RNA-seq transcriptomic profiling of crassulacean acid metabolism pathway in Dendrobium catenatum

Abstract

The regulation of crassulacean acid metabolism (CAM) pathway has recently become a topic of intensive research and has been explored in terms of several aspects, including phylogenetics, genomics, and transcriptomics. Orchidaceae, which contains approximately 9,000 CAM species, is one of the largest lineages using this special photosynthetic pathway. However, no comprehensive transcriptomic profiling focused on CAM regulation in orchid species had previously been performed. In this report, we present two Illumina RNA-seq datasets, including a total of 24 mature leaf samples with 844.4 million reads, from Dendrobium catenatum (Orchidaceae), a facultative CAM species. The first dataset was generated from a time-course experiment based on the typical CAM phases in a diel. The second was derived from an experiment on drought stress and stress removal. A series of quality assessments were conducted to verify the reliability of the datasets. These transcriptomic profiling datasets will be useful to explore and understand the essence of CAM regulation.

Figure 1. Overview of the experimental design and analysis pipeline.

(a) The sampling scheme based on typical CAM phases according to the CO₂ exchange rate during a natural day-night cycle. (b) The sampling scheme under sustained drought stress and stress removal. (c) Flow chart of the D. catenatum RNA-seq experiments and data analyses. Green arrows indicate sample collection times, and yellow arrows indicate watering times. Black bars indicate dark periods.

Figure 2. Quality assessment metrics for RNA-seq data.

The per base sequence quality (left), per sequence quality scores (middle), and per sequence GC content (right) across all samples of Dataset I (a) and Dataset II (b).

Figure 3. Three-dimensional PCA plots.

(a) Dataset I and (b) Dataset II.