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United States Department of Agriculture

Agricultural Research Service

Title: Chloroplast Sequence Evolution: a New Pattern of Nucleotide Substitutions in the Cucurbitaceae

Authors
item Decker-Walters, Deena - THE CUCURBIT NETWORK FL
item Chung, Sang-Min - UNIV OF WI MADISON
item Staub, Jack

Submitted to: Journal of Molecular Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 15, 2004
Publication Date: June 5, 2004
Citation: Decker-Walters, D., Chung, S., Staub, J.E. 2004. Chloroplast sequence evolution: a new pattern of nucleotide substitutions in the cucurbitaceae. Journal of Molecular Evolution. 58:606-614.

Interpretive Summary: The substance DNA is in the cells of all living organisms and controls how organisms function. Genes are made up of DNA and genes are located on chromosomes which are part of the nucleus (center) of every cell. DNA is composed of nucleic acids that are in four basic classes and are designated A (adenine), T (thymine), C (cytosine), and G (guanine). The nucleic acids are arranged in different orders or sequences to form genes. It is important to know the order of these nucleic acids because of their importance in heredity (how genes are passed on from generation to generation). Genes can mutate or change their nucleotide sequence and such changes can be positive (improve the organism), neutral (have no effect on the organism), or negative (cause the organism to be less efficient). It is important to know how these changes take place in order to understand why plants change form through mutation. Thus, and experiment was conducted determine the type and frequency of mutation in plants using various plant species in the family Cucurbitaceae, some of which have economic importance such as cucumber and melon. Data indicate that most of plant species examined have the same types of mutations. This means that they were afected by the same evolutionary mechanisms that caused the mutations that were observed in the DNA of these species. This information will help plant geneticists better understand why plant forms are different so that plant species such as cucumber and melon can be modified more efficiently through plant breeding. This increase in efficiency will eventually allow for more effective development of cultivars with improved economically important traits to improve the U.S. grower's competitive advantage in the worldwide market place.

Technical Abstract: Nucleotide substitutions (i.e., point mutations) are the primary driving force in generating DNA variation upon which selection can act. Substitutions called transitions, which entail exchanges between purines (A=adenine, G=guanine) or pyrimidines (C=cytosine, T=thymine), typically outnumber transversions (e.g., exchanges between a purine and a pyrimidine) in a DNA strand. With an increasing number of plant studies revealing a transversion rather than transition bias, we chose to perform a detailed substitution analysis for the plant family Cucurbitaceae. We generated a phylogenetic tree for 19 taxa of the tribe Benincaseae and related genera and then scored conservative substitution changes (e.g., those not exhibiting convergences or reversals) from the unambiguous branches of the tree. Neither the transition or (A+T)/(G+C) biases found in previous studies were supported by our overall data. More importantly, we found a novel and symmetrical substitution bias in which Gs had been preferentially replaced by A, As by C, Cs by T, and Ts by G, resulting in the G'A'C'T'G substitution series. Understanding this pattern will lead to new hypotheses concerning cpDNA evolution, which in turn will affect the choices of substitution models and other tree-building algorithms for phylogenetic analyses based on nucleotide data.

Last Modified: 4/21/2014
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