Quick and efficient approach to develop genomic resources in orphan species: Application in Lavandula angustifolia

Abstract

Next-Generation Sequencing (NGS) technologies, by reducing the cost and increasing the throughput of sequencing, have opened doors to generate genomic data in a range of previously poorly studied species. In this study, we propose a method for the rapid development of a large-scale molecular resources for orphan species. We studied as an example the true lavender (Lavandula angustifolia Mill.), a perennial sub-shrub plant native from the Mediterranean region and whose essential oil have numerous applications in cosmetics, pharmaceuticals, and alternative medicines. The heterozygous clone “Maillette” was used as a reference for DNA and RNA sequencing. We first built a reference Unigene, compound of coding sequences, thanks to de novo RNA-seq assembly. Then, we reconstructed the complete genes sequences (with introns and exons) using an Unigene-guided DNA-seq assembly approach. This aimed to maximize the possibilities of finding polymorphism between genetically close individuals despite the lack of a reference genome. Finally, we used these resources for SNP mining within a collection of 16 commercial lavender clones and tested the SNP within the scope of a genetic distance analysis. We obtained a cleaned reference of 8, 030 functionally in silico annotated genes. We found 359K polymorphic sites and observed a high SNP frequency (mean of 1 SNP per 90 bp) and a high level of heterozygosity (more than 60% of heterozygous SNP per genotype). On overall, we found similar genetic distances between pairs of clones, which is probably related to the out-crossing nature of the species and the restricted area of cultivation. The proposed method is transferable to other orphan species, requires little bioinformatics resources and can be realized within a year. This is also the first reported large-scale SNP development on Lavandula angustifolia. All the genomics resources developed herein are publicly available and provide a rich pool of molecular resources to explore and exploit lavender genetic diversity in breeding programs.

Gene Expression of Monoterpene Synthases Is Affected Rhythmically during the Day in Lavandula angustifolia Flowers

“…Monoterpenes and other volatile organic compounds (VOCs) synthesis differ throughout plant development as a result of the differential gene expression patterns in distinct cell types [24]. Most likely, genes involved in the synthesis of VOCs are Several genomic and transcriptomics resources for L. angustifolia were developed to investigate the regulation of EO production in leaves and flowers [16][17][18][19][20]. Finally, the first chromosome-level genome assembly of L. angustifolia was recently reported [21].…”

“…Linalool, β-myrcene, geraniol and ocimene are derived from geranyl and linalyl cations [9,14]. Several genomic and transcriptomics resources for L. angustifolia were developed to investigate the regulation of EO production in leaves and flowers [16][17][18][19][20]. Finally, the first chromosome-level genome assembly of L. angustifolia was recently reported [21].…”

Challenges in Medicinal and Aromatic Plants DNA Barcoding—Lessons from the Lamiaceae

“…Rastogi et al [ 196 ] reported the comprehensive transcriptome analysis of Ocimum species and identified transcriptome SNPs and SSR markers that could be used for the identification of closely related taxa in the genus. Likewise, SNP data was discovered from transcriptome assemblies of Lavandula clones to differentiate between L. angustifolia and its hybrid L. latifolia [ 305 ].…”