Pinpointing genes underlying annual/perennial transitions with comparative genomics.

Andrew J Heidel,Laura E Rose,Christiane Kiefer,George Coupland

doi:10.1186/s12864-016-3274-1

Abstract

BackgroundTransitions between perennial and an annual life history occur often in plant lineages, but the genes that control whether a plant is an annual or perennial are largely unknown. To identify genes that confer differences between annuals and perennials we compared the gene content of four pairs of sister lineages (Arabidopsis thaliana/Arabidopsis lyrata, Arabis montbretiana/Arabis alpina, Arabis verna/Aubrieta parviflora and Draba nemorosa/Draba hispanica) in the Brassicaceae in which each pair contains one annual and one perennial, plus one extra annual species (Capsella rubella).ResultsAfter sorting all genes in all nine species into gene families, we identified five families in which well-annotated genes are present in the perennials A. lyrata and A. alpina, but are not present in any of the annual species. For the eleven genes in perennials in these families, an orthologous pseudogene or otherwise highly diverged gene was found in the syntenic region of the annual species in six cases. The five candidate families identified encode: a kinase, an oxidoreductase, a lactoylglutathione lyase, a F-box protein and a zinc finger protein. By comparing the active gene in the perennial to the pseudogene or heavily altered gene in the annual, dN and dS were calculated. The low dN/dS values in one kinase suggest that it became pseudogenized more recently, while the other kinase, F-box, oxidoreductase and zinc-finger became pseudogenized closer to the divergence between the annual-perennial pair.ConclusionsWe identified five gene families that may be involved in the life history switch from perennial to annual. Considering the dN and dS data and whether syntenic pseudogenes were found and the potential functions of the genes, the F-box family is considered the most promising candidate for future functional studies to determine if it affects life history.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3274-1) contains supplementary material, which is available to authorized users.

Highlights

Transitions between perennial and an annual life history occur often in plant lineages, but the genes that control whether a plant is an annual or perennial are largely unknown
In perennial Brassicaceae species this behavior is conferred by orthologues of the A. thaliana gene FLOWERING LOCUS C, which inhibit flowering until the plant is exposed to an extended period of cold that mimics winter, a process referred to as vernalization [20, 43]
Phylogenetic positions of species The phylogentic positions of all species used in this analysis were already known [13, 17, 18], but a phylogenetic tree was constructed to illustrate the phylogenetic parviflora), it is useful to consider those gene families present in the other perennials, but that were not detected in D. hispanica or A. parviflora

Summary

Introduction

Transitions between perennial and an annual life history occur often in plant lineages, but the genes that control whether a plant is an annual or perennial are largely unknown. Annuals have evolved many times from perennial ancestors [39] and the reverse has occurred probably to a more limited extent [3]. These switches between life histories have produced closely related species where one is an annual and one a perennial [10, 25]. In perennial Brassicaceae species this behavior is conferred by orthologues of the A. thaliana gene FLOWERING LOCUS C, which inhibit flowering until the plant is exposed to an extended period of cold that mimics winter, a process referred to as vernalization [20, 43]. Less is known about the genetics of other differences between annuals and perennials, such as senescence patterns

Objectives

Methods

Results

Conclusion