De novo sequencing of the Lavandula angustifolia genome reveals highly duplicated and optimized features for essential oil production
Lavenders (Lavandula: Lamiaceae) are economically important plants widely grown around the world for their essential oils (EOs), which contribute to the cosmetic, personal hygiene, and pharmaceutical industries. To better understand the genetic mechanisms involved in EO production, identify genes in...
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| Veröffentlicht in: | Planta 2019-01, Vol.249 (1), p.251-256 |
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| creator | Malli, Radesh P. N. Adal, Ayelign M. Sarker, Lukman S. Liang, Ping Mahmoud, Soheil S. |
| description | Lavenders (Lavandula: Lamiaceae) are economically important plants widely grown around the world for their essential oils (EOs), which contribute to the cosmetic, personal hygiene, and pharmaceutical industries. To better understand the genetic mechanisms involved in EO production, identify genes involved in important biological processes, and find genetic markers for plant breeding, we generated the first de novo draft genome assembly for L. angustifolia (Maillette). This high-quality draft reveals a moderately repeated (> 48% repeated elements) 870 Mbp genome, composed of over 688 Mbp of non-gap sequences in 84,291 scaffolds with an N50 value of 96,735 bp. The genome contains 62,141 protein-coding genes and 2003 RNA-coding genes, with a large proportion of genes showing duplications, possibly reflecting past genome polyploidization. The draft genome contains full-length coding sequences for all genes involved in both cytosolic and plastidial pathways of isoprenoid metabolism, and all terpene synthase genes previously described from lavenders. Of particular interest is the observation that the genome contains a high copy number (14 and 7, respectively) of DXS (1-deoxyxylulose-5-phosphate synthase) and HDR (4-hydroxy-3-methylbut-2-enyl diphosphate reductase) genes, encoding the two known regulatory steps in the plastidial isoprenoid biosynthetic pathway. The latter generates precursors for the production of monoterpenes, the most abundant essential oil constituents in lavender. Furthermore, the draft genome contains a variety of monoterpene synthase genes, underlining the production of several monoterpene essential oil constituents in lavender. Taken together, these findings indicate that the genome of L. angustifolia is highly duplicated and optimized for essential oil production. |
| doi_str_mv | 10.1007/s00425-018-3012-9 |
| format | Article |
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N. ; Adal, Ayelign M. ; Sarker, Lukman S. ; Liang, Ping ; Mahmoud, Soheil S.</creator><creatorcontrib>Malli, Radesh P. N. ; Adal, Ayelign M. ; Sarker, Lukman S. ; Liang, Ping ; Mahmoud, Soheil S.</creatorcontrib><description>Lavenders (Lavandula: Lamiaceae) are economically important plants widely grown around the world for their essential oils (EOs), which contribute to the cosmetic, personal hygiene, and pharmaceutical industries. To better understand the genetic mechanisms involved in EO production, identify genes involved in important biological processes, and find genetic markers for plant breeding, we generated the first de novo draft genome assembly for L. angustifolia (Maillette). This high-quality draft reveals a moderately repeated (> 48% repeated elements) 870 Mbp genome, composed of over 688 Mbp of non-gap sequences in 84,291 scaffolds with an N50 value of 96,735 bp. The genome contains 62,141 protein-coding genes and 2003 RNA-coding genes, with a large proportion of genes showing duplications, possibly reflecting past genome polyploidization. The draft genome contains full-length coding sequences for all genes involved in both cytosolic and plastidial pathways of isoprenoid metabolism, and all terpene synthase genes previously described from lavenders. Of particular interest is the observation that the genome contains a high copy number (14 and 7, respectively) of DXS (1-deoxyxylulose-5-phosphate synthase) and HDR (4-hydroxy-3-methylbut-2-enyl diphosphate reductase) genes, encoding the two known regulatory steps in the plastidial isoprenoid biosynthetic pathway. The latter generates precursors for the production of monoterpenes, the most abundant essential oil constituents in lavender. Furthermore, the draft genome contains a variety of monoterpene synthase genes, underlining the production of several monoterpene essential oil constituents in lavender. Taken together, these findings indicate that the genome of L. angustifolia is highly duplicated and optimized for essential oil production.