A telomere-to-telomere genome assembly of Asparagus cochinchinensis reveals the evolution of centromere and steroidal saponin biosynthesis

Telomere-to-Telomere Genome Assemblies of Coprinellus xanthothrix and Coprinellus saccharinus Reveal Chromosome-Scale Genome Architecture and Lineage-Specific Evolutionary Dynamics

Coprinellus comprises mushroom-forming saprotrophic fungi that colonize decomposing plant-derived substrates, yet chromosome-complete genomic resources for this genus remain limited. To resolve chromosome architecture and lineage-specific evolution in this fungal group, we generated chromosome-complete assemblies of Coprinellus xanthothrix and C. saccharinus by integrating Oxford Nanopore Technologies (ONT) long reads, DNA nanoball sequencing (DNBSEQ) short reads, Hi-C, and RNA-seq data. Each genome comprised 13 gapless chromosomes with all 26 telomeres recovered; assembly sizes were 46.92 and 54.81 Mb, with BUSCO completeness of 99.20% and 99.10%, respectively. The larger C. saccharinus genome was primarily associated with greater retroelement content, whereas functional annotation profiles and CAZyme repertoires were broadly comparable between species. Phylogenomic analyses grouped C. xanthothrix with C. radians and C. saccharinus with C. micaceus, with estimated divergence times of 54.4 and 32.8 Ma, respectively. Both divergence events occurred within the Paleogene. Gene family analyses identified lineage-specific expansions enriched in nucleotide metabolism, DNA replication and repair, glutathione metabolism, redox regulation, endocytosis, cytoskeletal organization, and cell-cycle processes. Synteny and Ks analyses further revealed chromosome-level rearrangements and lineage-specific small-scale duplication but no strong evidence of recent whole-genome duplication. Together, the temporal placement of these divergences and the associated genomic patterns raise a testable hypothesis that long-term climatic and vegetation reorganization, together with changes in plant-derived substrates and microhabitats, may have contributed to lineage establishment and ecological differentiation. However, because direct paleoecological evidence and functional validation are currently lacking, this proposed relationship should not be interpreted as causal. These chromosome-complete assemblies provide important resources for comparative genomics in Coprinellus and future experimental studies of saprotrophic adaptation.

Near-complete telomere-to-telomere genome assembly of a millennium-old ancient Pteroceltis tatarinowii (Qingtan, Cannabaceae) tree

Pteroceltis tatarinowii is a monotypic relict species endemic to China. It belongs to the genus Pteroceltis in the family Cannabaceae, and is an economically and culturally valuable fiber-producing tree species. We integrated PacBio HiFi, Oxford Nanopore Technology (ONT), and Hi-C chromatin conformation capture data to generate a near-complete telomere-to-telomere genome assembly of a millennium-old P. tatarinowii tree. The final assembly spanned approximately 689 Mb, with a contig N50 of 35.0 Mb; 99.88% of the sequences were successfully mapped onto chromosomes, with only two gaps remaining in the genome, showing a marked improvement in assembly continuity over previously published P. tatarinowii assemblies. We predicted a total of 47,241 protein-coding genes; repetitive sequences accounted for 48.37% of the genome, with long terminal repeat retrotransposons as the dominant component (18.92%). Benchmarking Universal Single-Copy Orthologs assessment confirmed genome completeness of 98.6% and gene annotation completeness of 98.7%. We resolved key complex genomic regions, including telomeres and centromeres, and this high-quality assembly provided a foundational genomic resource to clarify the taxonomic status of P. tatarinowii and formulate scientific genetic conservation strategies for this endangered relict species.

