Show simple item record

dc.contributor.authorNattamai Malli Pooranachandhiran, Radesh
dc.date.accessioned2021-11-22T14:28:56Z
dc.date.available2021-11-22T14:28:56Z
dc.identifier.urihttp://hdl.handle.net/10464/15436
dc.description.abstractLavender (Lavandula angustifolia) is a perennial plant native to the Mediterranean region, best known for its essential oil (EOs) that have numerous applications in the pharmaceutical, cosmetic and perfume industries. We performed sequencing of the L. angustifolia genome and report a detailed analysis of the assembled genome, focusing on genome size, ploidy, and repeat content. The lavender genome was estimated to be around 870 Mbp (1C=0.96 pg) using a quantitative PCR method. Genome size was further validated through analysis of raw genome sequences using Kmergenie, providing a conclusive end to the lavender genome size dispute. The repeat element composition of the genome was analyzed using de novo (RepeatModeler) and library-based methods (RepeatMasker) and was estimated to be around 45% of the full genome or ~57% of the non-gap genome sequences. Further characterization revealed Long Terminal Repeat (LTRs) retrotransposons as the major repeat type, which contribute to ~18% of the genome, followed by DNA transposons at ~8.5% of the genome. Interestingly, unlike most other plant genomes, the lavender genome has many more Copia than Gypsy elements, both showing a trend of recent increasing activity. Furthermore, these LTRs, especially Copia elements, have shown active participation in gene function including genes for essential oil production, with Copia elements contributing to ~30 % of the coding DNA sequence (CDS) regions, in addition to promoter, intron and untranslated (UTR) regions. The lavender genome also has an unusually high number of miniature inverted-repeat transposable elements (MITEs) compared to other model plant genomes, with the number being ~88,000, which is close to that (~90,000) of the much larger maize genome. Analysis also revealed the lavender genome with a high proportion at polyploidy level, which is strongly biased towards regions containing essential oil genes, with polyploidization events in the lavender genome occurred between 16 to 41 Mya. In conclusion, our results reveal the lavender genome to be highly duplicated and with past and ongoing active retrotransposition, making the genome optimized for EO production.en_US
dc.language.isoengen_US
dc.publisherBrock Universityen_US
dc.subjectLavandula angustifoliaen_US
dc.subjectIllumina sequencingen_US
dc.subjectgenome size estimationen_US
dc.subjectde novo genome assembly and annotationen_US
dc.subjectessential oil pathwaysen_US
dc.titleDe novo sequencing, annotation, and characterization of the genome of Lavandula angustifolia (Lavender)en_US
dc.typeElectronic Thesis or Dissertationen
dc.degree.namePh.D. Biotechnologyen_US
dc.degree.levelDoctoralen_US
dc.contributor.departmentCentre for Biotechnologyen_US
dc.degree.disciplineFaculty of Mathematics and Scienceen_US
refterms.dateFOA2021-11-22T14:28:57Z


Files in this item

Thumbnail
Name:
Brock_NattamaiMalliPooranachan ...
Size:
2.824Mb
Format:
PDF
Description:
Thesis

This item appears in the following Collection(s)

Show simple item record