Genome-wide investigation reveals high evolutionary rates in annual model plants

Jia-Xing Yue; Jinpeng Li; Dan Wang; Araki, Hitoshi; Dacheng Tian; Sihai Yang
January 2010
BMC Plant Biology;2010, Vol. 10, p242
Academic Journal
Background: Rates of molecular evolution vary widely among species. While significant deviations from molecular clock have been found in many taxa, effects of life histories on molecular evolution are not fully understood. In plants, annual/perennial life history traits have long been suspected to influence the evolutionary rates at the molecular level. To date, however, the number of genes investigated on this subject is limited and the conclusions are mixed. To evaluate the possible heterogeneity in evolutionary rates between annual and perennial plants at the genomic level, we investigated 85 nuclear housekeeping genes, 10 non-housekeeping families, and 34 chloroplast genes using the genomic data from model plants including Arabidopsis thaliana and Medicago truncatula for annuals and grape (Vitis vinifera) and popular (Populus trichocarpa) for perennials. Results: According to the cross-comparisons among the four species, 74-82% of the nuclear genes and 71-97% of the chloroplast genes suggested higher rates of molecular evolution in the two annuals than those in the two perennials. The significant heterogeneity in evolutionary rate between annuals and perennials was consistently found both in nonsynonymous sites and synonymous sites. While a linear correlation of evolutionary rates in orthologous genes between species was observed in nonsynonymous sites, the correlation was weak or invisible in synonymous sites. This tendency was clearer in nuclear genes than in chloroplast genes, in which the overall evolutionary rate was small. The slope of the regression line was consistently lower than unity, further confirming the higher evolutionary rate in annuals at the genomic level. Conclusions: The higher evolutionary rate in annuals than in perennials appears to be a universal phenomenon both in nuclear and chloroplast genomes in the four dicot model plants we investigated. Therefore, such heterogeneity in evolutionary rate should result from factors that have genome-wide influence, most likely those associated with annual/perennial life history. Although we acknowledge current limitations of this kind of study, mainly due to a small sample size available and a distant taxonomic relationship of the model organisms, our results indicate that the genome-wide survey is a promising approach toward further understanding of the mechanism determining the molecular evolutionary rate at the genomic level.


Related Articles

  • Developing a method for customized induction of flowering. Chin Chin Yeoh; Balcerowicz, Martin; Laurie, Rebecca; Macknight, Richard; Putterill, Joanna // BMC Biotechnology;2011, Vol. 11 Issue 1, p36 

    Background: The ability to induce flowering on demand is of significant biotechnological interest. FT protein has been recently identified as an important component of the mobile flowering hormone, florigen, whose function is conserved across the plant kingdom. We therefore focused on...

  • Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana. Yan, H. H.; Mudge, J.; Kim, D.-J.; Larsen, D.; Shoemaker, R. C.; Cook, D. R.; Young, N. D. // Theoretical & Applied Genetics;May2003, Vol. 106 Issue 7, p1256 

    A growing body of research indicates that microsynteny is common among dicot genomes. However, most studies focus on just one or a few genomic regions, so the extent of microsynteny across entire genomes remains poorly characterized. To estimate the level of microsynteny between Medicago...

  • The ELF4 gene controls circadian rhythms and flowering time in Arabidopsis thaliana. Doyle, Mark R.; Davis, Seth J.; Bastow, Ruth M.; McWatters, Harriet G.; Kozma-Bognár, László; Nagy, Ferenc; Millar, Andrew J.; Amasino, Richard M. // Nature;9/5/2002, Vol. 419 Issue 6902, p74 

    Describes the early flowering 4 (ELF4) gene and its role in the control of the circadian rhythm and flowering time of the Arabidopsis thaliana. Promotion of clock accuracy and sustained rhythms in the absence of daily light/dark cycles; Function of the circadian clock associated 1 gene expressed...

  • Light responses of a plastic plant. Millar, Andrew J. // Nature Genetics;Dec2001, Vol. 29 Issue 4, p357 

    Arabidopsis thaliana isolates from the wild vary enormously in their morphology and physiological responses to standard conditions, indicating that substantial genetic variation is accessible in this species. Natural variant alleles encoding two Arabidopsis photoreceptors, phytochrome A and...

  • Plant genetics: a decade of integration. Pruitt, Robert E.; Bowman, John L.; Grossniklaus, Ueli // Nature Genetics;Mar2003 Supplement, Vol. 33, p294 

    The last decade provided the plant science community with the complete genome sequence of Arabidopsis thaliana and rice, tools to investigate the function of potentially every plant gene, methods to dissect virtually any aspect of the plant life cycle, and a wealth of information on gene...

  • Heterogeneous Selection at Specific Loci in Natural Environments in Arabidopsis thaliana. Weinig, Cynthia; Dorn, Lisa A.; Kane, Nolan C.; German, Zachary M.; Halldorsdottir, Solveig S.; Ungerer, Mark C.; Toyonaga, Yuko; Mackay, Trudy F.c.; Purugganan, Michael D.; Schmitt, Johanna // Genetics;Sep2003, Vol. 165 Issue 1, p321 

    Reports that selection on quantitative trait loci (QTL) for fitness traits in the model plant species Arabidopsis thaliana differs among natural ecological settings and genetic backgrounds. Suggestion that the allelic fitness effects of two QTL reversed direction depending on the genotype at...

  • Genetic Architecture of Plastic Methyl Jasmonate Responses in Arabidopsis thaliana. Kliebenstein, Daniel J.; Figuth, Antje; Mitchell-Olds, Thomas // Genetics;Aug2002, Vol. 161 Issue 4, p1685 

    Examines the genetic architecture of plastic methyl jasmonate (MeJa) responses in Arabidopsis thaliana. Analysis of MeJa and salicylic acid cross-talk in glucosinolate regulation; Implications for glucosinolate physiology and functional understanding of Arabidopsis MeJa signal transduction.

  • Genetic variation within and among populations of Arabidopsis thaliana. Bergelson, Joy; Stahl, Eli; Dudek, Scott; Kreitman, Martin // Genetics;Mar98, Vol. 148 Issue 3, p1311 

    Presents a study which examined the genetic variation of Arabidopsis thaliana. Examination of the levels of nucleotide polymorphism within Arabidopsis thaliana; Method employed in this study; Results of this study.

  • Transcriptional profiling of Medicago truncatula meristematic root cells. Holmes, Peta; Goffard, Nicolas; Weiller, Georg F.; Rolfe, Barry G.; Imin, Nijat // BMC Plant Biology;2008, Vol. 8, Special section p1 

    Background: The root apical meristem of crop and model legume Medicago truncatula is a significantly different stem cell system to that of the widely studied model plant species Arabidopsis thaliana. In this study we used the Affymetrix Medicago GeneChip® to compare the transcriptomes of...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics