A first draft genome of Holm oak (Quercus ilexL.), the most representative species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem “dehesa”

Abstract

The holm oak (Quercus ilex L.) is the most representative species of the Mediterranean Basin and the agrosilvopastoral Spanish dehesa ecosystem. Being part of our life, culture, and subsistence since ancient times, it has great environmental and economic importance. More recently, there has been a renewed interest in using the Q. ilex acorn as a functional food due to its nutritional and nutraceutical properties. However, the holm oak and its related ecosystems are threatened by different factors, with oak decline syndrome and climate change being the most worrying on the short and medium term. Breeding programs informed by selection of elite genotypes seems to be the only plausible biotechnological solution to rescue populations under threat. To achieve this and other downstream analyses, we need a high-quality Q. ilex reference genome. Here, we introduce the first draft genome assembly of Q. ilex using long-read sequencing (PacBio). The assembled nuclear haploid genome has 530 contigs totaling 842.2 Mbp (N50 = 3.3 Mbp), of which 448.7 Mb (53%) are repetitive sequences. We annotated 39,443 protein-coding genes and Benchmarking Universal Single-Copy Orthologs analysis detected 412 out of 425 expected complete and single-copy genes (94.80%) within the Q. ilex genome. The chloroplast genome size was 142.3 Kbp with 149 protein-coding genes successfully annotated. This first draft should allow for the validation of -omics data as well as the identification and functional annotation of genes related to phenotypes of interest such as those associated to resilience against oak decline syndrome and climate change, higher acorn productivity and nutraceutical value.

An Overview of Oak Species in Pakistan: Past, Present, and Future Research Perspectives

“…This revealed the plasticity of the organ, tree variability, and differences between developmental stages. Later, the first transcriptome and metabolome of a tissue mix were obtained [59,60]; recently, the genome was sequenced [61]. In other Quercus spp., the first studies have mainly focused on the genome, as it is essential for comprehending its biology and functionality.…”