A novel phylogenetic tree based on the presence of protein domains in selected actinobacteria

Sarkar, Indrani; Gtari, Maher; Tisa, Louis S.; Sen, Arnab

doi:10.1007/s10482-018-1154-1

Cited by 8 publications

(9 citation statements)

References 22 publications

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“…In particular, the basidiomycete human pathogen C. neoformans (CNE) could even be grouped with the ascomycete human pathogen C. immitis (CIM) and its close relative Uncinocarpus reesii (URE) [ 29 ] in nuclear and mitochondrial PC-based trees ( Figure S2 ). Overall, similar to the observation in bacteria [ 30 ], PC-based phylogenies usually grouped fungi according to fungal lifestyles rather than their evolutionary relationships. However, considering that the closely related species SSC and BCI, CIM and URE, and even the yeast species are not always clustered together in different trees, the results also implicated that the species grouped in the same lineage do not always have more similar PC distributions than for species in different branches.…”

Section: Resultssupporting

confidence: 78%

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

Xiao

Tang

Wang

2020

JoF

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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.

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Section: Resultssupporting

confidence: 78%

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

Xiao

Tang

Wang

2020

JoF

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“…In the first statistic model, it records the domain content in a species [5, 6]. As shown in Figure 1, the species contains four proteins, each of which consists of more than one domain.…”

Section: Methodsmentioning

confidence: 99%

Taxonomy Analysis in Bacterial Kingdom based on Protein Domain: A Comparison Study

Wang¹,

Zhou

Yuan³

et al. 2021

Preprint

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It is important to conduct taxonomy research on the bacteria kingdom for deeper understanding, which can utilize the conserved genes, 16s rRNA, protein domain, and so on. Among them, the methods based on the protein domain has a direct relationship with phenotype. However, these methods still lack analysis of their biological significance, models evaluation and the comparison of taxonomy results. To this end, we propose a complete framework to standardize the process for taxonomy problem based on the protein functional domain. By applying it to bacteria kingdom and comparing the results with the NCBI taxonomy, we point out the most appropriate method in each step of the framework and evaluate models according to the biological significance. Finally, taxonomy suggestions and recommendations are proposed based on the phylogenetic tree generated by the framework with the most appropriate combination.

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“…Comparatively, the protein sequence can mask some gene-level differences for the reason that the same amino acid could be translated from different codons (Baldauf, Roger et al 2000, Brown, James et al 2001). Furthermore, the protein domain, as the basic functional unit of protein, is a bridge that can directly connect genetic information with phenotypes (Yang, Doolittle et al 2005, Kaoru, Fukami-Kobayashi et al 2007, Sarkar, Gtari et al 2019). It is inferred from a given sequence of amino acids, the length of which is usually between 50 to 350.…”

Section: Introductionmentioning

confidence: 99%

A Standardized Framework for Taxonomy Analysis in Bacterial Kingdom based on Protein Domain

Wang

Zhou

Yuan

et al. 2022

Preprint

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The taxonomy research on the bacterial kingdom is important and can be usually conducted by the analysis on conserved genes, 16s rRNA, protein domain, and so on. Comparatively, the protein domains maintain a most direct relationship with phenotypes. In this paper, based on the protein domain, we propose a 3-step framework to standardize the classification process of bacteria. Different model candidates are involved and discussed in each step. By comparing the classification results with existing taxonomy, we select the most appropriate candidate to improve the framework, and furthermore, discuss their biological significance. Finally, we put forward taxonomy suggestions based on the best classification results.

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A novel phylogenetic tree based on the presence of protein domains in selected actinobacteria

Cited by 8 publications

References 22 publications

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

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

Taxonomy Analysis in Bacterial Kingdom based on Protein Domain: A Comparison Study

A Standardized Framework for Taxonomy Analysis in Bacterial Kingdom based on Protein Domain

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