Chromosome-scale assembly of the Cupressus sempervirens genome unravels new insights into the evolutionary history of conifers

Conifers, which comprise nearly two-thirds of extant gymnosperm species, are ecologically and economically important but remain genomically understudied because of their exceptionally large, repeat-rich genomes. Here, we report a chromosome-level assembly of the haploid genome of Cupressus sempervirens generated using PacBio HiFi reads and scaffolded with optical and genetic maps. The 10 Gb assembly shows exceptional contiguity for a conifer genome (contig N50 = 29.8 Mb) and was organized into 11 pseudomolecules. Iso-Seq-supported annotation identified 42,980 protein-coding genes. Repetitive elements account for over 80% of the genome, with LTR retrotransposons alone representing 52.5%. Transposable elements (TE) are pervasive in both intergenic and genic regions and have a major impact on gene architecture: TE insertions within introns generate ultra-long introns, often exceeding 100 kb, and drive gene size expansion. Analyses of LTR retrotransposon dynamics indicate that genome enlargement in C. sempervirens was driven not by recent transpositional bursts, but by the long-term accumulation and incomplete removal of ancient LTR retrotransposons. Consistent with this pattern, paleogenomic reconstruction across representative gymnosperms found no evidence of whole-genome duplication in the Cupressus lineage. This reference genome provides a valuable resource for studying conifer genome evolution, gene structure, and traits of agronomic and ecological interest, including cypress pollinosis.

Complete telomere-to-telomere genome assembly of Guazuma ulmifolia uncovers evolutionary mechanisms, drought adaptation, and flavonoid biosynthesis

Haplotype-resolved genome of Forsythia suspensa reveals the reticulate evolution in Oleaceae and a novel gene cluster regulating stamen development.

The olive family (Oleaceae) comprises numerous species of economic, horticultural, and medicinal importance. Despite its significance, the evolutionary history of this complex family remains enigmatic. Here, we generated a high-quality haplotype-resolved genome of Forsythia suspensa, a distylous species that occupies a key phylogenetic position in Oleaceae. The two haplotypes exhibit significant allelic divergence with potential allele-specific regulation. We reconstructed the polyploidization history of Oleaceae by confirming and precisely dating a shared whole-genome triplication (WGT) and an independent whole-genome duplication (WGD) event. We revealed a complex reticulate evolution that gave rise to the tribe Oleeae: an initial hybridization between Forsythieae (♂) and Jasmineae (♀), a subsequent backcrossing event, and a final WGD. We identified a novel tandemly duplicated pectin methylesterase inhibitor (PMEI) gene cluster that regulates filament length and pollen size via restricting cell elongation in the long-styled morph. Dosage augmentation via stepwise cluster formation (0.99-3.83 Mya) may contribute to maintaining stamen traits of the long-styled morph. These FsPMEIs are co-expressed with many cell wall-related genes, suggesting a functional link in cell wall modification. Our study reveals the reticulate evolution in Oleaceae and a novel gene cluster controlling stamen development in F. suspensa, provides valuable haplotype-resolved genomic resources for heterostylous species, offering novel framework and molecular pathways to understand plant adaptive evolution.

Chromosome-scale genome assembly of Artabotrys hexapetalus provides insights into its evolution and terpenoid biosynthesis

Artabotrys hexapetalus is used as traditional Chinese medicine for the treatment of malaria. Its antimalarial activity has been shown to be the result of the sesquiterpene designated as yingzhaosu A (YZSA), which mainly occurs in the roots of A. hexapetalus. Despite its medicinal significance, the genetic basis and molecular mechanisms underlying the biosynthesis of its active terpenoids remain unclear. In this study, a high-quality chromosome-scale genome of A. hexapetalus was first reported. In total, 915.15 Mb of genome sequences were assembled, of which 911.58 Mb was sorted into 8 chromosomes. Phylogenetic analysis indicated that the divergence between the genera Artabotrys and Annona happened at approximately 45.77 million years ago (Mya) and the Annonaceae family diverged from other Magnolia species about 103.58 Mya. An ancient whole genome duplication (WGD) event was discovered in the A. hexapetalus genome, earlier than the divergence between Annonaceae and Magnoliaceae families. It correlates with a significant expansion of gene families related to secondary metabolism, especially the terpene synthase (TPS) and cytochrome P450 (P450) families. The analysis of TPS, P450, and 2-oxoglutarate/Fe(II)-dependent dioxygenase (2-ODD) gene families provides a foundation for future functional studies. Additionally, three putative terpene biosynthetic gene clusters were identified within the genome. Our work provides a foundation for elucidating the complete biosynthetic pathway of terpenoids in A. hexapetalus in the future.