 C05 | 6号 染色 体 C06 | 7号 染色 体 C07 | 8号 染色 体 C08 | 9号 染色 体 C09 | 10号 染色 体 C10 | 11号 染色 体 C11 | 12号 染色 体 C12 | 13号 染色 体 C13 | 统计 Total |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rnd-1_family-0 | 13 | 11 | 14 | 0 | 13 | 8 | 8 | 14 | 6 | 8 | 3 | 7 | 11 | 116 |
| rnd-3_family-15 | 14 | 9 | 8 | 0 | 10 | 1 | 9 | 17 | 6 | 6 | 8 | 10 | 13 | 111 |
| rnd-1_family-8 | 17 | 3 | 7 | 0 | 9 | 2 | 2 | 8 | 10 | 2 | 4 | 14 | 7 | 85 |
| rnd-4_family-276 | 5 | 0 | 7 | 0 | 0 | 0 | 7 | 6 | 3 | 6 | 2 | 6 | 6 | 48 |
| rnd-1_family-2 | 16 | 4 | 2 | 0 | 1 | 3 | 2 | 3 | 0 | 3 | 3 | 2 | 7 | 46 |
| rnd-4_family-1322 | 3 | 0 | 2 | 0 | 1 | 0 | 4 | 4 | 1 | 2 | 2 | 3 | 3 | 25 |
| rnd-1_family-20 | 3 | 1 | 2 | 0 | 0 | 0 | 1 | 3 | 2 | 3 | 4 | 1 | 0 | 20 |
| rnd-1_family-3 | 3 | 1 | 3 | 0 | 1 | 0 | 0 | 3 | 0 | 1 | 2 | 0 | 3 | 17 |
| rnd-1_family-146 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | 0 | 4 | 0 | 0 | 2 | 3 | 14 |
| rnd-1_family-1 | 0 | 2 | 1 | 0 | 0 | 1 | 2 | 2 | 3 | 0 | 0 | 1 | 1 | 13 |
| (CCTCAT)n | 2 | 3 | 0 | 0 | 1 | 2 | 0 | 2 | 0 | 1 | 0 | 2 | 0 | 13 |
| GA-rich | 1 | 1 | 1 | 1 | 2 | 0 | 0 | 0 | 0 | 0 | 3 | 1 | 1 | 11 |
| Total number | 108 | 60 | 57 | 65 | 60 | 51 | 58 | 81 | 62 | 71 | 81 | 70 | 74 | 898 |
| Percent (%) | 2.07 | 2.01 | 2.10 | 0.87 | 2.39 | 1.77 | 2.58 | 2.58 | 1.71 | 2.55 | 2.51 | 2.84 | 3.07 |
| 注：统计每条染色体着丝粒区域120 kb序列信息；The family of repeat sequences：显示同时出现在6条染色体着丝粒区域的family；Total number：统计120 kb区域的family总数；Percent：着丝粒重复序列长度占对应染色体长度比值 | |
| Note: 120 kb sequence information of centromere region of each chromosome was collected. The family of repeat sequences: Family that appear simultaneously in the centromere region of 6 chromosomes. Total number: The total number of family in the 120 kb area. Percent: The ratio of centromere repeat sequence length to corresponding chromosome length. |
Table 3 Results of genome prediction表3 基因预测结果 |
| 基因预测结果 Results of genome prediction | 基因组大小 Genome size (bp) |
|---|---|
| 预测基因 Predicted genes | 13 383 |
| 蛋白质编码基因 Protein conding genes | 13 179 |
| tRNA基因 tRNA genes | 204 |
| 平均基因长度 Average gene length | 1 652.64 |
| 平均CDS长度 Average CDS length | 1 323.79 |
| 每个基因的平均外显子数 Average exons per gene (个) | 4.81 |
| 平均外显子长度 Average exon length | 274.84 |
| 平均内含子长度 Average intron length | 327.61 |
Table 4 Information about genome repeat sequence表4 基因组重复序列信息 |
| 分类 Classification | 数量 Number | 长度 Length (Mb) | 占比 Per. (%) | ||
|---|---|---|---|---|---|
| 重复序列片段 Total repeat fraction | 14 213 | 5.63 | 12.32 | ||
| 分类I：反转录因子 Class I: Retroelement | 统计 Total | 4 297 | 4.45 | 9.72 | |
| LTR反转录转座子 LTR Retrotransposon | 统计 Total | 2 106 | 3.40 | 7.44 | |
| Ty1/Copia | 276 | 0.58 | 1.28 | ||
| Ty3/Gypsy | 670 | 1.77 | 3.87 | ||
| Others | 1 160 | 1.05 | 2.29 | ||
