Molecular evolution of psbA gene in ferns: unraveling selective pressure and co-evolutionary patternReportar como inadecuado

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BMC Evolutionary Biology

, 12:145

First Online: 16 August 2012Received: 12 March 2012Accepted: 08 August 2012DOI: 10.1186-1471-2148-12-145

Cite this article as: Sen, L., Fares, M.A., Su, YJ. et al. BMC Evol Biol 2012 12: 145. doi:10.1186-1471-2148-12-145


BackgroundThe 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.

ResultsWe 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.

ConclusionsThe 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.


FELFixed effects likelihood

IRsInverted repeat regions

LSCLarge single copy region

LRTLikelihood ratio test

MyaMillion 1 × 10 years ago

MI-EMutual information-entropy

MSAsMultiple sequence alignments

PS IIPhoto system II

RELRandom effects likelihood

RCW-MIRow and column weighing of mutual information

SLACSingle likelihood ancestor counting

TaAnnealing temperature.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2148-12-145 contains supplementary material, which is available to authorized users.

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Autor: Lin Sen - Mario A Fares - Ying-Juan Su - Ting Wang


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