Comparative Evolutionary Analysis of Chalcone Synthase and Alcohol Dehydrogenase Loci in Arabidopsis, Arabis, and Related Genera (Brassicaceae)

TLDR

Arabidopsis and Arabis belong to the Brassicaceae tribe Arabideae, with Arabis being polyphyletic and less closely related to Arabidopsis. The authors compared chalcone synthase and alcohol dehydrogenase gene sequences across 28 species and used fossil pollen to estimate a synonymous substitution rate of 1.5 × 10 substitutions per site per year. Chs is largely single‑copy while Adh shows duplications; phylogenies identify Arabidopsis lyrata, petraea, and halleri as closest relatives, Arabis is polyphyletic, and divergence from Arabidopsis thaliana occurred about 5 MYA and from Brassica about 24 MYA, with consistent timescales across data.

Abstract

We analyzed sequence variation for chalcone synthase (Chs) and alcohol dehydrogenase (Adh) loci in 28 species in the genera Arabidopsis and Arabis and related taxa from tribe Arabideae. Chs was single-copy in nearly all taxa examined, while Adh duplications were found in several species. Phylogenies constructed from both loci confirmed that the closest relatives of Arabidopsis thaliana include Arabidopsis lyrata, Arabidopsis petraea, and Arabidopsis halleri (formerly in the genus Cardaminopsis). Slightly more distant are the North American n = 7 Arabis (Boechera) species. The genus Arabis is polyphyletic—some unrelated species appear within this taxonomic classification, which has little phylogenetic meaning. Fossil pollen data were used to compute a synonymous substitution rate of 1.5 × 10 substitutions per site per year for both Chs and Adh. Arabidopsis thaliana diverged from its nearest relatives about 5 MYA, and from Brassica roughly 24 MYA. Independent molecular and fossil data from several sources all provide similar estimates of evolutionary timescale in the Brassicaceae.