| 非LTR反转录转座子 non-LTR Retrotransposon | 统计 Total | 1 283 | 0.75 | 1.64 | |
| LINE | 1 039 | 0.72 | 1.57 | ||
| SINE | 244 | 0.03 | 0.07 | ||
| 未分类的反转座子 Unclassified retroelement | 908 | 0.30 | 0.65 | ||
| 分类Ⅱ：DNA转座子 Class Ⅱ: DNA Transposon | 统计 Total | 1 149 | 0.56 | 1.23 | |
| TIR | CMC | 57 | 0.06 | 0.12 | |
| Tc1/Mariner | 63 | 0.05 | 0.12 | ||
| Others | 966 | 0.40 | 0.87 | ||
| 串联重复序列 Tandem repeats | 7 881 | 0.55 | 1.20 | ||
| 未知 Unkown | 169 | 0.14 | 0.31 | ||
Table 5 Number of allelic difference sites shared between Ganoderma lingzhi 13 and seven post-fruiting strains to be tested表5 灵芝13与7个待测菌株共有的等位差异位点数 |
| 待测菌株编号 The strain to be tested | 共有等位差异位点数 Number of shared allelic difference loci | 占比 Proportion (%) |
|---|---|---|
| SL9 | 75 174 | 23.56 |
| G.l0069 | 75 429 | 23.64 |
| 日芝 G. japonicum | 144 157 | 45.18 |
| G.l0051 | 76 450 | 23.96 |
| G.l0064 | 70 834 | 22.20 |
| G.l0081 | 76 865 | 24.09 |
| 杂交子12 Hybridons 12 | 89 500 | 28.05 |
| [1] |
Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging, sorting, etc.). However, the enormous amount of data produced by current sequencing technologies is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research.We introduce a software suite for programmers and end users that facilitates research analysis and data management using BAM files. BamTools provides both the first C++ API publicly available for BAM file support as well as a command-line toolkit.BamTools was written in C++, and is supported on Linux, Mac OSX and MS Windows. Source code and documentation are freely available at http://github.org/pezmaster31/bamtools.
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [2] |
A tandem repeat in DNA is two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats have been shown to cause human disease, may play a variety of regulatory and evolutionary roles and are important laboratory and analytic tools. Extensive knowledge about pattern size, copy number, mutational history, etc. for tandem repeats has been limited by the inability to easily detect them in genomic sequence data. In this paper, we present a new algorithm for finding tandem repeats which works without the need to specify either the pattern or pattern size. We model tandem repeats by percent identity and frequency of indels between adjacent pattern copies and use statistically based recognition criteria. We demonstrate the algorithm's speed and its ability to detect tandem repeats that have undergone extensive mutational change by analyzing four sequences: the human frataxin gene, the human beta T cellreceptor locus sequence and two yeast chromosomes. These sequences range in size from 3 kb up to 700 kb. A World Wide Web server interface atc3.biomath.mssm.edu/trf.html has been established for automated use of the program.
