The sage genome provides insight into the evolutionary dynamics of diterpene biosynthesis gene cluster in plants

Li, Chen-Yi; Yang, Lei; Liu, Yan; Xu, Zhou-Geng; Huang, Yanbo; Xu, Jian; Fan, Hang; Kong, Yu; Wei, Yukun; Hu, W. Z.; Zhao, Qing; Hu, Yonghong; Zhang, Yijing; Martin, Cathie; Chen, Xiaoya

doi:10.1016/j.celrep.2022.111236

Cited by 31 publications

(40 citation statements)

References 114 publications

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“…Transcriptome sequencing of other tissues of S. rosmarinus and JA treatments from NCBI: PRJNA80069. The genome sequence numbers or reference links used in the article are as follows: Tectona grandis (Zhao et al., 2019), Scutellaria barbata (Xu et al., 2020), Scutellaria baicalensis (Xu et al., 2020), Salvia bowleyana (Zheng et al., 2021), Salvia officinalis (Li et al., 2022), Salvia miltiorrhiza (Song et al., 2020), Salvia splendens (Jia et al., 2021), Origanum vulgare (Bornowski et al., 2020), and Callicarpa americana (Hamilton et al., 2020).…”

Section: Data Availability Statementmentioning

confidence: 99%

The chromosome‐scale assembly of the Salvia rosmarinus genome provides insight into carnosic acid biosynthesis

Han

Hou

et al. 2023

The Plant Journal

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SUMMARY Rosemary (Salvia rosmarinus) is considered a sacred plant because of its special fragrance and is commonly used in cooking and traditional medicine. Here, we report a high‐quality chromosome‐level assembly of the S. rosmarinus genome of 1.11 Gb in size; the genome has a scaffold N50 value of 95.5 Mb and contains 40 701 protein‐coding genes. In contrast to other diploid Labiataceae, an independent whole‐genome duplication event occurred in S. rosmarinus at approximately 15 million years ago. Transcriptomic comparison of two S. rosmarinus cultivars with contrasting carnosic acid (CA) content revealed 842 genes significantly positively associated with CA biosynthesis in S. rosmarinus. Many of these genes have been reported to be involved in CA biosynthesis previously, such as genes involved in the mevalonate/methylerythritol phosphate pathways and CYP71‐coding genes. Based on the genomes and these genes, we propose a model of CA biosynthesis in S. rosmarinus. Further, comparative genome analysis of the congeneric species revealed the species‐specific evolution of CA biosynthesis genes. The genes encoding diterpene synthase and the cytochrome P450 (CYP450) family of CA synthesis‐associated genes form a biosynthetic gene cluster (CPSs–KSLs–CYP76AHs) responsible for the synthesis of leaf and root diterpenoids, which are located on S. rosmarinus chromosomes 1 and 2, respectively. Such clustering is also observed in other sage (Salvia) plants, thus suggesting that genes involved in diterpenoid synthesis are conserved in the Labiataceae family. These findings provide new insights into the synthesis of aromatic terpenoids and their regulation.

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Section: Data Availability Statementmentioning

confidence: 99%

The chromosome‐scale assembly of the Salvia rosmarinus genome provides insight into carnosic acid biosynthesis

Han

Hou

et al. 2023

The Plant Journal

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Section: Introductionmentioning

confidence: 99%

“…The nuclear genome of S. officinalis was reported recently and revealed a genomic size of 480 Mb and seven chromosomes [ 10 ]. Two expression cascades have been identified as the regulating factors of the biosynthesis of shoot and root diterpenoids, particularly the diterpene biosynthesis gene cluster [ 10 ]. Furthermore, genetic and metabolomic studies have focused on discerning the genes and pathways that underpin volatile terpenoid biosynthesis [ 11 , 12 ] and the genetic diversity of seven S. officinalis populations in Greece [ 13 ].…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial Genome Sequence of Salvia officinalis (Lamiales: Lamiaceae) Suggests Diverse Genome Structures in Cogeneric Species and Finds the Stop Gain of Genes through RNA Editing Events

