Abstract
Cork oak (Quercus suber) is native to southwest Europe and northwest Africa where it plays a crucial environmental and economical role. To tackle the cork oak production and industrial challenges, advanced research is imperative but dependent on the availability of a sequenced genome. To address this, we produced the first draft version of the cork oak genome. We followed a de novo assembly strategy based on high-throughput sequence data, which generated a draft genome comprising 23,347 scaffolds and 953.3 Mb in size. A total of 79,752 genes and 83,814 transcripts were predicted, including 33,658 high-confidence genes. An InterPro signature assignment was detected for 69,218 transcripts, which represented 82.6% of the total. Validation studies demonstrated the genome assembly and annotation completeness and highlighted the usefulness of the draft genome for read mapping of high-throughput sequence data generated using different protocols. All data generated is available through the public databases where it was deposited, being therefore ready to use by the academic and industry communities working on cork oak and/or related species.
Highlights
Background & SummaryQuercus suber is an evergreen tree, commonly known as cork oak, which is native to the western Mediterranean Basin, especially southwest Europe, where it occurs in the coastal regions
Despite the economic relevance of cork production, no genetic breeding/selection schemes have so far been established in this species, compromising the development of genetically superior trees, able to produce high quality cork, displaying enhanced resistance to the (a)biotic stress factors they are exposed to and with potential to adapt to new forestry management practices that may be implemented in the future
The microsatellite markers used were selected from available literature, and included markers developed in Quercus mongolica[7], Quercus petraea[8], Quercus robur[9], Quercus macrocarpa[10], Quercus myrsinifolia[11], Castanea sativa[12] and two additional markers developed for cork oak at CEBAL and INIAV
Summary
Quercus suber is an evergreen tree, commonly known as cork oak, which is native to the western Mediterranean Basin, especially southwest Europe, where it occurs in the coastal regions. Over the last few years, a decline in cork oak populations has been observed, eventually as a result of agriculture intensification, biotic stresses, fires and climate changes. Cork quality, perhaps the most important trait in cork oak production, cannot be properly evaluated before at least 40 years of growth, due to the specificities of the production cycle This extremely long cycle represents a textbook scenario in which genetic markers associated with better cork quality can be highly beneficial. Using a validation approach based on the RNA-Seq data available for five cork oak tissues, a total of 33,658 predicted genes could be confirmed and classified as high confidence genes, since they presented assembled transcripts within the genome annotation coordinates
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