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [3] |
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [4] |
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [5] |
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [6] |
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the haplotypes to produce high-quality phased assemblies. Here we describe hifiasm, a de novo assembler that takes advantage of long high-fidelity sequence reads to faithfully represent the haplotype information in a phased assembly graph. Unlike other graph-based assemblers that only aim to maintain the contiguity of one haplotype, hifiasm strives to preserve the contiguity of all haplotypes. This feature enables the development of a graph trio binning algorithm that greatly advances over standard trio binning. On three human and five nonhuman datasets, including California redwood with a ~30-Gb hexaploid genome, we show that hifiasm frequently delivers better assemblies than existing tools and consistently outperforms others on haplotype-resolved assembly.
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [7] |
Macrofungi, as an important component in forest ecosystems, consist of most members of Basidiomycota and some members of Ascomycota, having important economical value and ecological functions. Extensive field investigations have been carried out in almost whole types of the Chinese forests during the past 30 years, and 112 000 specimens were collected. Based on morphological examination and phylogenetic analyses in combination with ecology and biogeography, 4 250 species belonging to 21 orders in Baidiomycota and Ascomycota were identified, including two new families, four new subfamilies, 69 new genera and 885 new species. Yunnan Province is the richest in macrofungal diversity among provinces or regions in China, and 314 new species were described from this province, accounting for 35% of all the new species described from China by the authors. Our studies have made contributions to deepening the understanding of global diversity of macrofungi. The names of some important Chinese medicinal fungi were revised, the diversity characteristics of Chinese poisonous mushrooms were revealed, and the pathogenetic wood-decaying species were ascertained. These data improved our knowledge on utilization of natural resources and protection of forest health. Based on molecular evidences, the origin of some forest representative fungal genera or species complex were deduced, and their dispersal and speciation were discussed, for the purposes of providing some data for evolutionary study at level of family, order or class of macrofungi henceforth. {{custom_citation.content}}
{{custom_citation.annotation}}
|
| [8] |
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [9] |
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [10] |
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [11] |
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [12] |
Genomics drives the current progress in molecular biology, generating unprecedented volumes of data. The scientific value of these sequences depends on the ability to evaluate their completeness using a biologically meaningful approach. Here, we describe the use of the BUSCO tool suite to assess the completeness of genomes, gene sets, and transcriptomes, using their gene content as a complementary method to common technical metrics. The chapter introduces the concept of universal single-copy genes, which underlies the BUSCO methodology, covers the basic requirements to set up the tool, and provides guidelines to properly design the analyses, run the assessments, and interpret and utilize the results.
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [13] |
HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. It includes a fast implementation of the iterative correction method and is based on a memory-efficient data format for Hi-C contact maps. In addition, HiC-Pro can use phased genotype data to build allele-specific contact maps. We applied HiC-Pro to different Hi-C datasets, demonstrating its ability to easily process large data in a reasonable time. Source code and documentation are available at http://github.com/nservant/HiC-Pro.
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [14] |
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [15] |
Silencing of transposable elements (TEs) is essential for maintaining genome stability. Plants use small RNAs (sRNAs) to direct DNA methylation to TEs (RNA-directed DNA methylation; RdDM). Similar mechanisms of epigenetic silencing in the fungal kingdom have remained elusive.We use sRNA sequencing and methylation data to gain insight into epigenetics in the dikaryotic fungus Puccinia graminis f. sp. tritici (Pgt), which causes the devastating stem rust disease on wheat. We use Hi-C data to define the Pgt centromeres and show that they are repeat-rich regions (~250 kb) that are highly diverse in sequence between haplotypes and, like in plants, are enriched for young TEs. DNA cytosine methylation is particularly active at centromeres but also associated with genome-wide control of young TE insertions. Strikingly, over 90% of Pgt sRNAs and several RNAi genes are differentially expressed during infection. Pgt induces waves of functionally diversified sRNAs during infection. The early wave sRNAs are predominantly 21 nts with a 5' uracil derived from genes. In contrast, the late wave sRNAs are mainly 22-nt sRNAs with a 5' adenine and are strongly induced from centromeric regions. TEs that overlap with late wave sRNAs are more likely to be methylated, both inside and outside the centromeres, and methylated TEs exhibit a silencing effect on nearby genes.We conclude that rust fungi use an epigenetic silencing pathway that might have similarity with RdDM in plants. The Pgt RNAi machinery and sRNAs are under tight temporal control throughout infection and might ensure genome stability during sporulation.© 2021. The Author(s).
