Genomic structure and diversity of oak populations in British parklands

Abstract

The largest populations of veteran oak trees in Europe are found in British parklands: managed wood pastures up to 1000 years old. Here, we present genomic evidence that parkland oak populations harbour considerable diversity and grew from local seed sources. We found some evidence for natural regeneration of offspring and for hybridization between pedunculate and sessile oak. We detected signatures of past gene flow between these two species and few regions of high differentiation within their genomes. Future expansion of this dataset may allow us to test for a genomic basis of acute oak decline, a syndrome of particular concern in parkland environments. Summary• The two predominant oak species in Europe, Quercus robur (English or pedunculate oak) and Quercus petraea (sessile oak), have a long history of human intervention.In Britain, a common management regime is parklands, often surrounding country houses. Little is known about how seeds were sourced for parkland oak populations nor the genetic diversity that they contain.• We sequenced the whole genomes of 386 trees from four British parkland sites to characterize the nuclear and chloroplast genetic structure and diversity of oak parkland populations. We assembled the chloroplast genomes and matched these to restriction enzyme fragment chloroplast haplotypes found in previous studies of ancient woodlands.• We found over two million high-quality nuclear single-nucleotide polymorphisms (SNPs), allowing us to identify 360 Q. robur, 10 Q. petraea and 16 hybrid individuals with confidence. We identified 81 coding regions exhibiting strong differentiation between the two species. We found evidence for selective sweeps in Q. robur near some regions containing genes with putative involvement in stress tolerance.• We detected a few very close relatives within some sites, suggesting natural regeneration or local seed planting. There was little differentiation among the Q. robur populations at the four sites. Chloroplast genomes found in each parkland

Evidence for the Widespread Occurrence of Bacteria Implicated in Acute Oak Decline from Incidental Genetic Sampling

“…This study makes use of data initially collected for an investigation of oak tree genomes in relation to Acute Oak Decline and a wider population study of oak trees at four sites where research and monitoring of AOD was already taking place [41]. These sites are Attingham Park in Shropshire, Langdale Wood in Herefordshire, Hatchlands Park in Surrey and Sheen Wood in Richmond Park, Greater London.…”

“…Of the successfully sequenced individual trees, 351 were Q. robur, 10 were Q. petraea and 16 were hybrids, according to genome-based analyses. A further 45 trees not included in Nocchi et al 2021 [41] were identified by morphology, 43 as Q. robur, and one as Q. petraea, making a total of 394 Q. robur, 11 Q. petraea, and 16 hybrids.…”

“…Here, we analyse a large short-read dataset based on high-throughput sequencing of DNA extracted from oak leaves and buds from five sites, including Acute Oak Decline symptomatic, asymptomatic and 'in remission' native oaks. This dataset was generated for the study of oak genomic variation [41], but here we examine the incidental evidence it may provide about the phyllosphere of the sequenced trees. We aim to discover whether the four AOD-associated bacteria, previously identified in stem bleeds, could be identified in these foliar data using metagenomic classification of reads that do not map to the oak genome.…”

Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood

“…For example, temperature‐induced fluctuating selection resulting in allele frequencies changes in some genomic subregions have been observed in three successive oak generations covering the transition from the last Little Ice Age to the modern era (Saleh et al, 2022). Present‐day populations have been intensively studied and show a clear population structure as well as examples of recent secondary contacts and adaptive introgression between species (Alberto et al, 2010; Degen et al, 2021; Lepais et al, 2009; Leroy, Louvet, et al, 2020; Nocchi et al, 2022). Genome‐wide population data suggests that secondary contacts took place in the course of the current interglacial period and that they are associated with environmental changes such as temperature and precipitation shifts, since Q. robur is more adapted to cooler and wetter climate whereas Q. petraea prefers a warmer climate and well‐drained soils (Leroy et al, 2017; Leroy, Rougemont, et al, 2020; Roloff et al, 2010).…”

Discarded sequencing reads uncover natural variation in pest resistance inThlaspi arvense

“…The goals of our study were thus two-fold: i) to contribute to a mechanistic understanding of pest resistance in Thlaspi arvense, and, more generally, ii) to explore whether non-target reads from plant sequencing can be used as proxies for studying plant biotic interactions. Considering that we are moving towards an increasingly sequencing-prone world, where more and larger datasets are being generated for many species (37)(38)(39)(40)(41)(42)(43), the use of non-target reads will likely have very broad potential.…”