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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Autor*in:	Lin Jia [verfasserIn] Ning Xu [verfasserIn] Bin Xia [verfasserIn] Wenjie Gao [verfasserIn] Qingran Meng [verfasserIn] Qiang Li [verfasserIn] Ying Sun [verfasserIn] Shoubin Xu [verfasserIn] Miao He [verfasserIn] Huiyan Gu [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2024

Schlagwörter:	Thymus mandschuricus phylogeny CYP450 terpenoid biosynthesis aroma production

Übergeordnetes Werk:	In: Frontiers in Plant Science - Frontiers Media S.A., 2011, 15(2024)
Übergeordnetes Werk:	volume:15 ; year:2024

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3389/fpls.2024.1368869

Katalog-ID:	DOAJ098598163

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520			\|a 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.
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spelling	10.3389/fpls.2024.1368869 doi (DE-627)DOAJ098598163 (DE-599)DOAJe1d5587971614b649f96a964b0c4cb37 DE-627 ger DE-627 rakwb eng SB1-1110 Lin Jia verfasserin aut Chromosome-level genome of Thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Thymus mandschuricus phylogeny CYP450 terpenoid biosynthesis aroma production Plant culture Ning Xu verfasserin aut Bin Xia verfasserin aut Wenjie Gao verfasserin aut Qingran Meng verfasserin aut Qiang Li verfasserin aut Ying Sun verfasserin aut Shoubin Xu verfasserin aut Miao He verfasserin aut Miao He verfasserin aut Huiyan Gu verfasserin aut In Frontiers in Plant Science Frontiers Media S.A., 2011 15(2024) (DE-627)662359240 (DE-600)2613694-6 1664462X nnns volume:15 year:2024 https://doi.org/10.3389/fpls.2024.1368869 kostenfrei https://doaj.org/article/e1d5587971614b649f96a964b0c4cb37 kostenfrei https://www.frontiersin.org/articles/10.3389/fpls.2024.1368869/full kostenfrei https://doaj.org/toc/1664-462X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 15 2024
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allfieldsGer	10.3389/fpls.2024.1368869 doi (DE-627)DOAJ098598163 (DE-599)DOAJe1d5587971614b649f96a964b0c4cb37 DE-627 ger DE-627 rakwb eng SB1-1110 Lin Jia verfasserin aut Chromosome-level genome of Thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Thymus mandschuricus phylogeny CYP450 terpenoid biosynthesis aroma production Plant culture Ning Xu verfasserin aut Bin Xia verfasserin aut Wenjie Gao verfasserin aut Qingran Meng verfasserin aut Qiang Li verfasserin aut Ying Sun verfasserin aut Shoubin Xu verfasserin aut Miao He verfasserin aut Miao He verfasserin aut Huiyan Gu verfasserin aut In Frontiers in Plant Science Frontiers Media S.A., 2011 15(2024) (DE-627)662359240 (DE-600)2613694-6 1664462X nnns volume:15 year:2024 https://doi.org/10.3389/fpls.2024.1368869 kostenfrei https://doaj.org/article/e1d5587971614b649f96a964b0c4cb37 kostenfrei https://www.frontiersin.org/articles/10.3389/fpls.2024.1368869/full kostenfrei https://doaj.org/toc/1664-462X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 15 2024
allfieldsSound	10.3389/fpls.2024.1368869 doi (DE-627)DOAJ098598163 (DE-599)DOAJe1d5587971614b649f96a964b0c4cb37 DE-627 ger DE-627 rakwb eng SB1-1110 Lin Jia verfasserin aut Chromosome-level genome of Thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Thymus mandschuricus phylogeny CYP450 terpenoid biosynthesis aroma production Plant culture Ning Xu verfasserin aut Bin Xia verfasserin aut Wenjie Gao verfasserin aut Qingran Meng verfasserin aut Qiang Li verfasserin aut Ying Sun verfasserin aut Shoubin Xu verfasserin aut Miao He verfasserin aut Miao He verfasserin aut Huiyan Gu verfasserin aut In Frontiers in Plant Science Frontiers Media S.A., 2011 15(2024) (DE-627)662359240 (DE-600)2613694-6 1664462X nnns volume:15 year:2024 https://doi.org/10.3389/fpls.2024.1368869 kostenfrei https://doaj.org/article/e1d5587971614b649f96a964b0c4cb37 kostenfrei https://www.frontiersin.org/articles/10.3389/fpls.2024.1368869/full kostenfrei https://doaj.org/toc/1664-462X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 15 2024
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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. 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callnumber-first	S - Agriculture
author	Lin Jia
spellingShingle	Lin Jia misc SB1-1110 misc Thymus mandschuricus misc phylogeny misc CYP450 misc terpenoid biosynthesis misc aroma production misc Plant culture Chromosome-level genome of Thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis
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topic_title	SB1-1110 Chromosome-level genome of Thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis Thymus mandschuricus phylogeny CYP450 terpenoid biosynthesis aroma production
topic	misc SB1-1110 misc Thymus mandschuricus misc phylogeny misc CYP450 misc terpenoid biosynthesis misc aroma production misc Plant culture
topic_unstemmed	misc SB1-1110 misc Thymus mandschuricus misc phylogeny misc CYP450 misc terpenoid biosynthesis misc aroma production misc Plant culture
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title	Chromosome-level genome of Thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis
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title_full	Chromosome-level genome of Thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis
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author_browse	Lin Jia Ning Xu Bin Xia Wenjie Gao Qingran Meng Qiang Li Ying Sun Shoubin Xu Miao He Huiyan Gu
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title_sort	chromosome-level genome of thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis
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title_auth	Chromosome-level genome of Thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis
abstract	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.
abstractGer	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.
abstract_unstemmed	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.
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title_short	Chromosome-level genome of Thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis
url	https://doi.org/10.3389/fpls.2024.1368869 https://doaj.org/article/e1d5587971614b649f96a964b0c4cb37 https://www.frontiersin.org/articles/10.3389/fpls.2024.1368869/full https://doaj.org/toc/1664-462X
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author2	Ning Xu Bin Xia Wenjie Gao Qingran Meng Qiang Li Ying Sun Shoubin Xu Miao He Huiyan Gu
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up_date	2024-07-03T18:11:46.779Z
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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. 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Chromosome-level genome of Thymus mandschuricus reveals molecular mechanism of aroma compounds biosynthesis

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