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [16] |
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [17] |
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [18] |
Centromeres are essential for proper chromosome segregation. Despite extensive research, centromere locations in yeast genomes remain difficult to infer, and in most species they are still unknown. Recently, the chromatin conformation capture assay, Hi-C, has been re-purposed for diverse applications, including de novo genome assembly, deconvolution of metagenomic samples and inference of centromere locations. We describe a method, Centurion, that jointly infers the locations of all centromeres in a single genome from Hi-C data by exploiting the centromeres' tendency to cluster in three-dimensional space. We first demonstrate the accuracy of Centurion in identifying known centromere locations from high coverage Hi-C data of budding yeast and a human malaria parasite. We then use Centurion to infer centromere locations in 14 yeast species. Across all microbes that we consider, Centurion predicts 89% of centromeres within 5 kb of their known locations. We also demonstrate the robustness of the approach in datasets with low sequencing depth. Finally, we predict centromere coordinates for six yeast species that currently lack centromere annotations. These results show that Centurion can be used for centromere identification for diverse species of yeast and possibly other microorganisms. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [19] |
More than 130 medicinal functions are thought to be produced by medicinal mushrooms (MMs) and fungi, including antitumor, immunomodulating, antioxidant, radical scavenging, cardiovascular, antihypercholesterolemic, antiviral, antibacterial, antiparasitic, antifungal, detoxification, hepatoprotective, antidiabetic, and other effects. Many, if not all, higher Basidiomycetes mushrooms contain biologically active compounds in fruit bodies, cultured mycelia, and cultured broth. Special attention has been paid to mushroom polysaccharides. Numerous bioactive polysaccharides or polysaccharide-protein complexes from MMs seem to enhance innate and cell-mediated immune responses, and they exhibit antitumor activities in animals and humans. While the mechanism of their antitumor actions is still not completely understood, stimulation and modulation of key host immune responses by these mushroom compounds seems to be central. Most important for modern medicine are polysaccharides and low-molecular weight secondary metabolites with antitumor and immunostimulating properties. More than 600 studies have been conducted worldwide, and numerous human clinical trials on MMs have been published. Several of the mushroom compounds have proceeded through phase I, II, and III clinical studies and are used extensively and successfully in Asia to treat various cancers and other diseases. The aim of this review is to provide an overview of and analyze the literature on clinical trials using MMs with human anticancer, oncoimmunological, and immunomodulatory activities. High-quality, long-term, randomized, double-blind, placebo-controlled clinical studies of MMs, including well-sized population studies are definitely needed in order to yield statistical power showing their efficacy and safety. Clinical trials must obtain sufficient data on the efficacy and safety of MM-derived drugs and preparations. Discussion of results based on clinical studies of the anticancer, oncoimmunological, and immunomodulating activity of MMs are highlighted. Epidemiological studies with MMs are also discussed.
