ArticlePloS one2016
De Novo Transcriptome Assembly and Characterization for the Widespread and Stress-Tolerant Conifer Platycladus orientalis.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 36 citations in OpenAlex.
- A chromosome-level genome assembly of Platycladus orientalis and comparative genomics reveal pivotal roles of transposable elements in gene duplication and pseudogenization across gymnosperm giga-genomes.Plant communications · 2026Article
- Dynamic changes of endogenous hormones and transcriptome analysis reveal the regulatory mechanism of gibberellin-promoted male cone formation in Platycladus orientalis.BMC plant biology · 2026Article
- Comparative transcriptome analysis reveals the key role of photosynthetic traits in the formation of differences in photothermal sensitivity in tobacco.BMC genomics · 2025Article
- Transcriptome characterisation and population genetics ofBiodiversity data journal · 2025Article
- Full-length transcriptome characterization ofFrontiers in genetics · 2024Article
- Transcriptome analysis reveals the accelerated expression of genes related to photosynthesis and chlorophyll biosynthesis contribution to shade-tolerant in Phoebe bournei.BMC plant biology · 2022Article
- Repetitive Elements, Sequence Turnover and Cyto-Nuclear Gene Transfer in Gymnosperm Mitogenomes.Frontiers in genetics · 2022Article
- Characterization and Analysis of the Full-Length Transcriptomes of Multiple Organs inInternational journal of molecular sciences · 2020Article
- On the Evolution and Functional Diversity of Terpene Synthases in the Pinus Species: A Review.Journal of molecular evolution · 2020Review
- Development of a Large Gene-Associated SSR Marker Set and in-Depth Genetic Characterization in Scarlet Sage.Frontiers in genetics · 2020Article
- Genome-Wide Variant Identification and High-Density Genetic Map Construction Using RADseq forG3 (Bethesda, Md.) · 2019Article
- Utilization of Tissue Ploidy Level Variation inG3 (Bethesda, Md.) · 2019Article
- A Comprehensive Survey on the Terpene Synthase Gene Family Provides New Insight into Its Evolutionary Patterns.Genome biology and evolution · 2019Article
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- Characterization and Application of EST-SSR Markers Developed From the Transcriptome ofFrontiers in genetics · 2019Article
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- Genetic evaluation of the breeding population of a valuable reforestation conifer Platycladus orientalis (Cupressaceae).Scientific reports · 2016Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Platycladus orientalis, of the family Cupressaceae, is a widespread conifer throughout China and is extensively used for ecological reforestation, horticulture, and in medicine. Transcriptome assemblies are required for this ecologically important conifer for understanding genes underpinning adaptation and complex traits for breeding programs. To enrich the species' genomic resources, a de novo transcriptome sequencing was performed using Illumina paired-end sequencing. In total, 104,073,506 high quality sequence reads (approximately 10.3 Gbp) were obtained, which were assembled into 228,948 transcripts and 148,867 unigenes that were longer than 200 nt. Quality assessment using CEGMA showed that the transcriptomes obtained were mostly complete for highly conserved core eukaryotic genes. Based on similarity searches with known proteins, 62,938 (42.28% of all unigenes), 42,158 (28.32%), and 23,179 (15.57%) had homologs in the Nr, GO, and KOG databases, 25,625 (17.21%) unigenes were mapped to 322 pathways by BLASTX comparison against the KEGG database and 1,941 unigenes involved in environmental signaling and stress response were identified. We also identified 43 putative terpene synthase (TPS) functional genes loci and compared them with TPSs from other species. Additionally, 5,296 simple sequence repeats (SSRs) were identified in 4,715 unigenes, which were assigned to 142 motif types. This is the first report of a complete transcriptome analysis of P. orientalis. These resources provide a foundation for further studies of adaptation mechanisms and molecular-based breeding programs.
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