</description><identifier>ISSN: 0032-0935</identifier><identifier>EISSN: 1432-2048</identifier><identifier>DOI: 10.1007/s00425-018-3012-9</identifier><identifier>PMID: 30269192</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Science + Business Media</publisher><subject>Agriculture ; Assembly ; Biological activity ; Biomedical and Life Sciences ; Constituents ; Copy number ; Ecology ; Economic importance ; Essential oils ; Forestry ; Gene sequencing ; Genes ; Genetic markers ; Genomes ; Lavandula ; Lavandula - genetics ; Lavandula - metabolism ; Life Sciences ; Metabolism ; Monoterpenes ; Oils & fats ; Oils, Volatile - metabolism ; ORIGINAL ARTICLE ; Personal hygiene ; Pharmaceutical industry ; Plant breeding ; Plant Sciences ; Polyploidy ; Proteins ; Reductase ; Reproduction (copying) ; Ribonucleic acid ; RNA ; Terpene synthase ; Terpenes - metabolism ; Terpenes and Isoprenoids</subject><ispartof>Planta, 2019-01, Vol.249 (1), p.251-256</ispartof><rights>The Author(s) 2018</rights><rights>Planta is a copyright of Springer, (2018). 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This high-quality draft reveals a moderately repeated (> 48% repeated elements) 870 Mbp genome, composed of over 688 Mbp of non-gap sequences in 84,291 scaffolds with an N50 value of 96,735 bp. The genome contains 62,141 protein-coding genes and 2003 RNA-coding genes, with a large proportion of genes showing duplications, possibly reflecting past genome polyploidization. The draft genome contains full-length coding sequences for all genes involved in both cytosolic and plastidial pathways of isoprenoid metabolism, and all terpene synthase genes previously described from lavenders. Of particular interest is the observation that the genome contains a high copy number (14 and 7, respectively) of DXS (1-deoxyxylulose-5-phosphate synthase) and HDR (4-hydroxy-3-methylbut-2-enyl diphosphate reductase) genes, encoding the two known regulatory steps in the plastidial isoprenoid biosynthetic pathway. 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N.</au><au>Adal, Ayelign M.</au><au>Sarker, Lukman S.</au><au>Liang, Ping</au><au>Mahmoud, Soheil S.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>De novo sequencing of the Lavandula angustifolia genome reveals highly duplicated and optimized features for essential oil production</atitle><jtitle>Planta</jtitle><stitle>Planta</stitle><addtitle>Planta</addtitle><date>2019-01-01</date><risdate>2019</risdate><volume>249</volume><issue>1</issue><spage>251</spage><epage>256</epage><pages>251-256</pages><issn>0032-0935</issn><eissn>1432-2048</eissn><abstract>Lavenders (Lavandula: Lamiaceae) are economically important plants widely grown around the world for their essential oils (EOs), which contribute to the cosmetic, personal hygiene, and pharmaceutical industries. To better understand the genetic mechanisms involved in EO production, identify genes involved in important biological processes, and find genetic markers for plant breeding, we generated the first de novo draft genome assembly for L. angustifolia (Maillette). This high-quality draft reveals a moderately repeated (> 48% repeated elements) 870 Mbp genome, composed of over 688 Mbp of non-gap sequences in 84,291 scaffolds with an N50 value of 96,735 bp. The genome contains 62,141 protein-coding genes and 2003 RNA-coding genes, with a large proportion of genes showing duplications, possibly reflecting past genome polyploidization. The draft genome contains full-length coding sequences for all genes involved in both cytosolic and plastidial pathways of isoprenoid metabolism, and all terpene synthase genes previously described from lavenders. Of particular interest is the observation that the genome contains a high copy number (14 and 7, respectively) of DXS (1-deoxyxylulose-5-phosphate synthase) and HDR (4-hydroxy-3-methylbut-2-enyl diphosphate reductase) genes, encoding the two known regulatory steps in the plastidial isoprenoid biosynthetic pathway. The latter generates precursors for the production of monoterpenes, the most abundant essential oil constituents in lavender. Furthermore, the draft genome contains a variety of monoterpene synthase genes, underlining the production of several monoterpene essential oil constituents in lavender. Taken together, these findings indicate that the genome of L. angustifolia is highly duplicated and optimized for essential oil production.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Science + Business Media</pub><pmid>30269192</pmid><doi>10.1007/s00425-018-3012-9</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Agriculture Assembly Biological activity Biomedical and Life Sciences Constituents Copy number Ecology Economic importance Essential oils Forestry Gene sequencing Genes Genetic markers Genomes Lavandula Lavandula - genetics Lavandula - metabolism Life Sciences Metabolism Monoterpenes Oils & fats Oils, Volatile - metabolism ORIGINAL ARTICLE Personal hygiene Pharmaceutical industry Plant breeding Plant Sciences Polyploidy Proteins Reductase Reproduction (copying) Ribonucleic acid RNA Terpene synthase Terpenes - metabolism Terpenes and Isoprenoids |
| title | De novo sequencing of the Lavandula angustifolia genome reveals highly duplicated and optimized features for essential oil production |
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