scholarly journals Distinguishing Regional from Within-Codon Rate Heterogeneity in DNA Sequence Alignments

2009 ◽  
pp. 187-198
Author(s):  
Alexander V. Mantzaris ◽  
Dirk Husmeier
Keyword(s):  
Dna Sequence ◽  
Rate Heterogeneity ◽  
Sequence Alignments

scholarly journals Rice pseudomolecule-anchored cross-species DNA sequence alignments indicate regional genomic variation in expressed sequence conservation

BMC Genomics ◽  
2007 ◽  
Vol 8 (1) ◽  
pp. 283 ◽  
Author(s):  
Ian Armstead ◽  
Lin Huang ◽  
Julie King ◽  
Helen Ougham ◽  
Howard Thomas ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Sequence Conservation ◽  
Genomic Variation ◽  
Sequence Alignments ◽  
Expressed Sequence

Isolation and characterization of chitinases from Verticillium lecanii

2005 ◽  
Vol 51 (12) ◽  
pp. 1045-1055 ◽  
Author(s):  
Zhen-Xiang Lu ◽  
André Laroche ◽  
Hung Chang Huang
Keyword(s):  
Molecular Mass ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Verticillium Lecanii ◽  
Phylogenetic Groups ◽  
Sequence Alignments ◽  
Chitin Binding Domain ◽  
Isolation And Characterization ◽  
Fungal Chitinases

Degenerate PCR primers corresponding to conserved domains of fungal chitinases were designed, and PCR was performed on genomic DNA of the entomogenous fungus Verticillium lecanii (Zimmermann) Viegas. Two distinct PCR fragments, chf1 and chf2, were isolated and used to identify two DNA contigs. Analyses of these two contigs revealed that we had obtained the full-length DNA sequence including the promoter, 5′ untranslated region, open reading frame (ORF), and 3′ untranslated regions for two distinct chitinase-like genes. These two genomic DNA sequences exhibited 51% identity at the amino acid (aa) level and were designed as acidic (chi1) and basic (chi2) chitinase-like genes. The isolated cDNA for chi1 gene is 1110 bp with a predicted protein of 370 aa and molecular mass of 40.93 kDa, and its ORF was uninterrupted in its corresponding genomic DNA sequence. The cDNA for the chi2 gene is 1269 bp, a predicted ORF of 423 aa and molecular mass of 45.95 kDa. In contrast, the ORF was interrupted by three introns in its corresponding genomic DNA. The basic chitinase gene (chi2) was successfully expressed in the Pichia pastoris system; optimum enzymatic activity was observed at 22 °C and at pH 7.5. CHI1 and CHI2 were clustered into two different phylogenetic groups according to their sequence alignments with 28 other fungal chitinases. A chitin-binding domain, comprising two sub-domains that exhibit similarities at the aa level to chitin binding domains in bacteria, was identified in 30 fungal chitinase sequences examined.Key words: fungus, chitin, cloning, sequencing, transformation, Pichia sp. expression.

scholarly journals Plastid phylogenomics of the Gynoxoid group (Senecioneae, Asteraceae) highlights the importance of motif-based sequence alignment amid low genetic distances

2021 ◽  
Author(s):  
Belen Escobari ◽  
Thomas Borsch ◽  
Taylor S. Quedensley ◽  
Michael Gruenstaeudl
Keyword(s):  
Dna Sequence ◽  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Intergenic Spacer ◽  
Genetic Distances ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Plastid Genomes ◽  
Tree Inference ◽  
The Impact

ABSTRACTPREMISEThe genus Gynoxys and relatives form a species-rich lineage of Andean shrubs and trees with low genetic distances within the sunflower subtribe Tussilaginineae. Previous molecular phylogenetic investigations of the Tussilaginineae have included few, if any, representatives of this Gynoxoid group or reconstructed ambiguous patterns of relationships for it.METHODSWe sequenced complete plastid genomes of 21 species of the Gynoxoid group and related Tussilaginineae and conducted detailed comparisons of the phylogenetic relationships supported by the gene, intron, and intergenic spacer partitions of these genomes. We also evaluated the impact of manual, motif-based adjustments of automatic DNA sequence alignments on phylogenetic tree inference.RESULTSOur results indicate that the inclusion of all plastid genome partitions is needed to infer fully resolved phylogenetic trees of the Gynoxoid group. Whole plastome-based tree inference suggests that the genera Gynoxys and Nordenstamia are polyphyletic and form the core clade of the Gynoxoid group. This clade is sister to a clade of Aequatorium and Paragynoxys and also includes some but not all representatives of Paracalia.CONCLUSIONSThe concatenation and combined analysis of all plastid genome partitions and the construction of manually curated, motif-based DNA sequence alignments are found to be instrumental in the recovery of strongly supported relationships of the Gynoxoid group. We demonstrate that the correct assessment of homology in genome-level plastid sequence datasets is crucial for subsequent phylogeny reconstruction and that the manual post-processing of multiple sequence alignments improves the reliability of such reconstructions amid low genetic distances between taxa.

scholarly journals Capturing heterotachy through multi-gamma site models

2015 ◽  
Author(s):  
Remco Bouckaert ◽  
Peter Lockhart
Keyword(s):  
Sequence Data ◽  
Computational Cost ◽  
Realistic Model ◽  
Rate Variation ◽  
Specific Rate ◽  
Data Sets ◽  
Sequence Evolution ◽  
Rate Heterogeneity ◽  
Real World Data ◽  
Sequence Alignments

Most methods for performing a phylogenetic analysis based on sequence alignments of gene data assume that the mechanism of evolution is constant through time. It is recognised that some sites do evolve somewhat faster than others, and this can be captured using a (gamma) rate heterogeneity model. Further, some species have shorter replication times than others, and this results in faster rates of substitution in some lineages. This feature of lineage specific rate variation can be captured to some extent, by using relaxed clock models. However, it is also clear that there are additional poorly characterised features of sequence data that can sometimes lead to extreme differences in lineage specific rates. This variation is poorly captured by constant time reversible substitution models. The significance of extreme lineage specific rate differences is that they lead both to errors in reconstructing evolutionary relationships as well as biased estimates for the age of ancestral nodes. We propose a new model that allows gamma rate heterogeneity to change on branches, thus offering a more realistic model of sequence evolution. It adds negligible computational cost to likelihood calculations. We illustrate its effectiveness with an example of green algae and land-plants. For many real world data sets, we find a much better fit with multi-gamma sites models as well as substantial differences in ancestral node date estimates.

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