Multilocus phylogenetic analysis with gene tree clustering

Yoshida, Ruriko; Fukumizu, Kenji; Vogiatzis, Chrysafis

doi:10.1007/s10479-017-2456-9

Cited by 12 publications

(11 citation statements)

References 58 publications

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“…Multiples alignments of the sequences were estimated using Muscle algorithm in MEGA v.7 and adjusted manually when necessary. For multilocus analysis, the loci were concatenated by the use of Sequence Matrix v.1.8 [43, 44]. The sequences’ access codes of deposit on GenBank are in Table 2.…”

Section: Resultsmentioning

confidence: 99%

Biodiversity and phylogeny of novel Trichoderma isolates from mangrove sediments and potential of biocontrol against Fusarium strains

et al. 2019

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Background: Studies carried out with novel 13 strains of Trichoderma, isolated from mangrove sediments (PE, Brazil) using morphophysiological and molecular characterization, followed evaluation of biocontrol using Fusarium strains isolated from Caatinga soil (PE, Brazil). Trichoderma strains were characterized by polyphasic taxonomic approach, and the extracted DNA was amplified with primers ITS 1 and 4, and sequenced. The biocontrol evaluation was conducted at 24 and 48 h of growth intervals by Tukey test, with a significance of 5%. Antibiosis tests were assessed in vitro by dual plate and partition plate techniques against Fusarium strains. Results: Trichoderma molecular identification, sequences of 500 bp were amplified, deposited into GenBank, and used for phylogenetic analyses. The strains were identified as T. asperellum (10), as T. harzianum (2) and one as T. longibrachiatum. Growth rate presented an average of 0.1207 cm h −1 for Trichoderma and lower growth rate of 0.031 cm h −1 for Fusarium spp., respectively. Antibiosis tests presented the best antagonist level of efficiency for T. asperellum UCP 0149 against F. solani UCP 1395 (82.2%) and F. solani UCP 1075 (70.0%), followed by T. asperellum UCP 0319 against F. solani UCP1083 (73.4%) and T. asperellum UCP 0168 against F. solani UCP1098 (71.5%), respectively. Conclusions: The data obtained in this study as tool for identification of novel Trichoderma strains serve as basis for development of several sustainable use for biotechnological processes. Those Trichoderma strains found promising for the management antagonistic potential and interaction could aid the conduct of biotechnological biocontrol of contaminants, and improve environmental conditions for the health of plants.

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Section: Resultsmentioning

confidence: 99%

Biodiversity and phylogeny of novel Trichoderma isolates from mangrove sediments and potential of biocontrol against Fusarium strains

et al. 2019

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“…Furthermore, Latimeria chalumnae appears as sister to ray-finned fish (Actinopterygii). For decades, the phylogenetic position of Latimeria was subject to debate, but recent studies provide evidence for a closer relationship of Latimeria to tetrapods (Takezaki and Nishihara, 2016; Yoshida et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

The Orphan Cytokine Receptor CRLF3 Emerged With the Origin of the Nervous System and Is a Neuroprotective Erythropoietin Receptor in Locusts

Hahn

Büschgens

Schwedhelm-Domeyer

et al. 2019

Front. Mol. Neurosci.

