Chromosome-Scale Genome Assembly Provides Insights into Fresh Pine Wood Decay Strategies of the Wolfiporia hoelen

被引:0
|
作者
Yang, Chi [1 ]
Xiao, Donglai [1 ]
Jiang, Xiaoling [1 ]
Li, Yaru [1 ]
Liu, Xiaoyu [1 ]
Lin, Hui [1 ]
Liu, Chuansen [2 ]
Ma, Lu [1 ]
机构
[1] Fujian Acad Agr Sci, Inst Edible Mushroom, Natl & Local Joint Engn Res Ctr Breeding & Cultiva, Fuzhou 350014, Peoples R China
[2] Agr & Rural Bur Datian Cty, Sanming 366100, Peoples R China
关键词
Wolfiporia hoelen; genome; chromosome; pine sawdust decay; comparative genomics; COCOS; IDENTIFICATION; TRANSCRIPTOME; PREDICTION; DNA; CLASSIFICATION; TRITERPENOIDS; SCLEROTIA; MYCELIA; GENES;
D O I
10.3390/horticulturae10070703
中图分类号
S6 [园艺];
学科分类号
0902 ;
摘要
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.
引用
收藏
页数:16
相关论文
共 50 条
  • [41] The chromosome-scale reference genome for the pinfish (Lagodon rhomboides) provides insights into their evolutionary and demographic history
    Eaton, Katherine M.
    Krabbenhoft, Trevor J.
    Backenstose, Nathan J. C.
    Bernal, Moises A.
    G3-GENES GENOMES GENETICS, 2024, 14 (07):
  • [42] Chromosome-scale assembly of the African yam bean genome
    Waweru, Bernice
    Njaci, Isaac
    Paliwal, Rajneesh
    Maranga, Mary
    Muli, Collins
    Murungi, Edwin
    Kaimenyi, Davies
    Lyimo, Beatus
    Nigussie, Helen
    Ahadi, Bwihangane Birindwa
    Assefa, Ermias
    Ishag, Hassan
    Olomitutu, Oluwaseyi
    Abberton, Michael
    Darby, Christopher
    Uauy, Cristobal
    Yao, Nasser
    Adewale, Daniel
    Emmrich, Peter
    Entfellner, Jean-Baka Domelevo
    Shorinola, Oluwaseyi
    SCIENTIFIC DATA, 2024, 11 (01)
  • [43] A chromosome-scale genome assembly of mungbean (Vigna radiata)
    Khanbo, Supaporn
    Phadphon, Poompat
    Naktang, Chaiwat
    Sangsrakru, Duangjai
    Waiyamitra, Pitchaporn
    Narong, Nattapol
    Yundaeng, Chutintorn
    Tangphatsornruang, Sithichoke
    Laosatit, Kularb
    Somta, Prakit
    Pootakham, Wirulda
    PEERJ, 2024, 12
  • [44] A draft chromosome-scale genome assembly of a commercial sugarcane
    Jeremy R. Shearman
    Wirulda Pootakham
    Chutima Sonthirod
    Chaiwat Naktang
    Thippawan Yoocha
    Duangjai Sangsrakru
    Nukoon Jomchai
    Sissades Tongsima
    Jittima Piriyapongsa
    Chumpol Ngamphiw
    Nanchaya Wanasen
    Kittipat Ukoskit
    Prapat Punpee
    Peeraya Klomsa-ard
    Klanarong Sriroth
    Jisen Zhang
    Xingtan Zhang
    Ray Ming
    Somvong Tragoonrung
    Sithichoke Tangphatsornruang
    Scientific Reports, 12
  • [45] A Chromosome-Scale Genome Assembly of the Okapi (Okapia johnstoni)
    Winter, Sven
    Coimbra, Raphael T. F.
    Helsen, Philippe
    Janke, Axel
    JOURNAL OF HEREDITY, 2022, 113 (05) : 568 - 576
  • [46] Chromosome-scale assembly and annotation of the perennial ryegrass genome
    Nagy, Istvan
    Veeckman, Elisabeth
    Liu, Chang
    Van Bel, Michiel
    Vandepoele, Klaas
    Jensen, Christian Sig
    Ruttink, Tom
    Asp, Torben
    BMC GENOMICS, 2022, 23 (01)
  • [47] The chromosome-scale assembly of the Salvia plebeia genome provides insight into the biosynthesis and regulation of rosmarinic acid
    Dai, Yiqun
    He, Mengqian
    Liu, Hui
    Zeng, Huihui
    Wang, Kaixuan
    Wang, Rui
    Ma, Xiaojing
    Zhu, Yan
    Xie, Guoyong
    Zhao, Yucheng
    Qin, Minjian
    PLANT BIOTECHNOLOGY JOURNAL, 2025,
  • [48] A new chromosome-scale genome of wild Brassica oleracea provides insights into the domestication of Brassica crops
    Ji, Gaoxiang
    Long, Ying
    Cai, Guangqin
    Wang, Aihua
    Yan, Guixin
    Li, Hao
    Gao, Guizhen
    Xu, Kun
    Huang, Qian
    Chen, Biyun
    Li, Lixia
    Li, Feng
    Nishio, Takeshi
    Shen, Jinxiong
    Wu, Xiaoming
    JOURNAL OF EXPERIMENTAL BOTANY, 2024, 75 (10) : 2882 - 2899
  • [49] Chromosome-scale genome assembly and annotation of Cotoneaster glaucophyllus
    Meng, Kaikai
    Liao, Wenbo
    Wei, Shaolong
    Chen, Sufang
    Li, Mingwan
    Ma, Yongpeng
    Fan, Qiang
    SCIENTIFIC DATA, 2024, 11 (01)
  • [50] Chromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication Signature
    Shen, Lian-Ying
    Luo, Hang
    Wang, Xiao-Ling
    Wang, Xue-Meng
    Qiu, Xiao-Jing
    Liu, Hui
    Zhou, Shan-Shan
    Jia, Kai-Hua
    Nie, Shuai
    Bao, Yu-Tao
    Zhang, Ren-Gang
    Yun, Quan-Zheng
    Chai, Ying-Hui
    Lu, Jin-Ying
    Li, Yu
    Zhao, Shu-Wei
    Mao, Jian-Feng
    Jia, Shan-Gang
    Mao, Yong-Min
    FRONTIERS IN PLANT SCIENCE, 2021, 12