De Novo Transcriptome Assembly and Characterization for the Widespread and Stress-Tolerant Conifer Platycladus orientalis

• Published in: PloS one Vol. 11; no. 2; p. e0148985
• Main Authors: Hu, Xian-Ge, Liu, Hui, Jin, YuQing, Sun, Yan-Qiang, Li, Yue, Zhao, Wei, El-Kassaby, Yousry A, Wang, Xiao-Ru, Mao, Jian-Feng
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 16.02.2016; Public Library of Science (PLoS)
• Subjects: Adaptation; Adaptation, Physiological - genetics; Alkyl and Aryl Transferases - genetics; Alkyl and Aryl Transferases - metabolism; Analysis; Biology and Life Sciences; Bioremediation; Biosynthesis; Breeding; Chinese arbor vitae; Chinese medicine; Coniferophyta - classification; Coniferophyta - genetics; cupressaceae; Databases, Genetic; Ecology; Education; Engineering; Environmental science; Forestry; Gene expression; Gene Expression Profiling; Genes; Genes, Plant; Genetics; Genomes; Genomics; Germplasm; High-Throughput Nucleotide Sequencing; Homology; Horticulture; Laboratories; Microsatellite Repeats; Molecular Sequence Annotation; Phylogeny; Physiological aspects; Platycladus orientalis; Proteins; Quality assessment; Quality control; Reforestation; Research and Analysis Methods; RNA, Messenger - genetics; RNA, Messenger - metabolism; Simple sequence repeats; Stress, Physiological; Studies; Terpene synthase; Transcriptome; Trees; China; Beijing China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0148985

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.