Abstract
Limestone Karst areas possess high levels of biodiversity and endemism. Primulina is a typical component of Karst endemic floras. The high species richness and wide distribution in various Karst microenvironments make the genus an idea model for studying speciation and local adaptation. In this study, we obtained 10 full-length sequences of the phytochrome PHYE from available transcriptome resources of Primulina and amplified partial sequences of PHYE from the genomic DNA of 74 Primulina species. Then, we used maximum-likelihood approaches to explore molecular evolution of PHYE in this Karst cave plant. The results showed that PHYE was dominated by purifying selection in both data sets, and two sites were identified as potentially under positive selection. Furthermore, the ω ratio varies greatly among different functional domains of PHYE and among different species lineages. These results suggest that potential positive selection in PHYE might have played an important role in the adaption of Primulina to heterogeneous light environments in Karst regions, and different species lineages might have been subjected to different selective pressures.
Highlights
Light is the source of energy, and a very important environmental factor for plant growth and survival
The phytochrome apoprotein genes have been classified into four or five gene subfamilies based on sequence similarity to the five phytochrome genes of Arabidopsis: PHYA, PHYB, PHYC, PHYD, and PHYE [3]
The PHYB and PHYD subfamilies are evolutionarily related to PHYE, whereas PHYA and PHYC are related to each other and formed an ancient evolutionary clade [3, 4]
Summary
Light is the source of energy, and a very important environmental factor for plant growth and survival. Phytochromes are specialized photosensors that perceive and interpret light signals from the environment to regulate plant growth and development throughout the whole life cycle [1]. The phytochrome apoprotein genes have been classified into four or five gene subfamilies based on sequence similarity to the five phytochrome genes of Arabidopsis: PHYA, PHYB, PHYC, PHYD, and PHYE [3]. The PHYB and PHYD subfamilies are evolutionarily related to PHYE, whereas PHYA and PHYC are related to each other and formed an ancient evolutionary clade [3, 4]. As the three typical isoforms of phytochromes that are expressed widely in seed plants, the function and evolution of PHYA, PHYB and PHYC have been extensively studied
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