Duplication, divergence and persistence in the Phytochrome photoreceptor gene family of cottons (Gossypium spp.)

Abstract

Background: Phytochromes are a family of red/far-red photoreceptors that regulate a number of important developmental traits in cotton (Gossypium spp.), including plant architecture, fiber development, and photoperiodic flowering. Little is known about the composition and evolution of the phytochrome gene family in diploid (G. herbaceum, G. raimondii) or allotetraploid (G. hirsutum, G. barbadense) cotton species. The objective of this study was to obtain a preliminary inventory and molecular-evolutionary characterization of the phytochrome gene family in cotton.

Results: We used comparative sequence resources to design low-degeneracy PCR primers that amplify genomic sequence tags (GSTs) for members of the PHYA, PHYB/D, PHYC and PHYE gene sub-families from A- and D-genome diploid and AD-genome allotetraploid Gossypium species. We identified two paralogous PHYA genes (designated PHYA1 and PHYA2) in diploid cottons, the result of a Malvaceae-specific PHYA gene duplication that occurred approximately 14 million years ago (MYA), before the divergence of the A- and D-genome ancestors. We identified a single gene copy of PHYB, PHYC, and PHYE in diploid cottons. The allotetraploid genomes have largely retained the complete gene complements inherited from both of the diploid genome ancestors, with at least four PHYA genes and two genes encoding PHYB, PHYC and PHYE in the AD-genomes. We did not identify a PHYD gene in any cotton genomes examined.

Conclusions: Detailed sequence analysis suggests that phytochrome genes retained after duplication by segmental duplication and allopolyploidy appear to be evolving independently under a birth-and-death-process with strong purifying selection. Our study provides a preliminary phytochrome gene inventory that is necessary and sufficient for further characterization of the biological functions of each of the cotton phytochrome genes, and for the development of 'candidate gene' markers that are potentially useful for cotton improvement via modern marker-assisted selection strategies.

Figure 1

Gene diagrams and PCR amplicons used in this study. Model gene structures are derived from Arabidopsis thaliana annotations (At1g09570, At2g18790. At5g35840, At4g18130). The PHYB 2.1 kb sequenced fragment represents a composite of several overlapping amplicons.

Figure 2

Unrooted NJ tree of Gossypium spp. PHYA-related genes based on a ~315 bp consensus alignment of amplification products from the hinge region. Distances (uncorrected "p") and most parsimonious number of nt changes are indicated for each branch (to the left and to the right of the/, respectively). Branch lengths of less than 0.001 substitutions per site are not shown. Bootstrap support (500 replicates) is indicated where >50%.

Figure 3

Unrooted NJ tree of Gossypium spp. PHYB-related genes based on the consensus alignment of the ~2.1 kb merged amplicons. Distances (uncorrected "p") and most parsimonious number of nucleotide changes are indicated for each branch (to the left and to the right of the/, respectively). Branch lengths of less than 0.001 substitutions per site are not shown. Bootstrap support (500 replicates) is indicated where >50%.

Figure 4

Unrooted NJ tree of Gossypium spp. PHYC-related genes based on a 1022 bp consensus alignment of amplification products from primers PHYdeg-F and PHYC_1R_DFCI. Distances (uncorrected "p") and most parsimonious number of nucleotide changes are indicated for each branch (to the left and to the right of the/, respectively). Bootstrap support (500 replicates) is indicated where >50%.

Figure 5

Unrooted NJ tree of Gossypium spp. PHYE-related genes based on a 270 bp consensus alignment of amplification products from the hinge region. Distances (uncorrected "p") and most parsimonious number of nucleotide changes are indicated for each branch. Branch lengths of less than 0.001 substitutions per site are not indicated. Bootstrap support (500 replicates) is indicated where >50%.

Figure 6

Unrooted NJ tree of phytochrome genes of A. thaliana and cottons (Gossypium spp.) based on a 358 bp consensus alignment of amplification products from the hinge regions. Kimura two-parameter distances are shown for each branch. All internal branches had 100% bootstrap support (500 replicates). 1A, 1B, 1C and 1E denote gene divergence events likely resulting from speciation. 2 and 3 denote gene divergence events likely resulting from gene duplication. All Gossypium phytochrome genes are included within clusters (indicated by ovals).