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [20] |
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [21] |
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [22] |
才晓玲, 何伟, 安福全, 2016. 灵芝种质资源研究进展. 现代农业科技, 2016(6): 99-100
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [23] |
戴玉成, 杨祝良, 崔宝凯, 吴刚, 袁海生, 周丽伟, 何双辉, 葛再伟, 吴芳, 魏玉莲, 员瑗, 司静, 2021. 中国森林大型真菌重要类群多样性和系统学研究. 菌物学报, 40: 770-805
大型真菌主要为担子菌门的真菌和少数为子囊菌门的真菌,该类真菌具有重要的经济价值和生态功能,主要生长在森林生态系统中。30年来作者对我国几乎所有类型森林生态中的大型真菌进行了系统调查和采集,共采集标本11.2万号。基于对这些材料的形态学及分子系统学研究,并结合生态学和生物地理学特征,共鉴定出中国森林大型真菌4 250种,隶属于担子菌门和子囊菌门的21个目,发现和发表2个新科、4个新亚科、69个新属和885个新种。云南省是我国森林大型真菌最丰富的省份,描述于该省的新种有314种,占作者发表的全部中国新种的35%。这些研究为深入认识全球大型真菌物种多样性提供了中国的贡献,更新了我国重要食药用菌名称,揭示了我国毒蘑菇多样性基本特征,系统论述了我国森林病原菌的物种多样性,为资源利用、森林健康和保护提供了科学依据;论述了森林大型真菌代表性类群在种和属级水平的起源和演化,为今后开展重要类群科级、目级甚至纲级的系统进化关系提供了重要数据。
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [24] |
李绩, 2007. 我国食用菌菌种知识产权保护和现状分析. 中国发明与专利, 2007(8): 48-49
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [25] |
刘晓柳, 钟灿, 谢景, 侯凤飞, 戴甲木, 张水寒, 金剑, 2022. 药食用菌新品种保护及DUS测试指南研制现状与展望. 中草药, 53(4): 1173-1180
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [26] |
戚爱华, 孙艳霞, 李威, 车晓蕾, 连丰, 2018. 灵芝的药用价值. 农村经济与科技, 29(10): 141-142
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [27] |
孙缘缘, 2019. 论我国在“一带一路”沿线的自主知识产权保护. 广西质量监督导报, 2019(3): 207-208
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [28] |
张清洋, 李文学, 杨军, 盛立柱, 朱姝蕊, 朱星考, 2020. 我国食药用菌新品种保护现状与基本对策——以植物新品种保护条例为法律渊源. 食药用菌, 28(2): 98-102
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| [29] |
左洪波, 夏伯阳, 王夕亮, 李华利, 苏小林, 刘红粉, 2021. 灵芝产区种质资源调查及杂交育种研究. 现代农业研究, 27(3): 109-110
{{custom_citation.content}}
{{custom_citation.annotation}}
|
| {{custom_ref.label}} |
{{custom_citation.content}}
{{custom_citation.annotation}}
|
PDF(1014 KB)
Collection(s)
Table 1 Genomic information of Ganoderma lingzhi 13-5
Fig. 1 Evaluation results of genome completeness and accuracy of Ganoderma lingzhi 13-5. A: Heatmap of the Hi-C crosslinking. The color in the figure increases with the intensity of interaction; The coordinate and ordinate indicate the N * bin position on the genome; B: Results of the BUSCO assessment. C: Intact orthologous genes; S: Single copy orthologous genes; D: Multiple copy ortholog genes; F: Fragmented genes; M: Missing genes.Fig. 2 Location information of centromere of each chromosome in the genome. Abscissa: Length of each chromosome; Ordinate: Hi-C interaction value, higher value indicates stronger cross-link signal.Fig. 3 Proportion of centromere repeats.Table 2 Centromere characteristics of each chromosome in the genomeTable 3 Results of genome predictionFig. 4 Genome chromosome average gene density distribution map.Table 4 Information about genome repeat sequenceFig. 5 Distribution of chromosome repeat content in the genome.Fig. 6 Venn diagram between five repeating strains. LZ1-5: Duplicate strain 1-5.Fig. 7 SNP calling results of the first chromosome of five repeating strains.Table 5 Number of allelic difference sites shared between Ganoderma lingzhi 13 and seven post-fruiting strains to be testedFig. 8 SNP calling results of the first chromosome of Ganoderma lingzhi 13 and seven post-fruiting strains.Fig. 9 Construction and application of genome-wide molecular markers.
/
| 〈 |
|
〉 |
