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

• Published in: PloS one 2020-12, Vol.15 (12), p.e0243853-e0243853
• Main Authors: Fopa Fomeju, Berline, Brunel, Dominique, Bérard, Aurélie, Rivoal, Jean-Baptiste, Gallois, Philippe, Le Paslier, Marie-Christine, Bouverat-Bernier, Jean-Pierre
• Format: Article
• Language: English
• Subjects: Assembly; Base Sequence; Bioinformatics; Biology and Life Sciences; Breeding; Cloning; Computer Simulation; Cosmetics; Cultivation; Deoxyribonucleic acid; DNA; DNA sequencing; DNA, Plant - genetics; Essential oils; Exons; Exons - genetics; Flowers & plants; Gene polymorphism; Gene sequencing; Genes; Genetic analysis; Genetic aspects; Genetic distance; Genetic diversity; Genetic testing; Genome, Plant; Genomes; Genomics; Genomics - methods; Herbal medicine; Heterozygosity; High-throughput screening (Biochemical assaying); Introns; Introns - genetics; Lavandula; Lavandula - genetics; Lavandula angustifolia; Methods; Molecular Sequence Annotation; Next-generation sequencing; Nucleotide sequence; Oils & fats; Phylogeny; Polymorphism; Polymorphism, Single Nucleotide - genetics; Principal Component Analysis; Research and Analysis Methods; Ribonucleic acid; RNA; RNA-Seq; Single-nucleotide polymorphism; Species; Transcriptome - genetics
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0243853

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.