Phylogenetic inference from conserved sites alignments

Grundy, William Noble; Naylor, Gavin J. P.

doi:10.1002/(sici)1097-010x(19990815)285:2<128::aid-jez5>3.0.co;2-c

Cited by 20 publications

(5 citation statements)

References 31 publications

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“…An often-debated issue in the phylogenetics community is whether the removal of ambiguous regions in sequence alignments actually leads to more accurate trees [4], [27], [29], [32], [43]. We demonstrate here that masking by ZORRO significantly improved the tree accuracy as long as the sequences are sufficiently long and divergent.…”

Section: Discussionmentioning

confidence: 73%

“…Knowing the quality of the individual position is important as “poorly” aligned columns are more likely to contribute noise than signal. Detecting and removing ambiguously aligned regions, a step known as masking and trimming in molecular phylogenetics, increases the signal-to-noise ratio and improves the discriminatory power of phylogenetic methods [27], [28], [29]. Traditionally, masking and trimming of regions thought to be poorly aligned were done as part of manual curation process.…”

Section: Introductionmentioning

confidence: 99%

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Accounting For Alignment Uncertainty in Phylogenomics

2012

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Uncertainty in multiple sequence alignments has a large impact on phylogenetic analyses. Little has been done to evaluate the quality of individual positions in protein sequence alignments, which directly impact the accuracy of phylogenetic trees. Here we describe ZORRO, a probabilistic masking program that accounts for alignment uncertainty by assigning confidence scores to each alignment position. Using the BALIBASE database and in simulation studies, we demonstrate that masking by ZORRO significantly reduces the alignment uncertainty and improves the tree accuracy.

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Section: Discussionmentioning

confidence: 73%

Section: Introductionmentioning

confidence: 99%

Accounting For Alignment Uncertainty in Phylogenomics

2012

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“…Evolutionary relationship between pedigree and ancestor based on conserved and variable regions in sequences of genes. But accurate phylogenetic analysis depends upon highly-conserved and motif regions of molecular sequence ( Grundy and Naylor, 1999 ). Higher variable regions in 16S rRNA lead to inconsistency and lesser discrimination between species of different bacteria.…”

Section: Discussionmentioning

confidence: 99%

Pseudomonas spp. Mediate defense response in sugarcane through differential exudation of root phenolics

Shair

Yasmin

Hassan

et al. 2021

Saudi Journal of Biological Sciences

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Pseudomonas spp., a ubiquitous biocontrol agent, protects the plants from phytopathogens by suppressing them directly by reinforcing the plant’s intrinsic defense mechanism. Root exudated phenolics play an important role in establishing the rhizobacteria population and cross the host boundaries in beneficial plant–microbe interaction. In this study, Pseudomonas spp. HU-8 & HU-9 antagonized the sugarcane red rot pathogen ( C. falcatum ) and showed a positive chemotactic response against different concentrations (10–30 µM) of synthetic phenolic acids like p -coumaric, vanillic, and 3,4 di-hydroxybenzoic acid. In a pot experiment, they effectively colonized the sugarcane rhizosphere and mediated defense response in sugarcane plants challenged with red rot pathogen C. falcatum by regulating the exudation of root phenolics under hydroponic conditions. They significantly induced the activity of the antioxidant enzymes CAT (1.24–1.64 fold), PO (0.78–1.61 fold), PAL (0.77–0.97 fold), and PPO (3.67–3.73 fold) over untreated plants in sugarcane. They also induced the total phenolic contents (TPC) in sugarcane in the presence (6.56–10.29 mg/g GAE) and absence (2.89–4.16 mg/g GAE) of the pathogen quantified through the Folin-Ciocalteu (FC) method. However, their effect was lower than that of the pathogen (4.34–8 mg/g GAE). The Pseudomonas spp. significantly colonized the sugarcane rhizosphere by maintaining a cell population of (1.0E + 07–1.3E + 08 CFU/mL). A significant positive Pearson’s correlation was observed between the root exudated total phenolic contents, antioxidant enzymatic activities, and rhizospheric population of inoculated bacteria. The 16S rRNA and rpoD gene analysis showed sequence conservation (C: 0.707), average number of nucleotide differences (k: 199.816), nucleotide diversity, (Pi): 0.09819), average number of informative nucleotide sites per site (Psi: 0.01275), GC content (0.57), and polymorphic sites (n = 656). These diverse Pseudomonas spp. could be an ideal bio-inoculants for a broad range of hosts especially graminaceous crops.

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“…In a multiple sequence alignment, there are historical signals, such as the number of nucleotide substitutions, that are typically proportional to the divergence time, and non-historical signals that are typically not proportional to the divergence time [ 1 ]. Non-historical signals include compositional bias [ 2 , 3 , 4 ] and conflicting signals between codons and amino acids (AAs) [ 2 , 3 , 5 , 6 ].…”

Section: Introductionmentioning

confidence: 99%

Improving Phylogenetic Signals of Mitochondrial Genes Using a New Method of Codon Degeneration

Xia

2020

Life

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Recovering deep phylogeny is challenging with animal mitochondrial genes because of their rapid evolution. Codon degeneration decreases the phylogenetic noise and bias by aiming to achieve two objectives: (1) alleviate the bias associated with nucleotide composition, which may lead to homoplasy and long-branch attraction, and (2) reduce differences in the phylogenetic results between nucleotide-based and amino acid (AA)-based analyses. The discrepancy between nucleotide-based analysis and AA-based analysis is partially caused by some synonymous codons that differ more from each other at the nucleotide level than from some nonsynonymous codons, e.g., Leu codon TTR in the standard genetic code is more similar to Phe codon TTY than to synonymous CTN codons. Thus, nucleotide similarity conflicts with AA similarity. There are many such examples involving other codon families in various mitochondrial genetic codes. Proper codon degeneration will make synonymous codons more similar to each other at the nucleotide level than they are to nonsynonymous codons. Here, I illustrate a “principled” codon degeneration method that achieves these objectives. The method was applied to resolving the mammalian basal lineage and phylogenetic position of rheas among ratites. The codon degeneration method was implemented in the user-friendly and freely available DAMBE software for all known genetic codes (genetic codes 1 to 33).

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Phylogenetic inference from conserved sites alignments

Abstract: Includes 8 figures and 3 tables.

Cited by 20 publications

References 31 publications

Accounting For Alignment Uncertainty in Phylogenomics

Accounting For Alignment Uncertainty in Phylogenomics

Pseudomonas spp. Mediate defense response in sugarcane through differential exudation of root phenolics

Improving Phylogenetic Signals of Mitochondrial Genes Using a New Method of Codon Degeneration

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