A molecular phylogenomic analysis of the ILRI-like family of IAA amidohydrolase genes

James J. Campanella, Daniel Larko, John Smalley

Research output: Contribution to journalArticle

34 Citations (Scopus)

Abstract

The ILR1-like family of hydrolase genes was initially isolated in Arabidopsis thaliana and is thought to help regulate levels of free indole-3-acetic-acid. We have investigated how this family has evolved in dicotyledon, monocotyledon and gymnosperm species by employing the GenBank and TIGR databases to retrieve orthologous genes. The relationships among these sequences were assessed employing phylogenomic analyses to examine molecular evolution and phylogeny. The members of the ILR1-like family analysed were ILL1, ILL2, ILL3, ILL6, ILR1. and IAR3. Present evidence suggests that IAR3 has undergone the least evolution and is most conserved. This conclusion is based on IAR3 having the largest number of total interspecific orthologues, orthologous species and unique orthologues. Although less conserved than IAR3, DNA and protein sequence analyses of ILL1 and ILR1 suggest high conservation. Based on this conservation, IAR3, ILL1 and ILR1 may have had major roles in the physiological evolution of 'higher' plants. ILL3 is least conserved, with the fewest orthologous species and orthologues. The monocotyledonous orthologues for most family-members examined have evolved into two separate molecular clades from dicotyledons, indicating active evolutionary change. The monocotyledon clades are: (a) those possessing a putative endoplasmic reticulum localizing signal; and (b) those that are putative cytoplasmic hydrolases. IAR3, ILL1 and ILL6 are all highly orthologous to a gene in the gymnosperm Pinus taeda, indicating an ancient enzymatic activity. No orthologues could be detected in Chlamydomonas, moss and fern databases.

Original languageEnglish
Pages (from-to)584-600
Number of pages17
JournalComparative and Functional Genomics
Volume4
Issue number6
DOIs
StatePublished - 1 Dec 2003

Fingerprint

Amidohydrolases
Gymnosperms
Hydrolases
Pinus taeda
Databases
Genes
Ferns
Chlamydomonas
Bryophyta
Molecular Evolution
Nucleic Acid Databases
Protein Sequence Analysis
Phylogeny
DNA Sequence Analysis
Arabidopsis
Endoplasmic Reticulum

Keywords

  • Arabidopsis
  • Auxin regulation
  • IAA amidohydrolase
  • ILR1-like family
  • Phylogenetics
  • Phylogenomics

Cite this

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title = "A molecular phylogenomic analysis of the ILRI-like family of IAA amidohydrolase genes",
abstract = "The ILR1-like family of hydrolase genes was initially isolated in Arabidopsis thaliana and is thought to help regulate levels of free indole-3-acetic-acid. We have investigated how this family has evolved in dicotyledon, monocotyledon and gymnosperm species by employing the GenBank and TIGR databases to retrieve orthologous genes. The relationships among these sequences were assessed employing phylogenomic analyses to examine molecular evolution and phylogeny. The members of the ILR1-like family analysed were ILL1, ILL2, ILL3, ILL6, ILR1. and IAR3. Present evidence suggests that IAR3 has undergone the least evolution and is most conserved. This conclusion is based on IAR3 having the largest number of total interspecific orthologues, orthologous species and unique orthologues. Although less conserved than IAR3, DNA and protein sequence analyses of ILL1 and ILR1 suggest high conservation. Based on this conservation, IAR3, ILL1 and ILR1 may have had major roles in the physiological evolution of 'higher' plants. ILL3 is least conserved, with the fewest orthologous species and orthologues. The monocotyledonous orthologues for most family-members examined have evolved into two separate molecular clades from dicotyledons, indicating active evolutionary change. The monocotyledon clades are: (a) those possessing a putative endoplasmic reticulum localizing signal; and (b) those that are putative cytoplasmic hydrolases. IAR3, ILL1 and ILL6 are all highly orthologous to a gene in the gymnosperm Pinus taeda, indicating an ancient enzymatic activity. No orthologues could be detected in Chlamydomonas, moss and fern databases.",
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A molecular phylogenomic analysis of the ILRI-like family of IAA amidohydrolase genes. / Campanella, James J.; Larko, Daniel; Smalley, John.

In: Comparative and Functional Genomics, Vol. 4, No. 6, 01.12.2003, p. 584-600.

Research output: Contribution to journalArticle

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