Comparative Mitogenomics Provides Valuable Insights for the Phylogeny and New DNA Barcodes of Ganoderma
文献类型： 外文期刊
作者： Chen, Ti-Qiang 1 ; Yang, Chi 1 ; Xu, Xiao-Lan 2 ; Yang, Lin 3 ; He, Huan-Qing 4 ; Weng, Meng-Ting 1 ; Ying, Zheng-He 1 ; Shi, Xiao-Kun 1 ; Ding, Meng-Guang 1 ;
作者机构： 1.Fujian Acad Agr Sci, Inst Edible & Med Mushroom, Fuzhou 350014, Peoples R China
2.Fujian Agr & Forestry Univ, Coll Bee Sci & Biomed, Fuzhou 350002, Peoples R China
3.Chengdu Jinxu Biotechnol Co Ltd, Chengdu 610021, Peoples R China
4.Guangdong Acad Agr Sci, Inst Vegetable Res, Guangzhou 510640, Peoples R China
关键词：
期刊名称：JOURNAL OF FUNGI （ 影响因子：4.0； 五年影响因子：4.5 ）
ISSN：
年卷期： 2024 年 10 卷 11 期
页码：
收录情况： SCI
摘要： Ganoderma is the most important genus in the family Ganodermataceae; many species have attracted much attention and widely cultivated because of their medicinal values, but so far, not a sequenced mitogenome derived from dikaryon strains has been explicitly recorded. Herein, four novel mitogenomes of commonly cultivated Ganoderma (G. leucocontextum H4, G. lucidum G6, G. sinense MZ96 and G. tsugae SS) were de novo assembled and given detail functional annotations. Collinearity analysis revealed that the four mitogenomes shared 82.93-92.02% similarity with their corresponding reference mitogenomes at the nucleotide level. A total of 15 core protein-coding genes (PCGs), along with rrnL and rrnS (mtLSU and mtSSU) were chosen as potential candidates for constructing their individual phylogenetic trees. These trees were compared with those derived from the concatenated sequences of 15 core PCGs. And finally, we found that the atp9 and nad4L were the most reliable markers for the phylogenetic analysis of Ganoderma and chosen as standard sequences to generate new DNA barcodes. This finding was further verified by comparing it against almost all available Ganoderma mitogenomes in the NCBI, with Trametes versicolor (Polyporaceae) and Rigidoporus microporus (Meripilaceae) as two outgroups. A total of 52 mitogenomes from three families were highly conserved, with identical gene lengths for atp9 (222 bp) and nad4L (267 bp). These genes were capable of distinguish distinctly different various species, which are grouped into separate clades within the phylogenetic trees. The closest related clades (I and II), including at least 30 samples of the three classical taxonomic species (G. lingzhi, G. sichuanense and G. lucidum), differed in only one SNP. The single base mutation rate increased with the evolutionary divergence of the phylogenetic clades, from two to three SNPs in earlier clades (e.g., clade IV containing G. leucocontextum) to five to six SNPs in later clades (e.g., clade X containing G. sinense). Despite these variations between species, the atp9 and nad4L genes of Ganoderma mitogenomes consistently encoded the same ATP synthase F0 subunit c (73 aa) and NADH dehydrogenase subunit 4L (88 aa). These two genes have been identified as reliable markers of new DNA barcodes, offering valuable insights and contributing significantly to understanding the evolutionary relationships and phylogeny of the Ganoderma genus and even the Ganodermataceae family.
- 相关文献
作者其他论文 更多>>
-
Long non-coding RNAs and their potential function in response to postharvest senescence of Sparassis latifolia during cold storage
作者：Weng, Mengting;Zhang, Di;Wang, Hongyu;Yang, Chi;Lin, Hongyi;Lin, Yanquan;Weng, Mengting;Zhang, Di;Wang, Hongyu;Yang, Chi;Lin, Hongyi;Lin, Yanquan;Pan, Yanfang
关键词：
-
Chromosome-Scale Genome Assembly Provides Insights into Fresh Pine Wood Decay Strategies of the Wolfiporia hoelen
作者：Yang, Chi;Xiao, Donglai;Jiang, Xiaoling;Li, Yaru;Liu, Xiaoyu;Lin, Hui;Ma, Lu;Liu, Chuansen
关键词：Wolfiporia hoelen; genome; chromosome; pine sawdust decay; comparative genomics
-
Comparative genomics reveals ample evidence to Ganoderma sinense cultivars for molecular identification and new FIP exploration
作者：Chen, Ti-Qiang;Yang, Chi;Ying, Zheng-He;Shi, Xiao-Kun;Ding, Meng-Guang;Xu, Xiao-Lan;Yang, Lin
关键词：Ganoderma sinense; Dikaryotic genome; Comparative genomics; Homologous polygenes; Fungal immunoregulatory protein; Molecular identification
-
Screening and Characterization of a New Iflavirus Virus in the Fruit Tree Pest Pyrops candelaria
作者：Lin, Hong;Song, Weitao;Yang, Chi;Yao, Yanfang;Hao, Ling;Wu, Dandan;Wang, Shihua;Xiong, Jun;Zhuang, Zhenhong;Ma, Dongmei;Liu, Renyi;Xiao, Jiajing;Jiang, Jimou;Ma, Rui
关键词：iflavirus; Pyrops candelaria; virus; insect; distribution
-
Role of RNA Modifications, Especially m6A, in Aflatoxin Biosynthesis of Aspergillus flavus
作者：Yang, Chi;Wu, Dandan;Lin, Hong;Ma, Dongmei;Fu, Wangzhuo;Yao, Yanfang;Pan, Xiaohua;Wang, Shihua;Zhuang, Zhenhong;Yang, Chi;Wu, Dandan;Ma, Dongmei;Fu, Wangzhuo;Yao, Yanfang;Pan, Xiaohua;Wang, Shihua;Zhuang, Zhenhong;Yang, Chi;Ma, Dongmei
关键词：Aspergillus flavus; RNAmodifications; m6A; temperature; aflatoxin; aflQ
-
SWD1 epigenetically chords fungal morphogenesis, aflatoxin biosynthesis, metabolism, and virulence of Aspergillus flavus
作者：Pan, Xiaohua;Hao, Ling;Yang, Chi;Lin, Hong;Wu, Dandan;Chen, Xuan;Zhang, Mengjuan;Ma, Dongmei;Wang, Yu;Fu, Wangzhuo;Yao, Yanfang;Wang, Shihua;Zhuang, Zhenhong;Pan, Xiaohua;Hao, Ling;Yang, Chi;Lin, Hong;Wu, Dandan;Chen, Xuan;Zhang, Mengjuan;Ma, Dongmei;Wang, Yu;Fu, Wangzhuo;Yao, Yanfang;Wang, Shihua;Zhuang, Zhenhong;Pan, Xiaohua;Yang, Chi;Ma, Dongmei
关键词：SWD1; Aspergillus flavus; Aflatoxins; Histone methylation; Metabolomics
-
Chromosome-level assembly of Dictyophora rubrovolvata genome using third-generation DNA sequencing and Hi-C analysis
作者：Ma, Lu;Yang, Chi;Xiao, Donglai;Liu, Xiaoyu;Jiang, Xiaoling;Lin, Hui;Ying, Zhenghe;Lin, Yanquan;Ma, Lu;Yang, Chi;Xiao, Donglai;Liu, Xiaoyu;Jiang, Xiaoling;Lin, Hui;Ying, Zhenghe;Lin, Yanquan;Lin, Yanquan
关键词：Dictyophora rubrovolvata; whole-genome sequencing; functional annotation; lignocellulose degradation; CAZymes
