Evolutionary analysis of LP3 gene family in conifers: an ASR homolog

Abstract

Drought has long been established as a major environmental stress for plants which have in turn developed several coping strategies, ranging from physiological to molecular mechanisms. LP3; a homolog of the Abscisic Acid, Stress and Ripening (ASR) gene was first detected in tomato; and has been shown to be present in four different isoforms in loblolly pine called LP3-0, LP3-1, LP3-2 and LP3-3. While ASR has already been extensively studied notably in tomato, the same cannot be said of LP3. Like ASR, the different LP3 isoforms have been shown to be upregulated in response to water deficit stress and to also act as transcription factors for genes likely involved in hexose transport. In this study we have investigated the evolutionary history of LP3 gene family, with the aim of relating it to that of ASR from a phylogenetic perspective and comparing the differences in selective pressure and codon usage. Phylogenetic analyses of different LP3 homologs compared to ASR show that LP3 is less divergent across species than ASR and that even when comparing the different sub-sections of the gene the divergence rate of LP3 is lower than that of ASR. Analysis of different gene parameters showed that there were differences in GC1% and GC2% but not in total or GC3% content. All genes had a relatively high CAI value associated with a low to moderate ENC value, which is indicative of high translation efficiency found in highly expressed genes. Analysis of codon usage also showed that LP3 preferentially uses different codons than ASR. Selective pressure analysis across most of the LP3 and ASR genes used in this study showed that these genes were principally undergoing purifying selection, with the exception of LP3-3 which seems to be undergoing diversifying selection most probably due to the fact that it likely recently diverged from LP3-0. This study thus provides insight in how ASR and LP3 have diverged from each other while remaining homologous.