Abstract
Pseudotaxus chienii, a rare tertiary relict species with economic and ecological value, is a representative of the monotypic genus Pseudotaxus that is endemic to China. P. chienii can adapt well to habitat isolation and ecological heterogeneity under a variety of climate and soil conditions, and is able to survive in harsh environments. However, little is known about the molecular and genetic resources of this long-lived conifer. Herein, we sequenced the transcriptomes of four organs of P. chienii using the PacBio Isoform Sequencing and Illumina RNA Sequencing platforms. Based on the PacBio Iso-Seq data, we obtained 44,896, 58,082, 50,485, and 67,638 full-length unigenes from the root, stem, leaf, and strobilus, respectively, with a mean length of 2692 bp, and a mean N50 length of 3010.75 bp. We then comprehensively annotated these unigenes. The number of organ-specific expressed unigenes ranged from 4393 in leaf to 9124 in strobilus, suggesting their special roles in physiological processes, organ development, and adaptability in the different four organs. A total of 16,562 differentially expressed genes (DEGs) were identified among the four organs and clustered into six subclusters. The gene families related to biotic/abiotic factors, including the TPS, CYP450, and HSP families, were characterized. The expression levels of most DEGs in the phenylpropanoid biosynthesis pathway and plant–pathogen interactions were higher in the root than in the three other organs, suggesting that root constitutes the main organ of defensive compound synthesis and accumulation and has a stronger ability to respond to stress. The sequences were analyzed to predict transcription factors, long non-coding RNAs, and alternative splicing events. The expression levels of most DEGs of C2H2, C3H, bHLH, and bZIP families in the root and stem were higher than those in the leaf and strobilus, indicating that these TFs may play a crucial role in the survival of the root and stem. These results comprise the first comprehensive gene expression profiles obtained for different organs of P. chienii. Our findings will facilitate further studies on the functional genomics, adaptive evolution, and phylogeny of P. chienii, and lay the foundation for the development of conservation strategies for this endangered conifer.
Highlights
Pseudotaxus chienii (Taxaceae), a rare tertiary relict species, is a representative of the monotypic genus Pseudotaxus that is endemic to China [1]
Based on PacBio Isoform Sequencing (Iso-Seq), 3,589,223, 4,242,683, 4,905,002, and 5,427,724 subreads representing 8.21, 8.35, 11.42, and 11.22 Gbp were generated for the root, stem, leaf, and strobilus, with a mean length of 2289, 1968, 2328, and 2068 bp, respectively (Table S1)
Based on the iterative clustering for error correction (ICE) algorithm and the polishing of the Arrow algorithm, 80,434, 92,515, 142,159, and 126,538 high-quality (HQ), FL, and polished consensus isoforms were generated for the root, stem, leaf, and strobilus, respectively (Table S1)
Summary
Pseudotaxus chienii (Taxaceae), a rare tertiary relict species, is a representative of the monotypic genus Pseudotaxus that is endemic to China [1]. The distinguishing feature of this species is the presence of a white aril and two distinct white stomatal bands on the underside of mature leaves [1]. This species is a dioecious evergreen woody shrub or tree that grows in subtropical mountain forests [2]. Similar findings have been reported for conifers, such as white spruce (Picea glauca) [9], maritime pine (Pinus pinaster) [10], and Norway spruce (Picea abies) [11] These findings suggest that the consideration of multiple organs, including the determination of organ-specific expression patterns, is a powerful approach to characterizing the transcriptomic complexity across a whole organism. The current work attempts to fill this gap by studying the multiple organ transcriptomes of P. chienii
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