气候变化领域集成服务门户(CCPortal): Telomere-to-Telomere Genome Assembly of Tibetan Medicinal Mushroom Ganoderma leucocontextum and the First Copia Centromeric Retrotransposon in Macro-Fungi Genome

CCPortal

DOI	10.3390/jof10010015
	Telomere-to-Telomere Genome Assembly of Tibetan Medicinal Mushroom Ganoderma leucocontextum and the First Copia Centromeric Retrotransposon in Macro-Fungi Genome
	Wang, Miao; Meng, Guoliang; Yang, Ying; Wang, Xiaofang; Xie, Rong; Dong, Caihong
发表日期	2024
EISSN	2309-608X
卷号	10 期号:1
英文摘要	A complete telomere-to-telomere (T2T) genome has been a longstanding goal in the field of genomic research. By integrating high-coverage and precise long-read sequencing data using multiple assembly strategies, we present here the first T2T gap-free genome assembly of Ganoderma leucocontextum strain GL72, a Tibetan medicinal mushroom. The T2T genome, with a size of 46.69 Mb, consists 13 complete nuclear chromosomes and typical telomeric repeats (CCCTAA)n were detected at both ends of 13 chromosomes. The high mapping rate, uniform genome coverage, a complete BUSCOs of 99.7%, and base accuracy exceeding 99.999% indicate that this assembly represents the highest level of completeness and quality. Regions characterized by distinct structural attributes, including highest Hi-C interaction intensity, high repeat content, decreased gene density, low GC content, and minimal or no transcription levels across all chromosomes may represent potential centromeres. Sequence analysis revealed the first Copia centromeric retrotransposon in macro-fungi genome. Phylogenomic analysis identified that G. leucocontextum and G. tsugae diverged from the other Ganoderma species approximately 9.8-17.9 MYA. The prediction of secondary metabolic clusters confirmed the capability of this fungus to produce a substantial quantity of metabolites. This T2T gap-free genome will contribute to the genomic 'dark matter' elucidation and server as a great reference for genetics, genomics, and evolutionary studies of G. leucocontextum.
关键词	Ganoderma centromere Copia telomere-to-telomere
英文关键词	SEQUENCE; PROTEIN; ALIGNMENT; ACCURATE; REVEALS; IDENTIFICATION; TRITERPENOIDS; PREDICTION; SELECTION; ELEMENTS
WOS研究方向	Microbiology ; Mycology
WOS记录号	WOS:001153071800001
来源期刊	JOURNAL OF FUNGI
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/283855
作者单位	Chinese Academy of Sciences; Institute of Microbiology, CAS; Chinese Academy of Sciences; University of Chinese Academy of Sciences, CAS; Tibet Academy of Agriculture & Animal Husbandry Sciences
推荐引用方式 GB/T 7714	Wang, Miao,Meng, Guoliang,Yang, Ying,et al. Telomere-to-Telomere Genome Assembly of Tibetan Medicinal Mushroom Ganoderma leucocontextum and the First Copia Centromeric Retrotransposon in Macro-Fungi Genome[J],2024,10(1).
APA	Wang, Miao,Meng, Guoliang,Yang, Ying,Wang, Xiaofang,Xie, Rong,&Dong, Caihong.(2024).Telomere-to-Telomere Genome Assembly of Tibetan Medicinal Mushroom Ganoderma leucocontextum and the First Copia Centromeric Retrotransposon in Macro-Fungi Genome.JOURNAL OF FUNGI,10(1).
MLA	Wang, Miao,et al."Telomere-to-Telomere Genome Assembly of Tibetan Medicinal Mushroom Ganoderma leucocontextum and the First Copia Centromeric Retrotransposon in Macro-Fungi Genome".JOURNAL OF FUNGI 10.1(2024).