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Open Access Research article

Molecular evolution of psbA gene in ferns: unraveling selective pressure and co-evolutionary pattern

Lin Sen12, Mario A Fares34, Ying-Juan Su5 and Ting Wang2*

Author Affiliations

1 State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China

2 CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China

3 Integrative Systems Biology Group, Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia (UPV)), Valencia, Spain

4 Evolutionary Genetics and Bioinformatics Laboratory, Department of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland

5 State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China

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BMC Evolutionary Biology 2012, 12:145  doi:10.1186/1471-2148-12-145

Published: 16 August 2012

Abstract

Background

The photosynthetic oxygen-evolving photo system II (PS II) produces almost the entire oxygen in the atmosphere. This unique biochemical system comprises a functional core complex that is encoded by psbA and other genes. Unraveling the evolutionary dynamics of this gene is of particular interest owing to its direct role in oxygen production. psbA underwent gene duplication in leptosporangiates, in which both copies have been preserved since. Because gene duplication is often followed by the non-fictionalization of one of the copies and its subsequent erosion, preservation of both psbA copies pinpoint functional or regulatory specialization events. The aim of this study was to investigate the molecular evolution of psbA among fern lineages.

Results

We sequenced psbA , which encodes D1 protein in the core complex of PSII, in 20 species representing 8 orders of extant ferns; then we searched for selection and convolution signatures in psbA across the 11 fern orders. Collectively, our results indicate that: (1) selective constraints among D1 protein relaxed after the duplication in 4 leptosporangiate orders; (2) a handful positively selected codons were detected within species of single copy psbA, but none in duplicated ones; (3) a few sites among D1 protein were involved in co-evolution process which may intimate significant functional/structural communications between them.

Conclusions

The strong competition between ferns and angiosperms for light may have been the main cause for a continuous fixation of adaptive amino acid changes in psbA , in particular after its duplication. Alternatively, a single psbA copy may have undergone bursts of adaptive changes at the molecular level to overcome angiosperms competition. The strong signature of positive Darwinian selection in a major part of D1 protein is testament to this. At the same time, species own two psbA copies hardly have positive selection signals among the D1 protein coding sequences. In this study, eleven co-evolving sites have been detected via different molecules, which may be more important than others.