Skip to main content
Log in

Expression Patterns of Duplicate Genes in the Developing Root in Arabidopsis thaliana

  • Published:
Journal of Molecular Evolution Aims and scope Submit manuscript

Abstract

Data on gene expression in the development of the root in Arabidopsis thaliana were used to test for expression profile differences among multi-gene families and to examine the extent to which expression differences accompanied coding sequences divergence within families. Significant differences among families were observed on two principal axes, accounting for over 80% of the variance in the expression data. The number of synonymous nucleotide substitutions per synonymous site (d S ) and the number of nonsynonymous nucleotide substitutions per nonsynonymous site (d N ) were estimated between the members of two-member families (N = 428) and between phylogenetically independent sister pairs (N = 190) of sequences within larger families. Ribosomal proteins and a few other proteins were exceptional in showing highly divergent expression patterns in spite of very low levels of amino acid sequence divergence, as indicated by the low d N relative to d S . However, the majority of gene duplicates showed relatively high levels of amino acid sequence divergence without appreciable change in expression pattern in the cell types analyzed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5

Similar content being viewed by others

References

  • SF Altschul TL Madden AA Schäffer J Zhang Z Zhang W Miller DJ Lipman (1997) ArticleTitleGapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 25 3389–3402 Occurrence Handle1:CAS:528:DyaK2sXlvFyhu7w%3D Occurrence Handle9254694

    CAS  PubMed  Google Scholar 

  • K Birnbaum DE Shasha JY Wang JW Jung GM Lambert DW Galbraith PN Benfrey (2003) ArticleTitleA gene expression map of the Arabidopsis root Science 302 1956–1960 Occurrence Handle10.1126/science.1090022 Occurrence Handle1:CAS:528:DC%2BD3sXps1ams7k%3D Occurrence Handle14671301

    Article  CAS  PubMed  Google Scholar 

  • G Blanc K Wolfe (2004) ArticleTitleFunctional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution Plant Cell 16 1679–1691 Occurrence Handle10.1105/tpc.021410

    Article  Google Scholar 

  • J-F Bonello H-G Opsahl-Ferstad P Perez C Dumas PM Rogowsky (2000) ArticleTitleEsr genes show different levels of expression in the same region of maize endosperm Gene 246 219–227

    Google Scholar 

  • TF Duda SuffixJr SR Palumbi (2004) ArticleTitleGene expression and feeding ecology: evolution of piscivory in the venomous gastropod genus Conus Proc R Soc Lond B 271 1165–1174

    Google Scholar 

  • J Felsenstein (1985a) ArticleTitleConfidence limits on phylogenies: an approach using the bootstrap Evolution 39 783–791

    Google Scholar 

  • J Felsenstein (1985b) ArticleTitlePhylogenies and the comparative method Am Nat 125 1–15

    Google Scholar 

  • A Force M Lynch FB Pickett A Amores Y Yan J Postlethwait (1999) ArticleTitlePreservation of duplicate genes by complementary degenerative mutations Genetics 151 1531–1545 Occurrence Handle1:CAS:528:DyaK1MXisV2rs7o%3D Occurrence Handle10101175

    CAS  PubMed  Google Scholar 

  • RE Hill ND Hastie (1987) ArticleTitleAccelerated evolution in the reactive center regions of serine protease inhibitors Nature 326 96–99 Occurrence Handle10.1038/326096a0 Occurrence Handle1:CAS:528:DyaL2sXktVWktb8%3D Occurrence Handle3493437

    Article  CAS  PubMed  Google Scholar 

  • AL Hughes (1994) ArticleTitleThe evolution of functionally novel proteins after gene duplication Proc R Soc Lond B 256 119–124 Occurrence Handle1:CAS:528:DyaK2MXmsFSktw%3D%3D Occurrence Handle8029240

    CAS  PubMed  Google Scholar 

  • AL Hughes (1999) Adaptive evolution of genes and genomes Oxford University Press New York

    Google Scholar 

  • AL Hughes R Friedman (2004) ArticleTitleDifferential loss of ancestral gene families as a source of genomic divergence in animals Proc R Soc Lond B (Suppl) 271 S107–S109

    Google Scholar 

  • AL Hughes M Nei (1989) ArticleTitleEvolution of the major histocompatibility complex: Independent origin of nonclassical class I genes in different groups of animals Mol Biol Evol 6 559–579 Occurrence Handle1:CAS:528:DyaK3cXhsVGr Occurrence Handle2484936

    CAS  PubMed  Google Scholar 

  • AL Hughes JA Green H Piontkivska RM Roberts (2003) ArticleTitleAspartic proteinase phylogeny and the origin of pregnancy-associated glycoproteins Mol Biol Evol 20 1940– 1945

    Google Scholar 

  • M Ito Y Ichinose H Kato T Shiraishi T Yamada (1997) ArticleTitleMolecular evolution and functional relevance of the chalcone synthase genes of pea Mol Gen Genet 255 28–37

    Google Scholar 

  • RA Jensen (1976) ArticleTitleEnzyme recruitment and the evolution of new function Annu Rev Microbiol 30 409–425

    Google Scholar 

  • R Johnson D Wichern (1992) Applied multivariate statistical methods, 3rd ed Prentice Hall Englewood Cliffs, NJ

    Google Scholar 

  • M Kimura (1977) ArticleTitlePreponderance of synonymous changes as evidence for the neutral theory of molecular evolution Nature 267 275–276

