染色体尺度的基因组组装揭示了褐斑梭菌(Wolfiporia hoelen)的新松木腐烂策略

Chi Yang, Donglai Xiao, Xiaoling Jiang, Yaru Li, Xiaoyu Liu, Hui Lin, Chuansen Liu, Lu Ma
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引用次数: 0

摘要

枸杞子(Wolfiporia hoelen (Fr.) Y.C. Dai & V. Papp)是一种重要的传统中药,具有多种药理作用。本研究利用 PacBio 长读取测序、Illumina 短读取测序和 Hi-C 测序相结合的方法,生成了枸杞菌株闽灵 A5 的高质量染色体组基因组。基因组中有 112 个等位基因,总长度为 62.95 Mb,等位基因 N50 长度为 4.21 Mb。平均 GC 含量为 51.89%。根据 Hi-C 数据,我们对 CCS 数据进行了校正,并将其支架化为 14 个假染色体。该基因组包含 44.37% 的重复序列和 12,670 个编码蛋白质的基因,其中 86.53% 的基因(10,963 个)可在 KOG、GO、Pfam、Swissprot、TrEMBL、NR 和 KEGG 数据库中的至少一个数据库中进行功能注释。此外,在 W. hoelen 基因组中还发现了 240 个转移 RNA、97 个核糖体 RNA 和 103 个其他非编码 RNA。还发现了 755 个假基因,平均长度为 2665.51 bp。此外,CAZymes、TCDB、PHI、P450 和 DFVF 数据库分别注释了 398、100、2837、519 和 2068 个基因。W. hoelen 的一个显著特征是它能在新鲜松木锯屑的基质中生长。通过分析其在各种纯木锯屑培养基上的生长情况,我们发现 W. hoelen 和 Sparassis latifolia 在松木锯屑上的生长情况与在阔叶木锯屑上的生长情况相似,而 Pleurotus ostreatus、P. eryngii 和 Cyclocybe aegerita 在阔叶木锯屑上的生长速度则较慢。通过对这五种蘑菇形成真菌的正交组进行功能注释分析,确定了 645 个正交组在 W. hoelen 和 S. latifolia 中特别常见。这些特定直向群中的基因在 12 个途径中明显富集,包括类固醇生物合成、抗生素生物合成和酪氨酸代谢。高质量的基因组和比较基因组分析结果极大地促进了我们对松柏生物学基础知识的了解,同时也为开发创新生物技术方法提供了宝贵的见解,这些方法旨在提高松柏的高效和可持续利用。
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Chromosome-Scale Genome Assembly Provides Insights into Fresh Pine Wood Decay Strategies of the Wolfiporia hoelen
The sclerotia of Wolfiporia hoelen (Fr.) Y.C. Dai & V. Papp is an important traditional Chinese medicine with diverse pharmacological properties. This study utilized a combination of PacBio Long-Read Sequencing, Illumina Short-Read Sequencing, and Hi-C Sequencing to generate a high-quality chromosome-level genome assembly of a W. hoelen strain Minling A5. There were 112 contigs in the genome, with 62.95 Mb in total length and 4.21 Mb in length for the contig N50. The average GC content was 51.89%. Based on Hi-C data, we corrected the CCS data and scaffolded them into 14 pseudo-chromosomes. The genome contained 44.37% repetitive sequences and 12,670 protein-coding genes, 86.53% (10,963) of which could be functionally annotated in at least one of the KOG, GO, Pfam, Swissprot, TrEMBL, NR, and KEGG databases. In addition, 240 transfer RNAs, 97 ribosomal RNAs, and 103 other non-coding RNAs were identified in the W. hoelen genome. A total of 755 pseudogenes were also identified, with an average length of 2665.51 bp. Further, there were 398, 100, 2837, 519, and 2068 genes annotated by CAZymes, TCDB, PHI, P450, and DFVF databases, respectively. One notable attribute of W. hoelen is its capacity to thrive in a substrate of fresh pine sawdust. Through an analysis of the growth on various pure wood sawdust culture media, we found that the growth of W. hoelen and Sparassis latifolia on pine sawdust was similar to that on broad-leaved wood sawdust, while the growth of Pleurotus ostreatus, P. eryngii, and Cyclocybe aegerita was slower than that on broad-leaved wood sawdust. By the functional annotation analysis of orthogroups in these five mushroom-forming fungi, it was determined that 645 orthogroups were specifically common in W. hoelen and S. latifolia. The genes in these specific orthogroups were significantly enriched in 12 pathways, including steroid biosynthesis, biosynthesis of antibiotics, and tyrosine metabolism. The high-quality genome and comparative genome analysis results significantly contribute to advancing our foundational knowledge of W. hoelen biology, while also offering valuable insights for the development of innovative biotechnological approaches aimed at enhancing the efficient and sustainable utilization of Pinus.
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