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Comparative Analysis of the Receptor-Like Kinase Family in Arabidopsis and Rice
It is found that rice (Oryza sativa) has nearly twice as many RLK/Pelle members as Arabidopsis does, and it is not simply a consequence of a larger predicted gene number in rice. Expand
Uncovering Small RNA-Mediated Responses to Phosphate Deficiency in Arabidopsis by Deep Sequencing1[W][OA]
Deep sequencing of Arabidopsis small RNAs revealed an increased abundance of TAS4-derived trans-acting small interfering RNAs (ta-siRNAs) in Pi-deficient shoots and uncovered an autoregulatory mechanism of PAP1/MYB75 via miR828 and Tas4-siR81(−) that regulates the biosynthesis of anthocyanin. Expand
Fundamentals of molecular evolution
Introduction Genes, Genetic Codes, and Mutation Dynamics of Genes in Populations Evolutionary Change in Nucleotide Sequences Rates and Patterns of Nucleotide Substitution Molecular Phylogenetics GeneExpand
Rates of Nucleotide Substitution in Angiosperm Mitochondrial DNA Sequences and Dates of Divergence Between Brassica and Other Angiosperm Lineages
Abstract. We obtained 16 nucleotide sequences (∼1400 bp each) of the first intron of the mitochondrial (mt) gene for NADH subunit 4 (nad4) from 10 species of Brassicaceae. Using these new sequencesExpand
Unbiased estimation of the rates of synonymous and nonsynonymous substitution
A new method that gives unbiased estimates is proposed and an application of the new and the old method to 14 pairs of mouse and rat genes shows that the new method gives aKS value very close to the number of substitutions per fourfold degenerate site whereas the oldmethod gives a value 30% higher. Expand
Role of duplicate genes in genetic robustness against null mutations
A genome-wide evaluation of the role of duplicate genes in genetic robustness against null mutations shows that there is a significantly higher probability of functional compensation for a duplicate gene than for a singleton, a high correlation between the frequency of compensation and the sequence similarity of two duplicates, and a higher probability for a severe fitness effect when the duplicate copy that is more highly expressed is deleted. Expand
An evolutionary perspective on synonymous codon usage in unicellular organisms
Observed patterns of synonymous codon usage are explained in terms of the joint effects of mutation, selection, and random drift, and a measure of directional synonymous-codon usage bias, the Codon Adaptation Index, has been developed. Expand
Dating the Monocot–Dicot Divergence and the Origin of Core Eudicots Using Whole Chloroplast Genomes
It is proposed that monocots branched off from dicots 140–150 Myr ago, at least 50 Myr younger than previous estimates based on the molecular clock hypothesis, and that the core eudicots diverged 100–115 Myr ago (Albian–Aptian of the Cretaceous). Expand
Mutation rates differ among regions of the mammalian genome
It is proposed that the differences arising because mutation patterns vary with the timing of replication of different chromosomal regions in the germline can account for both the origin of isochores in mammalian genomes and the observation that silent nucleotide substitutions in different mammalian genes do not have the same molecular clock. Expand
Low nucleotide diversity in chimpanzees and bonobos.
This study sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees and found that the pi value for bonobos is only 0.078%, even somewhat lower than that for humans for the same 50 segments, which is puzzling. Expand