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The orphan cytokine receptor-like factor 3 (CRLF3) was identified as a neuroprotective erythropoietin receptor in locust neurons and emerged with the evolution of the eumetazoan nervous system. Human CRLF3 belongs to class I helical cytokine receptors that mediate pleiotropic cellular reactions to injury and diverse physiological challenges. It is expressed in various tissues including the central nervous system but its ligand remains unidentified. A CRLF3 ortholog in the holometabolous beetle Tribolium castaneum was recently shown to induce anti-apoptotic mechanisms upon stimulation with human recombinant erythropoietin. To test the hypothesis that CRLF3 represents an ancient cell-protective receptor for erythropoietin-like cytokines, we investigated its presence across metazoan species. Furthermore, we examined CRLF3 expression and function in the hemimetabolous insect Locusta migratoria. Phylogenetic analysis of CRLF3 sequences indicated that CRLF3 is absent in Porifera, Placozoa and Ctenophora, all lacking the traditional nervous system. However, it is present in all major eumetazoan groups ranging from cnidarians over protostomians to mammals. The CRLF3 sequence is highly conserved and abundant amongst vertebrates. In contrast, relatively few invertebrates express CRLF3 and these sequences show greater variability, suggesting frequent loss due to low functional importance. In L. migratoria, we identified the transcript Lm-crlf3 by RACE-PCR and detected its expression in locust brain, skeletal muscle and hemocytes. These findings correspond to the ubiquitous expression of crlf3 in mammalian tissues. We demonstrate that the sole addition of double-stranded RNA to the culture medium (called soaking RNA interference) specifically interferes with protein expression in locust primary brain cell cultures. This technique was used to knock down Lm-crlf3 expression and to abolish its physiological function. We confirmed that recombinant human erythropoietin rescues locust brain neurons from hypoxia-induced apoptosis and showed that this neuroprotective effect is absent after knocking down Lm-crlf3. Our results affirm the erythropoietin-induced neuroprotective function of CRLF3 in a second insect species from a different taxonomic group. They suggest that the phylogenetically conserved CRLF3 receptor may function as a cell protective receptor for erythropoietin or a structurally related cytokine also in other animals including vertebrate and mammalian species.

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“…where Depth is the depth of the species tree, Population Size is the effective population size (N e ) and C is a parameter, which we varied from 0.6 to 6.0 as in [45], [46].…”

Section: Simulationsmentioning

confidence: 99%

CURatio: Genome-Wide Phylogenomic Analysis Method Using Ratios of Total Branch Lengths

Kang

Moore

Schardl

et al. 2020

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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Evolutionary hypotheses provide important underpinnings of biological and medical sciences, and comprehensive, genome-wide understanding of evolutionary relationships among organisms are needed to test and refine such hypotheses. Theory and empirical evidence clearly indicate that phylogenies (trees) of different genes (loci) should not display precisely matching topologies. The main reason for such phylogenetic incongruence is reticulated evolutionary history of most species due to meiotic sexual recombination in eukaryotes, or horizontal transfers of genetic material in prokaryotes. Nevertheless, many genes should display topologically related phylogenies, and should group into one or more (for genetic hybrids) clusters in poly-dimensional "tree space". Unusual evolutionary histories or effects of selection may result in "outlier" genes with phylogenies that fall outside the main distribution(s) of trees in tree space. We present a new phylogenomic method, CURatio, which uses ratios of total branch lengths in gene trees to help identify phylogenetic outliers in a given set of ortholog groups from multiple genomes. An advantage of CURatio over other methods is that genes absent from and/or duplicated in some genomes can be included in the analysis. We conducted a simulation study under the coalescent model, and showed that, given sufficient species depth and topological difference, these ratios are significantly higher for the "outlier" gene phylogenies. Also, we applied CURatio to a set of annotated genomes of the fungal family, Clavicipitaceae, and identified alkaloid biosynthesis genes as outliers, probably due to a history of duplication and loss.

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Multilocus phylogenetic analysis with gene tree clustering

Cited by 12 publications

References 58 publications

Biodiversity and phylogeny of novel Trichoderma isolates from mangrove sediments and potential of biocontrol against Fusarium strains

Biodiversity and phylogeny of novel Trichoderma isolates from mangrove sediments and potential of biocontrol against Fusarium strains

The Orphan Cytokine Receptor CRLF3 Emerged With the Origin of the Nervous System and Is a Neuroprotective Erythropoietin Receptor in Locusts

CURatio: Genome-Wide Phylogenomic Analysis Method Using Ratios of Total Branch Lengths

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