Cargando…

Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function

BACKGROUND: The analysis of synonymous and nonsynonymous rates of DNA change can help in the choice among competing explanations for rate variation, such as differences in constraint, mutation rate, or the strength of genetic drift. Nonphotosynthetic plants of the Orobanchaceae have increased rates...

Descripción completa

Detalles Bibliográficos
Autores principales: Young, Nelson D, dePamphilis, Claude W
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC554776/
https://www.ncbi.nlm.nih.gov/pubmed/15713237
http://dx.doi.org/10.1186/1471-2148-5-16
_version_ 1782122520222105600
author Young, Nelson D
dePamphilis, Claude W
author_facet Young, Nelson D
dePamphilis, Claude W
author_sort Young, Nelson D
collection PubMed
description BACKGROUND: The analysis of synonymous and nonsynonymous rates of DNA change can help in the choice among competing explanations for rate variation, such as differences in constraint, mutation rate, or the strength of genetic drift. Nonphotosynthetic plants of the Orobanchaceae have increased rates of DNA change. In this study 38 taxa of Orobanchaceae and relatives were used and 3 plastid genes were sequenced for each taxon. RESULTS: Phylogenetic reconstructions of relative rates of sequence evolution for three plastid genes (rbcL, matK and rps2) show significant rate heterogeneity among lineages and among genes. Many of the non-photosynthetic plants have increases in both synonymous and nonsynonymous rates, indicating that both (1) selection is relaxed, and (2) there has been a change in the rate at which mutations are entering the population in these species. However, rate increases are not always immediate upon loss of photosynthesis. Overall there is a poor correlation of synonymous and nonsynonymous rates. There is, however, a strong correlation of synonymous rates across the 3 genes studied and the lineage-speccific pattern for each gene is strikingly similar. This indicates that the causes of synonymous rate variation are affecting the whole plastid genome in a similar way. There is a weaker correlation across genes for nonsynonymous rates. Here the picture is more complex, as could be expected if there are many causes of variation, differing from taxon to taxon and gene to gene. CONCLUSIONS: The distinctive pattern of rate increases in Orobanchaceae has at least two causes. It is clear that there is a relaxation of constraint in many (though not all) non-photosynthetic lineages. However, there is also some force affecting synonymous sites as well. At this point, it is not possible to tell whether it is generation time, speciation rate, mutation rate, DNA repair efficiency or some combination of these factors.
format Text
id pubmed-554776
institution National Center for Biotechnology Information
language English
publishDate 2005
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-5547762005-03-18 Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function Young, Nelson D dePamphilis, Claude W BMC Evol Biol Research Article BACKGROUND: The analysis of synonymous and nonsynonymous rates of DNA change can help in the choice among competing explanations for rate variation, such as differences in constraint, mutation rate, or the strength of genetic drift. Nonphotosynthetic plants of the Orobanchaceae have increased rates of DNA change. In this study 38 taxa of Orobanchaceae and relatives were used and 3 plastid genes were sequenced for each taxon. RESULTS: Phylogenetic reconstructions of relative rates of sequence evolution for three plastid genes (rbcL, matK and rps2) show significant rate heterogeneity among lineages and among genes. Many of the non-photosynthetic plants have increases in both synonymous and nonsynonymous rates, indicating that both (1) selection is relaxed, and (2) there has been a change in the rate at which mutations are entering the population in these species. However, rate increases are not always immediate upon loss of photosynthesis. Overall there is a poor correlation of synonymous and nonsynonymous rates. There is, however, a strong correlation of synonymous rates across the 3 genes studied and the lineage-speccific pattern for each gene is strikingly similar. This indicates that the causes of synonymous rate variation are affecting the whole plastid genome in a similar way. There is a weaker correlation across genes for nonsynonymous rates. Here the picture is more complex, as could be expected if there are many causes of variation, differing from taxon to taxon and gene to gene. CONCLUSIONS: The distinctive pattern of rate increases in Orobanchaceae has at least two causes. It is clear that there is a relaxation of constraint in many (though not all) non-photosynthetic lineages. However, there is also some force affecting synonymous sites as well. At this point, it is not possible to tell whether it is generation time, speciation rate, mutation rate, DNA repair efficiency or some combination of these factors. BioMed Central 2005-02-15 /pmc/articles/PMC554776/ /pubmed/15713237 http://dx.doi.org/10.1186/1471-2148-5-16 Text en Copyright © 2005 Young and dePamphilis; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Young, Nelson D
dePamphilis, Claude W
Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function
title Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function
title_full Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function
title_fullStr Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function
title_full_unstemmed Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function
title_short Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function
title_sort rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC554776/
https://www.ncbi.nlm.nih.gov/pubmed/15713237
http://dx.doi.org/10.1186/1471-2148-5-16
work_keys_str_mv AT youngnelsond ratevariationinparasiticplantscorrelatedanduncorrelatedpatternsamongplastidgenesofdifferentfunction
AT depamphilisclaudew ratevariationinparasiticplantscorrelatedanduncorrelatedpatternsamongplastidgenesofdifferentfunction