Characterization and functional analysis of the Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) gene family in poplar

Chen, Nan; Qi, Qi; Li, Shuang; Ruan, Brent; Jiang, Xiangning; Gai, Ying

doi:10.7717/peerj.10741

Cited by 13 publications

(8 citation statements)

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“…Dirigent protein not only plays an important role in the synthesis of plant secondary metabolites, but also participates in the plant stress resistance in Arabidopsis thaliana (Modolo et al, 2020). Hydroxycinnamoyl transferase (HCT) divides the mass flux to H, G and S units in monolignol biosynthesis and affects lignin content in Populus (Chao et al, 2021). In addition to A .…”

Section: Discussionmentioning

confidence: 99%

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The first high‐quality chromosomal genome assembly of a medicinal and edible plant Arctium lappa

Yang

Xing

et al. 2021

Molecular Ecology Resources

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Arctium lappa has a long medicinal and edible history with great economic importance.Here, the first high-quality chromosome-level draft genome of A. lappa was presented by the Illumina and PacBio sequencing data. The assembled genome was approximately 1.79 Gb with a N50 contig size of 6.88 Mb. Approximately 1.70 Gb (95.4%) of the contig sequences were anchored onto 18 chromosomes using Hi-C data; the scaffold N50 was improved to be 91.64 Mb. Furthermore, we obtained 1.12 Gb (68.46%) of repetitive sequences and 32,771 protein-coding genes; 616 positively selected candidate genes were identified. Among candidate genes related to lignan biosynthesis, the following were found to be highly correlated with the accumulation of arctiin: 4-coumarate-CoA ligase (4CL), dirigent protein (DIR), and hydroxycinnamoyl transferase (HCT). Additionally, we compared the transcriptomes of A. lappa roots at three different developmental stages and identified 8,943 differentially expressed genes (DEGs) in these tissues. These data can be utilized to identify genes related to A. lappa quality or provide a basis for molecular identification and comparative genomics among related species.

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Section: Discussionmentioning

confidence: 99%

“…Hydroxycinnamoyl transferase (HCT) divides the mass flux to H, G and S units in monolignol biosynthesis and affects lignin content in Populus (Chao et al, 2021). In addition to A. lappa, other plants of the Asteraceae are also enriched in these genes.…”

Section: Discussionmentioning

confidence: 99%

The first high‐quality chromosomal genome assembly of a medicinal and edible plant Arctium lappa

Yang

Xing

et al. 2021

Molecular Ecology Resources

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“…Phylogenetic analysis showed that the PAL genes were clustering with the reported PAL from monocotyledonous cereal crops, like rice and triticum, rather than the PAL from dicotyledonous plants such as Arabidopsis ( Zhu et al., 1995 ; Liao et al., 1996 ) ( Figure 3D ). Si016926m clustering with the HCT/HQT genes that had been reported to transfer hydroxycinnamate to shikimate or quinine, and is involved in the formation of phenolic acid ( Chao et al., 2021 ) ( Figure 3E ).…”

Section: Resultsmentioning

confidence: 99%

QTL analysis of important agronomic traits and metabolites in foxtail millet (Setaria italica) by RIL population and widely targeted metabolome

Wei

Li³

et al. 2023

Front. Plant Sci.

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As a bridge between genome and phenotype, metabolome is closely related to plant growth and development. However, the research on the combination of genome, metabolome and multiple agronomic traits in foxtail millet (Setaria italica) is insufficient. Here, based on the linkage analysis of 3,452 metabolites via with high-quality genetic linkage maps, we detected a total of 1,049 metabolic quantitative trait loci (mQTLs) distributed in 11 hotspots, and 28 metabolite-related candidate genes were mined from 14 mQTLs. In addition, 136 single-environment phenotypic QTL (pQTLs) related to 63 phenotypes were identified by linkage analysis, and there were 12 hotspots on these pQTLs. We futher dissected 39 candidate genes related to agronomic traits through metabolite-phenotype correlation and gene function analysis, including Sd1 semidwarf gene, which can affect plant height by regulating GA synthesis. Combined correlation network and QTL analysis, we found that flavonoid-lignin pathway maybe closely related to plant architecture and yield in foxtail millet. For example, the correlation coefficient between apigenin 7-rutinoside and stem diameter reached 0.98, and they were co-located at 41.33-44.15 Mb of chromosome 5, further gene function analysis revealed that 5 flavonoid pathway genes, as well as Sd1, were located in this interval . Therefore, the correlation and co-localization between flavonoid-lignins and plant architecture may be due to the close linkage of their regulatory genes in millet. Besides, we also found that a combination of genomic and metabolomic for BLUP analysis can better predict plant agronomic traits than genomic or metabolomic data, independently. In conclusion, the combined analysis of mQTL and pQTL in millet have linked genetic, metabolic and agronomic traits, and is of great significance for metabolite-related molecular assisted breeding.

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“…Previously, p -hydroxyphenyl (H), guaiacyl (G), and syringyl (S) lignin were the only known lignin monomers. Recent studies have reported that catechyl (C) and 5 - Hydroxy -guaiacyl (5H) monomers contribute to lignin polymerization in some plant species [ 17 , 18 , 19 , 20 ]. A total of 11 lignin family enzymes and 24 metabolites are currently associated with the lignin pathway [ 17 , 18 , 19 , 20 ].…”

Section: Introductionmentioning

confidence: 99%

Lignin and Its Pathway-Associated Phytoalexins Modulate Plant Defense against Fungi

Ninkuu

Yan

et al. 2022

JoF

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Fungi infections cause approximately 60–70% yield loss through diseases such as rice blast, powdery mildew, Fusarium rot, downy mildew, etc. Plants naturally respond to these infections by eliciting an array of protective metabolites to confer physical or chemical protection. Among plant metabolites, lignin, a phenolic compound, thickens the middle lamella and the secondary cell walls of plants to curtail fungi infection. The biosynthesis of monolignols (lignin monomers) is regulated by genes whose transcript abundance significantly improves plant defense against fungi. The catalytic activities of lignin biosynthetic enzymes also contribute to the accumulation of other defense compounds. Recent advances focus on modifying the lignin pathway to enhance plant growth and defense against pathogens. This review presents an overview of monolignol regulatory genes and their contributions to fungi immunity, as reported over the last five years. This review expands the frontiers in lignin pathway engineering to enhance plant defense.

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Characterization and functional analysis of the Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) gene family in poplar

Cited by 13 publications

References 50 publications

The first high‐quality chromosomal genome assembly of a medicinal and edible plant Arctium lappa

The first high‐quality chromosomal genome assembly of a medicinal and edible plant Arctium lappa

QTL analysis of important agronomic traits and metabolites in foxtail millet (Setaria italica) by RIL population and widely targeted metabolome

Lignin and Its Pathway-Associated Phytoalexins Modulate Plant Defense against Fungi

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