CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes

Xu, Zhonghui; Hao, Bailin

doi:10.1093/nar/gkp278

Cited by 163 publications

(156 citation statements)

References 19 publications

(30 reference statements)

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“…Phylogenetic analysis. A phylogenetic tree based on the comparison of whole proteomes of G. margarita and various fungal genomes was constructed using CVTree v3 using the default parameters (Xu and Hao, 2009 Other bioinformatic techniques. Unless otherwise stated, further graphical outputs were generated with scripts as available in DESEQ2 package vignette (Love et al, 2013).…”

Section: Generation Of Data Bioinformatics and Phylogenetic Analysesmentioning

confidence: 99%

Symbiosis with an endobacterium increases the fitness of a mycorrhizal fungus, raising its bioenergetic potential

et al. 2015

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Arbuscular mycorrhizal fungi (AMF) occur in the rhizosphere and in plant tissues as obligate symbionts, having key roles in plant evolution and nutrition. AMF possess endobacteria, and genome sequencing of the endobacterium Candidatus Glomeribacter gigasporarum revealed a reduced genome and a dependence on the fungal host. To understand the effect of bacteria on fungal fitness, we used next-generation sequencing to analyse the transcriptional profile of Gigaspora margarita in the presence and in the absence of its endobacterium. Genomic data on AMF are limited; therefore, we first generated a gene catalogue for G. margarita. Transcriptome analysis revealed that the endobacterium has a stronger effect on the pre-symbiotic phase of the fungus. Coupling transcriptomics with cell biology and physiological approaches, we demonstrate that the bacterium increases the fungal sporulation success, raises the fungal bioenergetic capacity, increasing ATP production, and eliciting mechanisms to detoxify reactive oxygen species. By using TAT peptide to translocate the bioluminescent calcium reporter aequorin, we demonstrated that the line with endobacteria had a lower basal intracellular calcium concentration than the cured line. Lastly, the bacteria seem to enhance the fungal responsiveness to strigolactones, the plant molecules that AMF perceive as branching factors. Although the endobacterium exacts a nutritional cost on the AMF, endobacterial symbiosis improves the fungal ecological fitness by priming mitochondrial metabolic pathways and giving the AMF more tools to face environmental stresses. Thus, we hypothesise that, as described for the human microbiota, endobacteria may increase AMF innate immunity.

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Section: Generation Of Data Bioinformatics and Phylogenetic Analysesmentioning

confidence: 99%

Symbiosis with an endobacterium increases the fitness of a mycorrhizal fungus, raising its bioenergetic potential

et al. 2015

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“…GMR22 and 20 complete genome sequences of Streptomyces. Phylogeny tree was created using CV tree with a k-value of 6 (Xu and Hao, 2009) with Bacillus subtilis natto BEST195 as an outgroup and visualized with MEGA 6.06 (Tamura et al, 2013). Identification, annotation, and analysis of gene cluster involved in the biosynthesis of secondary metabolites and predictions core structure produced done by using antiSMASH 3.0.…”

Section: Analysis Of Whole Genome Phylogenetic Tree Of Gmr22mentioning

confidence: 99%

“…GMR22 and other 20 completed genomic sequences of Streptomyces. Phylogeny tree was created using CVtree with a k-value of 6 (Xu and Hao, 2009) with Bacillus subtilis natto BEST195 as an out-group and was visualized with MEGA 6.06 (Tamura et al, 2013). (Figures 2 and 3).…”

Section: Analysis Of Whole Genome Phylogenetic Tree Of Gmr22mentioning

confidence: 99%

SECONDARY BIOACTIVE METABOLITE GENE CLUSTERS IDENTIFICATION OF ANTICANDIDA-PRODUCING Streptomyces Sp. GMR22 ISOLATED FROM WANAGAMA FOREST AS REVEALED BY GENOME MINING APPROACH

Herdini

Miceli

Hariwiyanto

et al. 2017

Indonesian J. Pharm.

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Streptomyces are a group of Gram-positive bacteria belonging to the Actinobacteria class, which are among the most important bacteria for producing secondary bioactive metabolites such as antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. Recently, we have isolated the Streptomyces sp. GMR22 from Cajuput rhizospheric soil at Wanagama Forest, Indonesia. GMR22 produced a secondary metabolite that inhibited Candida albicans with IC 50 of 62.5μg/mL. The objective of this work was to reveal the novel secondary metabolites from GMR22 by genome mining approach. The antiSMASH 3.0 was used to predict gene clusters that encode the biosynthetic pathways of secondary metabolites in the genome of GMR22, and their core chemical structures. The phylogenomic analysis showed that GMR22 was closely related to Streptomyces bingchenggensis BCW1, as well as to the large genome size (9.5-12.7Mbp) groups of Streptomyces. AntiSMASH 3.0 analysis revealed that the genome of Streptomyces sp. GMR22 harbored at least 63 gene clusters that encode the biosynthetic pathways of secondary metabolites. It was the highest number of gene clusters had been observed among the members of Streptomyces groups, with polyketide synthetase (PKS) was predicted as the major groups of the identified gene cluster products. The results suggested that GMR22 could be a strong potential candidate for secondary bioactive metabolites source.

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“…Currently, the CV method has been applied to the phylogenetic study of viruses (Gao et al, 2003), chloroplasts (Chu et al, 2004), and prokaryotes . The CVTree server (Xu and Hao, 2009) that implements the method is available online (http://tlife.fudan.edu.cn/cvtree/), and we used its default settings. The trees generated using the 2 methods were displayed using Tree Explorer in Molecular Evolutionary Genetics Analysis 4 (Tamura et al, 2007).…”

Section: (Equation 1)mentioning

confidence: 99%

Co-evolution of genomic islands and their bacterial hosts revealed through phylogenetic analyses of 17 groups of homologous genomic islands

Guo¹,

Wu²,

Wang³

et al. 2012

Genet. Mol. Res.

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ABSTRACT. Horizontal gene transfer is an important mechanism for the evolution of microbial genomes, and many horizontal gene transfer events are facilitated by genomic islands (GIs). Until now, few reports have provided evidence for the co-evolution of horizontally transferred genes and their hosts. We obtained 17 groups of homologous GIs, all of which appear in 8 or more bacterial strains of the same species or genus. Using phylogenetic analyses, we found that the topological structure of a distance tree based on the proteins of each group of homologous GIs was consistent with that based on the complete proteomes of the hosts. This result clearly indicates that GIs and their bacterial hosts have co-evolved. In addition to presenting and providing evidence for a novel concept, i.e., the co-evolution of GIs and their bacterial hosts, we also describe a new and interesting detail for the phylogenetic analysis of horizontally transferred genes: consistent phylogenetic trees can be obtained by focusing on homologous GIs despite the commonly accepted theory that the phylogenies of horizontally transferred sequences and host organisms should be inconsistent.

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CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes

Cited by 163 publications

References 19 publications

Symbiosis with an endobacterium increases the fitness of a mycorrhizal fungus, raising its bioenergetic potential

Symbiosis with an endobacterium increases the fitness of a mycorrhizal fungus, raising its bioenergetic potential

SECONDARY BIOACTIVE METABOLITE GENE CLUSTERS IDENTIFICATION OF ANTICANDIDA-PRODUCING Streptomyces Sp. GMR22 ISOLATED FROM WANAGAMA FOREST AS REVEALED BY GENOME MINING APPROACH

Co-evolution of genomic islands and their bacterial hosts revealed through phylogenetic analyses of 17 groups of homologous genomic islands

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