Yang

Chen

et al. 2023

IJMS

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Our previous study was the first to confirm that the predominant conformation of mitochondrial genome (mitogenome) sequence of Salvia species contains two circular chromosomes. To further understand the organization, variation, and evolution of Salvia mitogenomes, we characterized the mitogenome of Salvia officinalis. The mitogenome of S. officinalis was sequenced using Illumina short reads and Nanopore long reads and assembled using a hybrid assembly strategy. We found that the predominant conformation of the S. officinalis mitogenome also had two circular chromosomes that were 268,341 bp (MC1) and 39,827 bp (MC2) in length. The S. officinalis mitogenome encoded an angiosperm-typical set of 24 core genes, 9 variable genes, 3 rRNA genes, and 16 tRNA genes. We found many rearrangements of the Salvia mitogenome through inter- and intra-specific comparisons. A phylogenetic analysis of the coding sequences (CDs) of 26 common protein-coding genes (PCGs) of 11 Lamiales species and 2 outgroup taxa strongly indicated that the S. officinalis was a sister taxon to S. miltiorrhiza, consistent with the results obtained using concatenated CDs of common plastid genes. The mapping of RNA-seq data to the CDs of PCGs led to the identification of 451 C-to-U RNA editing sites from 31 PCGs of the S. officinalis mitogenome. Using PCR amplification and Sanger sequencing methods, we successfully validated 113 of the 126 RNA editing sites from 11 PCGs. The results of this study suggest that the predominant conformation of the S. officinalis mitogenome are two circular chromosomes, and the stop gain of rpl5 was found through RNA editing events of the Salvia mitogenome.

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“…According to previous studies ( Supplementary Table 1 ), nuclear genomes of medicinal plants are usually diploids or polyploids with large genome sizes, high heterozygosity, and high repeat sequences proportion. It is also demonstrated that the GC content of nuclear genomes of many medicinal plants is generally lower than 50% on average and unevenly distributed in different chromosomes ( Shang et al., 2020 ; Sun et al., 2020 ; Wu et al., 2021b ; Li et al., 2022a ; Xu et al., 2022a ). These features have brought traditional short reads methods under challenge.…”

Section: Advantages and Challengesmentioning

confidence: 99%

Application of third-generation sequencing to herbal genomics

Gao

Xu²,

Xin³

et al. 2023

Front. Plant Sci.

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There is a long history of traditional medicine use. However, little genetic information is available for the plants used in traditional medicine, which limits the exploitation of these natural resources. Third-generation sequencing (TGS) techniques have made it possible to gather invaluable genetic information and develop herbal genomics. In this review, we introduce two main TGS techniques, PacBio SMRT technology and Oxford Nanopore technology, and compare the two techniques against Illumina, the predominant next-generation sequencing technique. In addition, we summarize the nuclear and organelle genome assemblies of commonly used medicinal plants, choose several examples from genomics, transcriptomics, and molecular identification studies to dissect the specific processes and summarize the advantages and disadvantages of the two TGS techniques when applied to medicinal organisms. Finally, we describe how we expect that TGS techniques will be widely utilized to assemble telomere-to-telomere (T2T) genomes and in epigenomics research involving medicinal plants.

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The sage genome provides insight into the evolutionary dynamics of diterpene biosynthesis gene cluster in plants

Cited by 31 publications

References 114 publications

The chromosome‐scale assembly of the Salvia rosmarinus genome provides insight into carnosic acid biosynthesis

The chromosome‐scale assembly of the Salvia rosmarinus genome provides insight into carnosic acid biosynthesis

Mitochondrial Genome Sequence of Salvia officinalis (Lamiales: Lamiaceae) Suggests Diverse Genome Structures in Cogeneric Species and Finds the Stop Gain of Genes through RNA Editing Events

Application of third-generation sequencing to herbal genomics

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