Congruence Amidst Discordance between Sequence and Protein-Content Based Phylogenies of Fungi

doi:10.3390/jof6030134

	Congruence Amidst Discordance between Sequence and Protein-Content Based Phylogenies of Fungi
	Xiao, Guohua 1,2; Tang, Guirong 2; Wang, Chengshu2,3,4
	2020-09
发表期刊	JOURNAL OF FUNGI
卷号	6 期号:3
发表状态	已发表
DOI	10.3390/jof6030134
摘要	Amid the genomic data explosion, phylogenomic analysis has resolved the tree of life of different organisms, including fungi. Genome-wide clustering has also been conducted based on gene content data that can lighten the issue of the unequal evolutionary rate of genes. In this study, using different fungal species as models, we performed phylogenomic and protein-content (PC)-based clustering analysis. The obtained sequence tree reflects the phylogenetic trajectory of examined fungal species. However, 15 PC-based trees constructed from the Pfam matrices of the whole genomes, four protein families, and ten subcellular locations largely failed to resolve the speciation relationship of cross-phylum fungal species. However, lifestyle and taxonomic associations were more or less evident between closely related fungal species from PC-based trees. Pairwise congruence tests indicated that a varied level of congruent or discordant relationships were observed between sequence- and PC-based trees, and among PC-based trees. It was intriguing to find that a few protein family and subcellular PC-based trees were more topologically similar to the phylogenomic tree than was the whole genome PC-based phylogeny. In particular, a most significant level of congruence was observed between sequence- and cell wall PC-based trees. Cophylogenetic analysis conducted in this study may benefit the prediction of the magnitude of evolutionary conservation, interactive associations, or networking between different family or subcellular proteins.
关键词	phylogenomics protein content phylogeny cophylogenetic analysis taxonomic association lifestyle association
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收录类别	SCI ; SCIE
语种	英语
资助项目	National Key R&D Programs of China[2018YFA0900502] ; Chinese Academy of Sciences[QYZDJ-SSW-SMC028]
WOS研究方向	Microbiology ; Mycology
WOS类目	Microbiology ; Mycology
WOS记录号	WOS:000580303000001
出版者	MDPI
引用统计
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/123935
专题	生命科学与技术学院_特聘教授组_王成树组
通讯作者	Wang, Chengshu
作者单位	1.Fudan Univ, Sch Comp Sci, Shanghai 200433, Peoples R China 2.Chinese Acad Sci, Shanghai Inst Plant Physiol & Ecol, CAS Ctr Excellence Mol Plant Sci, CAS Key Lab Insect Dev & Evolutionary Biol, Shanghai 200032, Peoples R China 3.Univ Chinese Acad Sci, CAS Ctr Excellence Biot interact, Beijing 100049, Peoples R China 4.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai 201210, Peoples R China
通讯作者单位	生命科学与技术学院
推荐引用方式 GB/T 7714	Xiao, Guohua,Tang, Guirong,Wang, Chengshu. Congruence Amidst Discordance between Sequence and Protein-Content Based Phylogenies of Fungi[J]. JOURNAL OF FUNGI,2020,6(3).
APA	Xiao, Guohua,Tang, Guirong,&Wang, Chengshu.(2020).Congruence Amidst Discordance between Sequence and Protein-Content Based Phylogenies of Fungi.JOURNAL OF FUNGI,6(3).
MLA	Xiao, Guohua,et al."Congruence Amidst Discordance between Sequence and Protein-Content Based Phylogenies of Fungi".JOURNAL OF FUNGI 6.3(2020).