Chromosome-level genome of Thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis
BackgroundThymus mandschuricus is an aromatic and medicinal plant with notable antibacterial and antioxidant properties. However, traditional breeding methods rely on phenotypic selection due to a lack of molecular resources. A high-quality reference genome is crucial for marker-assisted breeding, g...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2024-03-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1368869/full |
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| author | Lin Jia Ning Xu Bin Xia Wenjie Gao Qingran Meng Qiang Li Ying Sun Shoubin Xu Miao He Miao He Huiyan Gu |
| author_facet | Lin Jia Ning Xu Bin Xia Wenjie Gao Qingran Meng Qiang Li Ying Sun Shoubin Xu Miao He Miao He Huiyan Gu |
| author_sort | Lin Jia |
| collection | DOAJ |
| description | BackgroundThymus mandschuricus is an aromatic and medicinal plant with notable antibacterial and antioxidant properties. However, traditional breeding methods rely on phenotypic selection due to a lack of molecular resources. A high-quality reference genome is crucial for marker-assisted breeding, genome editing, and molecular genetics.ResultsWe utilized PacBio and Hi-C technologies to generate a high-quality chromosome-level reference genome for T. mandschuricus, with a size of 587.05 Mb and an N50 contig size of 8.41 Mb. The assembled genome contained 29,343 predicted protein-coding genes, and evidence of two distinct whole-genome duplications in T. mandschuricus was discovered. Comparative genomic analysis revealed rapid evolution of genes involved in phenylpropanoid biosynthesis and the CYP450 gene family in T. mandschuricus. Additionally, we reconstructed the gene families of terpenoid biosynthesis structural genes, such as TPS, BAHD, and CYP, and identified regulatory networks controlling the expression of aroma-synthesis genes by integrating transcriptome data from various organs and developmental stages. We discovered that hormones and transcription factors may collaborate in controlling aroma-synthesis gene expression.ConclusionThis study provides the first high-quality genome sequence and gene annotation for T. mandschuricus, an indigenous thyme species unique to China. The genome assembly and the comprehension of the genetic basis of fragrance synthesis acquired from this research could potentially serve as targets for future breeding programs and functional studies. |
| first_indexed | 2024-04-25T00:17:10Z |
| format | Article |
| id | doaj.art-e1d5587971614b649f96a964b0c4cb37 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-25T00:17:10Z |
| publishDate | 2024-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-e1d5587971614b649f96a964b0c4cb372024-03-13T04:18:46ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2024-03-011510.3389/fpls.2024.13688691368869Chromosome-level genome of Thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesisLin Jia0Ning Xu1Bin Xia2Wenjie Gao3Qingran Meng4Qiang Li5Ying Sun6Shoubin Xu7Miao He8Miao He9Huiyan Gu10School of Forestry, Northeast Forestry University, Harbin, ChinaSchool of Forestry, Northeast Forestry University, Harbin, ChinaCollege of Landscape Architecture, Northeast Forestry University, Harbin, ChinaSchool of Ecological Technology and Engineering, Shanghai Institute of Technology, Shanghai, ChinaSchool of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, ChinaCollege of Landscape Architecture, Northeast Forestry University, Harbin, ChinaCollege of Landscape Architecture, Northeast Forestry University, Harbin, ChinaHeilongjiang Academy of Forestry, Harbin, ChinaSchool of Forestry, Northeast Forestry University, Harbin, ChinaCollege of Landscape Architecture, Northeast Forestry University, Harbin, ChinaSchool of Forestry, Northeast Forestry University, Harbin, ChinaBackgroundThymus mandschuricus is an aromatic and medicinal plant with notable antibacterial and antioxidant properties. However, traditional breeding methods rely on phenotypic selection due to a lack of molecular resources. A high-quality reference genome is crucial for marker-assisted breeding, genome editing, and molecular genetics.ResultsWe utilized PacBio and Hi-C technologies to generate a high-quality chromosome-level reference genome for T. mandschuricus, with a size of 587.05 Mb and an N50 contig size of 8.41 Mb. The assembled genome contained 29,343 predicted protein-coding genes, and evidence of two distinct whole-genome duplications in T. mandschuricus was discovered. Comparative genomic analysis revealed rapid evolution of genes involved in phenylpropanoid biosynthesis and the CYP450 gene family in T. mandschuricus. Additionally, we reconstructed the gene families of terpenoid biosynthesis structural genes, such as TPS, BAHD, and CYP, and identified regulatory networks controlling the expression of aroma-synthesis genes by integrating transcriptome data from various organs and developmental stages. We discovered that hormones and transcription factors may collaborate in controlling aroma-synthesis gene expression.ConclusionThis study provides the first high-quality genome sequence and gene annotation for T. mandschuricus, an indigenous thyme species unique to China. The genome assembly and the comprehension of the genetic basis of fragrance synthesis acquired from this research could potentially serve as targets for future breeding programs and functional studies.https://www.frontiersin.org/articles/10.3389/fpls.2024.1368869/fullThymus mandschuricusphylogenyCYP450terpenoid biosynthesisaroma production |
| spellingShingle | Lin Jia Ning Xu Bin Xia Wenjie Gao Qingran Meng Qiang Li Ying Sun Shoubin Xu Miao He Miao He Huiyan Gu Chromosome-level genome of Thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis Frontiers in Plant Science Thymus mandschuricus phylogeny CYP450 terpenoid biosynthesis aroma production |
| title | Chromosome-level genome of Thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis |
| title_full | Chromosome-level genome of Thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis |
| title_fullStr | Chromosome-level genome of Thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis |
| title_full_unstemmed | Chromosome-level genome of Thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis |
| title_short | Chromosome-level genome of Thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis |
| title_sort | chromosome level genome of thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis |
| topic | Thymus mandschuricus phylogeny CYP450 terpenoid biosynthesis aroma production |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1368869/full |
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