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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.

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