A first draft genome of holm oak (Quercus ilex subsp. ballota), the most representative species of the Mediterranean forest and the Spanish agrosylvopastoral ecosystem “dehesa”.
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Resource type
Journal article
Date published
October 12, 2023
Abstract
The holm oak ( subsp. ) is the most representative species of the Mediterranean Basin and the agrosylvopastoral Spanish “ ” ecosystem. Being part of our life, culture, and subsistence since ancient times, it has significant environmental and economic importance. More recently, there has been a renewed interest in using the 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 in the short and medium term. Breeding programs informed by the selection of elite genotypes seem to be the most plausible biotechnological solution to rescue populations under threat. To achieve this and other downstream analyses, we need a high-quality and well-annotated reference genome. Here, we introduce the first draft genome assembly of using long-read sequencing (PacBio). The assembled nuclear haploid genome had 530 contigs totaling 842.2 Mbp (N50 = 3.3 Mbp), of which 448.7 Mb (53%) were repetitive sequences. We annotated 39,443 protein-coding genes of which 94.80% were complete and single-copy genes. Phylogenetic analyses showed no evidence of a recent whole-genome duplication, and high synteny of the 12 chromosomes between and and between and . 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 with resilience against oak decline syndrome and climate change and higher acorn productivity and nutraceutical value.
Funder
| Funder name | Awards |
Ministerio de Ciencia, Tecnología e Innovación, Spain | Ramón y Cajal (RYC-2017-23706) - Juan de la Cierva-Incorporación (IJC2018-035272-I) contract |
Junta de Andalucía, Spain | UCO_FEDER-18-12575795R grant - PROYEXCEL_00881 grant |
Ministerio de Economía y Competitividad, Spain | ENCINOMICS-2 PID 2019-109038RB-100 grant |
Journal title
Frontiers in Molecular Biosciences
Volume
10
Article number
1242943.
Publisher
Frontiers Media SA
Place of publication
Lausanne, Switzerland
eISSN
2296-889X
Date accepted
September 20, 2023
Official URL
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In Copyright
Additional information
IF = 6.113 (2022-2023)