Genome Dynamics Explain the Evolution of Flowering Time CCT Domain Gene Families in the Poaceae

James Cockram,Nils Stein,Donal M O'Sullivan,Stefan Taudien,Paul C Bailey,Thomas Thiel,Burkhard Steuernagel,Miguel A Blazquez

doi:10.1371/journal.pone.0045307

Abstract

Numerous CCT domain genes are known to control flowering in plants. They belong to the CONSTANS-like (COL) and PREUDORESPONSE REGULATOR (PRR) gene families, which in addition to a CCT domain possess B-box or response-regulator domains, respectively. Ghd7 is the most recently identified COL gene to have a proven role in the control of flowering time in the Poaceae. However, as it lacks B-box domains, its inclusion within the COL gene family, technically, is incorrect. Here, we show Ghd7 belongs to a larger family of previously uncharacterized Poaceae genes which possess just a single CCT domain, termed here CCT MOTIF FAMILY (CMF) genes. We molecularly describe the CMF (and related COL and PRR) gene families in four sequenced Poaceae species, as well as in the draft genome assembly of barley (Hordeum vulgare). Genetic mapping of the ten barley CMF genes identified, as well as twelve previously unmapped HvCOL and HvPRR genes, finds the majority map to colinear positions relative to their Poaceae orthologues. Combined inter-/intra-species comparative and phylogenetic analysis of CMF, COL and PRR gene families indicates they evolved prior to the monocot/dicot divergence ∼200 mya, with Poaceae CMF evolution described as the interplay between whole genome duplication in the ancestral cereal, and subsequent clade-specific mutation, deletion and duplication events. Given the proven role of CMF genes in the modulation of cereals flowering, the molecular, phylogenetic and comparative analysis of the Poaceae CMF, COL and PRR gene families presented here provides the foundation from which functional investigation can be undertaken.

Highlights

The control of flowering time is a crucial environmental adaptation in plants, as well as a major determinant of grain yield in cereal crops [1]
Poaceae COL genes With the recognition of the CCT MOTIF FAMILY (CMF) gene family, the rice COL gene family [13] should be reduced from sixteen (OsA-OsP) to fourteen members, due to the lack of B-box domains in OsH and Ghd7 (OsI)
Parsimonious analyses indicate the CMF family may have evolved from COL genes after the divergence of the cormophyte and streptophyte lineages, around 5002400 mya

Summary

Introduction

The control of flowering time is a crucial environmental adaptation in plants, as well as a major determinant of grain yield in cereal crops [1]. The observation that green micro-algae, but not earlier photosynthetic microorganisms such as diatoms and euglenoids, possess CO-like (COL) genes suggests that the gene family appeared during or soon after the endosymbiotic event in the photosynthetic lineage [5] and has evolved to regulate flowering in response to inductive daylengths in higher plants. CO belongs to a larger family of 17 COL genes, subdivided into three broad subgroups [11]. They encode proteins with a conserved region of 43 amino acids towards their carboxy-terminus, termed the CCT domain, which in arabidopsis interacts with CONSTITUITIVE PHOTOMORPHOGENIC 1 (COP1) protein to control CO stability [12]. Moench) all possessing five members [17,18,19,20]

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Results

Conclusion