Abstract
Cephalotaxus oliveri is a tertiary relict conifer endemic to China, regarded as a national second-level protected plant in China. This species has experienced severe changes in temperature and precipitation in the past millions of years, adapting well to harsh environments. In view of global climate change and its endangered conditions, it is crucial to study how it responds to changes in temperature and precipitation for its conservation work. In this study, single-molecule real-time (SMRT) sequencing and Illumina RNA sequencing were combined to generate the complete transcriptome of C. oliveri. Using the RNA-seq data to correct the SMRT sequencing data, the four tissues obtained 63,831 (root), 58,108 (stem), 33,013 (leaf) and 62,436 (male cone) full-length unigenes, with a N50 length of 2523, 3480, 3181, and 3267 bp, respectively. Additionally, 35,887, 11,306, 36,422, and 25,439 SSRs were detected for the male cone, leaf, root, and stem, respectively. The number of long non-coding RNAs predicted from the root was the largest (11,113), and the other tissues were 3408 (stem), 3193 (leaf), and 3107 (male cone), respectively. Functional annotation and enrichment analysis of tissue-specific expressed genes revealed the special roles in response to environmental stress and adaptability in the different four tissues. We also characterized the gene families and pathways related to abiotic factors. This work provides a comprehensive transcriptome resource for C. oliveri, and this resource will facilitate further studies on the functional genomics and adaptive evolution of C. oliveri.
Highlights
Cephalotaxus oliveri, a perennial shrub or small tree, belongs to the Genus Cephalotaxus sect
Based on single-molecule realtime (SMRT) sequencing technology, 560,605, 312,574, 353,127 and 213,338 polymerase reads were generated for the male cone, root, stem, and leaf
The benchmarking universal single-copy ortholog (BUSCO) software was used to evaluate the completeness of the three-generation full-length transcripts of C. oliveri. 902, 1048, 930 and 1015 complete core conserved genes were retrieved in the four tissues, which indicated the results of Iso-seq were good
Summary
Cephalotaxus oliveri, a perennial shrub or small tree, belongs to the Genus Cephalotaxus sect. C. oliveri has been regarded as a vulnerable species by International Union for Conservation of Nature (IUCN) due to the deforestation and overexploitation [2,3]. After the Quaternary, due to the influence of glacier activities, C. oliveri only survived in a small environment. As an old rare species with a long life, C. oliveri has experienced severe changes in temperature and precipitation over the past millions of years, adapting well to cold and arid environments [3]. In view of the continuous changes in the global climate, it is crucial to study how C. oliveri responds to the changes in temperature and precipitation for its conservation work. The molecular and genetic resources of this long-lived conifer are still blank, limiting the studies on molecular and genetic analysis
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