Open Access Research article

The temporal foliar transcriptome of the perennial C3 desert plant Rhazya stricta in its natural environment

Steven A Yates1, Igor Chernukhin1, Ruben Alvarez-Fernandez1, Ulrike Bechtold1, Mohammed Baeshen2, Nabih Baeshen2, Mohammad Z Mutwakil2, Jamal Sabir2, Tracy Lawson1 and Philip M Mullineaux1*

Author Affiliations

1 School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK

2 Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Kingdom of Saudi Arabia

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BMC Plant Biology 2014, 14:2  doi:10.1186/1471-2229-14-2

Published: 4 January 2014

Abstract

Background

The perennial species Rhazya stricta (R. stricta) grows in arid zones and carries out typical C3 photosynthesis under daily extremes of heat, light intensity and low humidity. In order to identify processes attributable to its adaptation to this harsh environment, we profiled the foliar transcriptome of apical and mature leaves harvested from the field at three time periods of the same day.

Results

Next generation sequencing was used to reconstruct the transcriptome and quantify gene expression. 28018 full length transcript sequences were recovered and 45.4% were differentially expressed (DE) throughout the day. We compared our dataset with microarray experiments in Arabidopsis thaliana (Arabidopsis) and other desert species to identify trends in circadian and stress response profiles between species. 34% of the DE genes were homologous to Arabidopsis circadian-regulated genes. Independent of circadian control, significant overlaps with Arabidopsis genes were observed only with heat and salinity/high light stress-responsive genes. Also, groups of DE genes common to other desert plants species were identified. We identified protein families specific to R. stricta which were found to have diverged from their homologs in other species and which were over -expressed at midday.

Conclusions

This study shows that temporal profiling is essential to assess the significance of genes apparently responsive to abiotic stress. This revealed that in R. stricta, the circadian clock is a major regulator of DE genes, even of those annotated as stress-responsive in other species. This may be an important feature of the adaptation of R. stricta to its extreme but predictable environment. However, the majority of DE genes were not circadian-regulated. Of these, some were common to other desert species and others were distinct to R. stricta, suggesting that they are important for the adaptation of such plants to arid environments.

Keywords:
Next generation sequencing; Transcriptomics; Circadian clock; Rhazya stricta; Perennial desert plants; Heat stress; Salinity stress; C3 photosynthesis