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

PloS One
Xian-Ge HuJian-Feng Mao

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 t...Continue Reading

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Citations

Jul 16, 2019·Genome Biology and Evolution·Shu-Ye JiangSrinivasan Ramachandran
Aug 21, 2019·G3 : Genes - Genomes - Genetics·Dario I OjedaTanja Pyhäjärvi
Feb 10, 2020·Journal of Molecular Evolution·Enrica AlicandriMario Ciaffi

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Datasets Mentioned

BETA
CBS100218

Methods Mentioned

BETA
RNA-Seq
PCR
genome-based prediction

Software Mentioned

Phyml
TRAPID
SSR Identification Tool ( SSRIT
CEGMA
BLASTX
Burrows tool ( BWA )
QDD
Clustalx
WEGO
FastQC

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