Characterization and Analysis of the Full-Length Transcriptomes of Multiple Organs in Pseudotaxus chienii (W.C.Cheng) W.C.Cheng

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.

Population transcriptomic sequencing reveals allopatric divergence and local adaptation in Pseudotaxus chienii (Taxaceae)

“…This result suggests that when the species adapts to the surrounding environment, gene expression and nucleotide diversity have a reciprocal relationship. This phenomenon might be attributed to gene duplication events occurring in the P. chienii genome during the evolutionary process [43]. Compared with single-copy genes, duplicated genes usually significantly increase the diversity of gene expression, while genetic diversity remains relatively weak [44].…”

First Multi-Organ Full-Length Transcriptome of Tree Fern Alsophila spinulosa Highlights the Stress-Resistant and Light-Adapted Genes

“…These results indicated that genome size did not correlate with transcriptome size and more genes were covered by multi-organ sequencing than by single organ sequencing. Similarly, the novel strategy of multi-organ FL transcriptome for gene analysis has been used for several nonmodel plants, including Asarum sieboldii (Chen et al, 2020), Pseudotaxus chienii (Liu et al, 2020), and Cephalotaxus oliveri (He et al, 2021).…”

SMRT and Illumina RNA-Seq Identifies Potential Candidate Genes Related to the Double Flower Phenotype and Unveils SsAP2 as a Key Regulator of the Double-Flower Trait in Sagittaria sagittifolia

“…The method of Liu et al [57] was used to obtain the total RNA of S. sagittifolia flower buds at different developmental stages. The integrity of the total RNA samples was monitored by the Agilent 2100 system, and the purity of the RNA samples was measured using NanoDrop spectroscopy (Novogene Company, Beijing, China).…”

“…The results predicted by both software packages as 'non-coding' were used as the final long noncoding (lnc)RNA result for the full-length transcriptome. The coding sequences were assembled using the software Cogent [62], and variable shear analysis was then performed by SUPPA [57] as a reference.…”