The lemon (Citrus limon; family Rutaceae) is one of the most important and popular fruit worldwide. Lemon also tolerates Huanglongbing disease, which is a devastating citrus disease. Here, we produced a gap-free and haplotype-resolved chromosome-scale genome assembly of the lemon by combining Pacific Biosciences circular consensus sequencing, Oxford Nanopore 50-kb ultra-long, and high-throughput chromatin conformation capture technologies. The assembly contained nine-pair chromosomes with a contig N50 of 35.6 Mb and zero gaps. While a total of 633.0 Mb genomic sequences were generated. The origination analysis identified 338.5 Mb genomic sequences originating from citron (53.5 %), 147.4 Mb from mandarin (23.3 %), and 147.1 Mb from pummelo (23.2 %). The genome included 30,528 protein-coding genes, and most of the assembled sequences were found to be repetitive sequences. Several significantly expanded gene families were associated with plant-pathogen interactions, plant hormone signal transduction, and the biosynthesis of major active components, such as terpenoids and flavor. Most HLB-tolerant genes were expanded in the lemon genome, such as 2-oxoglutarate (2OG) / Fe(II)-dependent oxygenase and constitutive disease resistance 1, cell wall-related genes, and lignin synthesis genes. Comparative transcriptomic analysis showed that the phloem regeneration and lower levels of phloem plugging are the elements that contribute to HLB tolerance in lemon. Our results provide insight into lemon genome evolution, active component biosynthesis, and genes associated with HLB tolerance.

Cyclocarya paliurus is a relict plant species that survived the last Glacial period and shows a population expansion recently. Its leaves have been traditionally used to treat obesity and diabetes with the well-known active ingredient cyclocaric acid B. Here, we present three C. paliurus genomes from two diploids with different flower morphs and one haplotype-resolved tetraploid assembly. Comparative genomic analysis revealed two rounds of recent whole-genome duplication events and identified 691 genes with dosage-effect that likely contribute to adaptive evolution through enhanced photosynthesis and increased accumulation of triterpenoids. Re-sequencing analysis of 45 accessions uncovered two bottlenecks, consistent with the known events of environmental changes, and many selectively swept genes involved in critical biological functions, including plant defense and secondary metabolism biosynthesis. We also proposed the biosynthesis pathway of cyclocaric acid B based on multi-omics data and identified key genes, in particular gibberellin related genes, associated with heterodichogamy in the species. Our research sheds light on evolutionary history and provides genomics resources to study the medicinal herb. External links: https://drive.google.com/file/d/1YDqAk_jvoX_ilb7kSxqs56QfbEiHj9Nm/view?usp=sharing https://pan.baidu.com/s/1XoKEQAjYw0GFgDYvdRT7aw, extraction number: bm0u