    Google Scholar 

  • N Kiyosawa T Watanabe K Sakumo M Kanbori N Niino K Ito T Yamoto S Manabe (2003) ArticleTitlePhylogenetic tree facilitates the understanding of gene expression data on drug metabolizing enzymes obtained by microarray analysis Toxicol Lett 145 281–289

    Google Scholar 

  • S Kumar K Tamura IB Jakobsen M Nei (2001) ArticleTitleMEGA2: Molecular evolutionary genetics analysis software Bioinformatics 17 1244–1245 Occurrence Handle10.1093/bioinformatics/17.12.1244 Occurrence Handle1:CAS:528:DC%2BD38XmtVCktQ%3D%3D Occurrence Handle11751241

    Article  CAS  PubMed  Google Scholar 

  • W-H Li (1982) ArticleTitleEvolutionary change of duplicate genes Isozymes 6 55–92 Occurrence Handle6187709

    PubMed  Google Scholar 

  • M Lynch A Force (2000) ArticleTitleThe probability of duplicate gene preservation by subfunctionalization Genetics 154 459–473 Occurrence Handle1:CAS:528:DC%2BD3cXms1KhsA%3D%3D Occurrence Handle10629003

    CAS  PubMed  Google Scholar 

  • M Nei (1969) ArticleTitleGene duplication and nucleotide substitution in evolution Nature 221 40–42 Occurrence Handle1:STN:280:CCaD283isVU%3D Occurrence Handle5782607

    CAS  PubMed  Google Scholar 

  • M Nei (1987) Molecular evolutionary genetics Columbia University Press New York

    Google Scholar 

  • S Ohno (1970) Evolution by gene duplication Springer-Verlag Berlin

    Google Scholar 

  • LE Orgel (1977) ArticleTitleGene-duplication and the origin of proteins with novel functions J Theor Biol 67 773

    Google Scholar 

  • SK Parker HW Detrich (1998) ArticleTitleEvolution, organization, and expression of α-tubulin genes in the Antarctic fish Notothenia coriiceps J Biol Chem 273 34358–34369

    Google Scholar 

  • F Rodrigues-Trelles R Tarrio FJ Ayala (2003) ArticleTitleEvolution of cis-regulatory regions versus codifying regions Int J Dev Biol 47 665–673

    Google Scholar 

  • N Saitou M Nei (1987) ArticleTitleThe neighbor-joining method: A new method for reconstructing phylogenetic trees Mol Biol Evol 4 406–425 Occurrence Handle1:STN:280:BieC1cbgtVY%3D Occurrence Handle3447015

    CAS  PubMed  Google Scholar 

  • M Shannon AT Hamilton L Gordon E Branscomb L Stubbs (2003) ArticleTitleDifferential expansion of zinc-finger transcription factor loci in homologous human and mouse gene clusters Genome Res 13 1097–1110 Occurrence Handle10.1101/gr.963903 Occurrence Handle1:CAS:528:DC%2BD3sXksFehu7k%3D Occurrence Handle12743021

    Article  CAS  PubMed  Google Scholar 

  • JD Thompson DG Higgins T Gibson (1994) ArticleTitleCLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 22 4673–4680 Occurrence Handle1:CAS:528:DyaK2MXitlSgu74%3D Occurrence Handle7984417

    CAS  PubMed  Google Scholar 

  • ML Ujwal AC McCormac A Goulding AM Kumar D Söll MJ Terry (2002) ArticleTitleDivergent regulation of the HEMA gene family encoding glutamyl-tRNA reductase in Arabidopsis thaliana: expression of HEMA2 is regulated by sugars, but is independent of light and plastid signaling Plant Mol Biol 50 83–91

    Google Scholar 

  • AN Vallejo LR Pease (1995) ArticleTitleStructure of the MHC A and B locus promoters in hominoids: Insights on the evolution of the class I MHC multigene family J Immunol 154 3912–3921

    Google Scholar 

  • Y Wen DM Irwin (1999) ArticleTitleMosaic evolution of ruminant stomach lysozyme genes Mol Phyl Evol 13 474–482

    Google Scholar 

  • Z Yang (1997) ArticleTitlePAML: A program package for phylogenetic analysis by maximum likelihood Comput Appl Biosci 13 555–556 Occurrence Handle1:CAS:528:DyaK2sXntlGnu7s%3D Occurrence Handle9367129

    CAS  PubMed  Google Scholar 

  • Z Yang R Nielsen (2000) ArticleTitleEstimating synonymous and nonsynonymous substitution rates under realistic evolutionary models Mol Biol Evol 17 32–43 Occurrence Handle1:CAS:528:DC%2BD3cXotF2qtA%3D%3D Occurrence Handle10666704

    CAS  PubMed  Google Scholar 

  • R Zhong Z-H Ye (2003) ArticleTitleThe SAC domain-containing protein gene family in Arabidopsis Plant Physiol 132 544–555

    Google Scholar 

Download references

Acknowledgments

This research was supported by Grant GM066710 to A.L.H. from the National Institutes of Health.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Austin L. Hughes.

Additional information

Reviewing Editor:Dr. Manyuan Long

Rights and permissions

Reprints and permissions

About this article

Cite this article

Hughes, A.L., Friedman, R. Expression Patterns of Duplicate Genes in the Developing Root in Arabidopsis thaliana. J Mol Evol 60, 247–256 (2005). https://doi.org/10.1007/s00239-004-0171-z

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00239-004-0171-z

Keywords

Navigation