Peanut or groundnut (Arachis hypogaea L.), a legume of South American origin, has high seed oil content (45-56%) and is a staple crop in semiarid tropical and subtropical regions, partially because of drought tolerance conferred by its geocarpic reproductive strategy. We present a draft genome of the peanut A-genome progenitor, Arachis duranensis, and 50,324 protein-coding gene models. Patterns of gene duplication suggest the peanut lineage has been affected by at least three polyploidizations since the origin of eudicots. Resequencing of synthetic Arachis tetraploids reveals extensive gene conversion in only three seed-to-seed generations since their formation by human hands, indicating that this process begins virtually immediately following polyploid formation. Expansion of some specific gene families suggests roles in the unusual subterranean fructification of Arachis. For example, the S1Fa-like transcription factor family has 126 Arachis members, in contrast to no more than five members in other examined plant species, and is more highly expressed in roots and etiolated seedlings than green leaves. The A. duranensis genome provides a major source of candidate genes for fructification, oil biosynthesis, and allergens, expanding knowledge of understudied areas of plant biology and human health impacts of plants, informing peanut genetic improvement and aiding deeper sequencing of Arachis diversity.

Plants of the Elaeagnaceae family are widely used to treat various health disorders owing to their natural phytochemicals. Seabuckthorn (Hippophae rhamnoides L.) is an economically and ecologically important species within the family with richness of biologically and pharmacologically active substances. Here, we present a chromosome-level genome assembly of seabuckthorn (http://hipp.shengxin.ren/), the first genome sequence of Elaeagnaceae, which has a total length of 849.04 Mb with scaffold N50 of 69.52 Mb and 30 864 annotated genes. Two sequential tetraploidizations with one occurring ~36-41 million years ago (Mya) and the last ~24-27 Mya were inferred, resulting in expansion of genes related to ascorbate and aldarate metabolism, lipid biosynthesis, and fatty acid elongation. Comparative genomic analysis reconstructed the evolutionary trajectories of the seabuckthorn genome with the predicted ancestral genome of 14 proto-chromosomes. Comparative transcriptomic and metabonomic analyses identified some key genes contributing to high content of polyunsaturated fatty acids and ascorbic acid (AsA). Additionally, we generated and analysed 55 whole-genome sequences of diverse accessions, and identified 9.80 million genetic variants in the seabuckthorn germplasms. Intriguingly, genes in selective sweep regions identified through population genomic analysis appeared to contribute to the richness of AsA and fatty acid in seabuckthorn fruits, among which GalLDH, GMPase and ACC, TER were the potentially major-effect causative genes controlling AsA and fatty acid content of the fruit, respectively. Our research offers novel insights into the molecular basis underlying phytochemical innovation of seabuckthorn, and provides valuable resources for exploring the evolution of the Elaeagnaceae family and molecular breeding.

Key message Genome-wide identification of the sea buckthorn GRAS genes and their transcription profiles in different organizations. Abstract GRAS proteins comprise a large family of transcription factors that experienced extensive replication, and play important roles in many aspects of growth regulatory and environmental signals. Sea buckthorn is a unique and valuable plant which has tremendous value for medical researching, ecological protection, and providing daily necessities. We identified, characterized, and distinguished duplication models of GRAS transcription factors in sea buckthorn. A systematic whole-genome analysis was performed to identify and characterize the GRAS gene family of sea buckthorn, especially the comparative genome method was used to demonstrate its different duplication models. We identified 62 sea buckthorn GRAS (HrGRAS) genes and renamed based on their respective chromosome distribution. Fifty-nine HrGRASs were classified into nine subgroups and three HrGRASs did not belong to any of the subfamilies according to their phylogenetic features. HrGRAS genes tend to have a representative GRAS domain, few introns, and unevenly distributed on chromosomes. Segmental duplication was the main driver of the GRAS gene family expansion, followed by whole-genome duplication (WGD) and tandem duplication, according to the results of comparative genome analysis. GRAS genes involved in duplication experienced strong purifying selection pressure according to the Ka/Ks ratios. The expression profile derived from transcriptome data shows the expression patterns of HrGRAS gene in different tissues and the characterization of differentially expressed genes. This systematic analysis provided a foundation to understand the expansion and potential functions of GRAS genes with an aim of sea buckthorn crop improvement.