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Summary White oak (Quercus alba) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important.We report the first haplotype‐resolved chromosome‐scale genome assembly ofQ. albaand conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. We investigate the genetic diversity of this widespread species and the phylogenetic relationships among oaks using whole genome data.Despite strongly conserved chromosome synteny and genome size acrossQuercus, certain gene families have undergone rapid changes in size, including defense genes. Unbiased annotation of resistance (R) genes across oaks revealed that the overall number of R genes is similar across species – as are the chromosomal locations of R gene clusters – but, gene number within clusters is more labile. We found thatQ. albahas high genetic diversity, much of which predates its divergence from other oaks and likely impacts divergence time estimations. Our phylogenetic results highlight widespread phylogenetic discordance across the genus.The white oak genome represents a major new resource for studying genome diversity and evolution inQuercus. Additionally, we show that unbiased gene annotation is key to accurately assessing R gene evolution inQuercus. 

Recent studies have demonstrated that it is a misconception that transcriptome sequencing requires tissue preserved at ultracold temperatures. Here, we outline the potential origins of this misconception and its possible role in biasing the geographic distribution of published plant transcriptomes. We highlight the importance of ensuring diverse sampling by providing an overview of the questions that transcriptomes can answer about the forces shaping the plant tree of life. We discuss how broadening transcriptome sequencing to include existing specimens will allow the eld to grow and more fully utilize biological collections. We hope this article encourages the expansion of the current trend in ‘herbariomics’ research to include whole-transcriptome sequencing of historical RNA. 

Abstract—Podostemaceae are a clade of aquatic flowering plants that form important components of tropical river ecosystems. Species in the family exhibit highly derived growth forms and high vegetative phenotypic plasticity, both of which contribute to taxonomic confusion. The backbone phylogeny of the family remains poorly resolved, many species remain to be included in a molecular phylogenetic analysis, and the monophyly of many taxa remains to be tested. To address these issues, we assembled sequence data for 73 protein-coding plastid genes from 132 samples representing 68 species (∼23% of described species) that span the breadth of most major taxonomic, morphological, and biogeographic groups of Podostemaceae. With these data, we conducted the first plastid phylogenomic analysis of the family with broad taxon sampling. These analyses resolved most nodes with high support, including relationships not recovered in previous analyses. No evidence of widespread, well-supported conflict among individual plastid genes and the concatenated phylogeny was observed. We present new evidence that four genera (Apinagia,Marathrum,Oserya, andPodostemum), as well as four species, are not monophyletic. In particular, we show thatPodostemum flagelliformeshould not be included inPodostemumand is better recognized asDevillea flagelliformis,and thatMarathrum capillaceumis embedded withinLophogynes.l. and should be recognized asLophogyne capillacea. We also place a previously unsampled and undescribed species that likely represents a new genus. In contrast to previous studies, the neotropical generaDiamantina,Ceratolacis,Cipoia,andPodostemumare resolved as successive sister groups to a clade of all paleotropical Podostemoideae taxa sampled, suggesting a single dispersal event from the neotropics to the paleotropics in the history of the subfamily. These results provide a strong basis for improving the classification of Podostemaceae and a framework for future phylogenomic studies of the clade employing data from the nuclear genome. 

Quercus alba L., also known as white oak, eastern white oak, or American white oak, is a quintessential North American species within the white oak section (Quercus) of the genus Quercus, subgenus Quercus. This species plays a vital role as a keystone species in eastern North American forests and plays a significant role in local and regional economies. As a long-lived woody perennial covering an extensive natural range, Q. alba’s biology is shaped by a myriad of adaptations accumulated throughout its natural history. Populations of Q. alba are crucial repositories of genetic, genomic, and evolutionary insights, capturing the essence of successful historical adaptations and ongoing responses to contemporary environmental challenges in the Anthropocene. This intersection offers an exceptional opportunity to integrate genomic knowledge with the discovery of climate-relevant traits, advancing tree improvement, forest ecology, and forest management strategies. This review provides a comprehensive examination of the current understanding of Q. alba’s biology, considering past, present, and future research perspectives. It encompasses aspects such as distribution, phylogeny, population structure, key adaptive traits to cyclical environmental conditions (including water use, reproduction, propagation, and growth), as well as the species’ resilience to biotic and abiotic stressors. Additionally, this review highlights the state-of-the-art research resources available for the Quercus genus, including Q. alba, showcasing developments in genetics, genomics, biotechnology, and phenomics tools. This overview lays the groundwork for exploring and elucidating the principles of longevity in plants, positioning Q. alba as an emerging model tree species, ideally suited for investigating the biology of climate-relevant traits. 

Chloroplasts and mitochondria each contain their own genomes, which have historically been and continue to be important sources of information for inferring the phylogenetic relationships among land plants. The organelles are predominantly inherited from the same parent, and therefore should exhibit phylogenetic concordance. In this study, we examine the mitochondrion and chloroplast genomes of 226 land plants to infer the degree of similarity between the organelles’ evolutionary histories. Our results show largely concordant topologies are inferred between the organelles, aside from four well-supported conflicting relationships that warrant further investigation. Despite broad patterns of topological concordance, our findings suggest that the chloroplast and mitochondrial genomes evolved with significant differences in molecular evolution. The differences result in the genes from the chloroplast and the mitochondrion preferentially clustering with other genes from their respective organelles by a program that automates selection of evolutionary model partitions for sequence alignments. Further investigation showed that changes in compositional heterogeneity are not always uniform across divergences in the land plant tree of life. These results indicate that although the chloroplast and mitochondrial genomes have coexisted for over 1 billion years, phylogenetically, they are still evolving sufficiently independently to warrant separate models of evolution. As genome sequencing becomes more accessible, research into these organelles’ evolution will continue revealing insight into the ancient cellular events that shaped not only their history, but the history of plants as a whole.