Identification, expression, and phylogenetic analyses of terpenoid biosynthesis-related genes in secondary xylem of loblolly pine (Pinus taeda L.) based on transcriptome analyses

Abstract

Loblolly pine (Pinus taeda L.) is one of the most important species for oleoresin (a mixture of terpenoids) in South China. The high oleoresin content of loblolly pine is associated with resistance to bark beetles and other economic benefits. In this study, we conducted transcriptome analyses of loblolly pine secondary xylem to gain insight into the genes involved in terpenoid biosynthesis. A total of 372 unigenes were identified as being critical for oleoresin production, including genes for ATP-binding cassette (ABC) transporters, the cytochrome P450 (CYP) protein family, and terpenoid backbone biosynthesis enzymes. Six key genes involved in terpenoid biosynthetic pathways were selected for multiple sequence alignment, conserved motif prediction, and phylogenetic and expression profile analyses. The protein sequences of all six genes exhibited a higher degree of sequence conservation, and upstream genes were relatively more conserved than downstream genes in terpenoid biosynthetic pathways. The N-terminal regions of these sequences were less conserved than the C-terminal ends, as the N-terminals were quite diverse in both length and composition. The phylogenetic analyses revealed that most genes originated from gene duplication after species divergence, and partial genes exhibited incomplete lineage sorting. In addition, the expression profile analyses showed that all six genes exhibited high expression levels during the high-oleoresin-yielding phase.

Genome structure and evolutionary history of frankincense producing Boswellia sacra

“…Resin from Boswellia has been viewed as one of the significant defense responses to wounding and pathogenic attacks ( Cabrita, 2018 ; Trapp and Croteau, 2001 ). Resin, synthesized via methylerythritol 4-phosphate (MEP) or mevalonic acid (MVA) pathways ( Bai et al., 2019 ; Mao et al., 2019 ), is transported to wounded sites through resin canals ( Khan et al., 2018b ; Mengistu et al., 2013 ). The resin is composed of more than 300 chemical constituents ( Al-Harrasi et al., 2019a ) identified as monoterpenes (KEGG pathway: map00902) and diterpenes (KEGG pathway: map00904), and triterpenes (KEGG pathway: map00909; map01062).…”

Genome-wide association study of terpenoids in resin reveals candidate genes for resin yield in Pinus massoniana

“…It has been reported that some members of the AP2 family are involved in the biosynthesis of various secondary metabolites including terpenoids (Udomsom et al, 2016;Paul et al, 2017;Zhang et al, 2019). ABC transporters are involved in the transportation of secondary metabolites in plants (Yazaki, 2006;Crouzet et al, 2013;Fu et al, 2017;Mao et al, 2019). It has been reported that ABC transporter is one of the important differentially expressed genes in P. massoniana (Liu et al, 2015).…”

Unravelling complex molecular mechanisms in pine with genome-wide association analysis and gene co-expression networks

“…Data available in the SRA database from three independent experiments were employed in this research [20][21][22] To detect correspondence of the transcripts to the genomic regions containing probes, all the assembled transcripts were aligned to the corresponding scaffolds with the BLASTn v.2.11.0 tool 59 , considering only alignments with a minimum e-value of 1e-30 and a transcript coverage of at least 75%.…”

“…LP has a complex, poorly characterized and extremely large genome (1C=21.6 Gb) 17,18 , which until now could be assembled into only a highly fragmented draft reference genome with more than one million scaffolds and up to an 82% content of various highly repetitive DNA elements 19 . Due to such complexity, most LP genomic studies have focused on the analysis of nuclear gene sequences, which are important for the application of genomic data to the improvement of this conifer [20][21][22][23] , even in cases of limited information 24 .…”