Lamiales is an order of core eudicots with abundant diversity, and many Lamiales plants have important medicinal and ornamental values. Here, we comparatively reanalyzed 11 Lamiales species with well-assembled genome sequences and found evidence that Lamiales plants, in addition to a hexaploidization or whole-genome triplication (WGT) shared by core eudicots, experienced further polyploidization events, establishing new groups in the order. Notably, we identified a whole-genome duplication (WGD) occurred just before the split of Scrophulariaceae from the other Lamiales families, such as Acanthaceae, Bignoniaceae, and Lamiaceae, suggesting its likely being the causal reason for the establishment and fast divergence of these families. We also found that a WGT occurred ∼68-78 Mya, near the split of Oleaceae from the other Lamiales families, implying that it may have caused their fast divergence and the establishment of the Oleaceae family. Then, by exploring and distinguishing intra- and inter-genomic chromosomal homology due to recursive polyploidization and speciation, respectively, we inferred that the Lamiales ancestral cell karyotype had 11 proto-chromosomes. We reconstructed the evolutionary trajectories from these proto-chromosomes to form the extant chromosomes in each Lamiales plant under study. We must note that most of the inferred 11 proto-chromosomes, duplicated during a WGD thereafter, have been well preserved in Jacaranda (Jacaranda mimosifolia) genome, showing the credibility of the present inference implementing a telomere-centric chromosome repatterning model. These efforts are important to understand genome repatterning after recursive polyploidization, especially shedding light on the origin of new plant groups and angiosperm cell karyotype evolution.

Rice (Oryza sativa) is one of the key staple crops, providing food for nearly half of the world’s population. The past twenty years have seen significant advances in understanding Oryza species through genome sequencing efforts. However, the stability of Oryza genomes during their divergence has not been well characterized. Here, by performing gene collinearity and comparative genomics analysis, we selected ten Oryza species and three other Poaceae species to check their genome stability, with Leersia perrieri as the reference. Intra- and intergenomic analysis showed a ~30% difference in homologous block numbers and a 35.7% difference in collinear gene numbers per block, indicating that Oryza genomes have undergone extensive DNA permutations. Notably, we found that Oryza chromosomes with smaller ordinal numbers have often preserved larger percentages of genes, while those with bigger numbers have undergone more gene losses. This unique observation may be explained by elevated gene losses incurred by illegitimate or homoeologous recombination between homoeologous chromosomes produced by the grass-common tetraploidization (GCT) ~100 million years ago (Mya), e.g., Chro. 11 and 12. However, the lowered gene loss rates in Chro. 1–3 could be explained by earlier restriction of illegitimate recombination after the GCT due to there often being (larger) neo-chromosomes produced by the fusion of ancestral chromosomes. The enriched NBS-LRR (nucleotide-binding site and leucine-rich repeat) genes in chromosomes 11 and 12 are another explanation for the above observation. Further evidence was obtained from other Poaceae plants. Moreover, we revealed around twice as many differences in tandem genes and their densities among Oryza plants, further showing their divergent levels of genome stability. The present efforts may contribute to the understanding of the stability of the Oryza genome and its formation, evolution, and functional innovation.

Gene conversion contributes to gene copy number changes, DNA mutations, and functional innovation and has been widely reported in three domains of life. However, it has hardly been described in Aspergillus, including industrially and commercially important or pathogenic fungi. Here, we revealed multiple sets of homologous genes located in a region of chromosome 1 of A. flavus, and its orthologous counterpart of A. oryzae. Phylogenetic analysis showed evidence of frequent gene (DNA) conversion between ectopic paralogs in each species, accompanied by prominent point mutations and DNA deletion (from several to hundreds of base pairs). At least two independent cases showed that the converted genes in A. oryzae have been repeatedly split into shorter genes by the introduction of stop codons, and then ectopic conversion rendered paralogous genes (regions) to have the same configuration of tandemly located new genes. Inference of nucleotide substitution and ancestral gene content showed that the conversion-affected regions have seen 3.48 times as many substitutions and 4–6 times as many gene losses compared to the non-affected regions. We predicted that a DNA loop between proximal regions, in the common ancestor and inherited by each species, facilitates ectopic gene (DNA) conversion and elevated rates of mutations and losses. Overall, we found that gene conversion proves to be a key factor resulting in genome instability, elevated gene evolutionary rates, and an effective avenue to produce new genes, likely leading to the speciation of two Aspergillus lineages.

The adzuki bean (Vigna angularis) is an economically and nutritionally significant legume species. Using a multi-strategy sequencing approach, a gapless, telomere-to-telomere (T2T) genome assembly of an elite cultivar, Jihong 16 (JH16), was generated. The genome size was 514.85 Mb, with a Contig N50 of 48.72 Mb, 3x longer than previous published genome. The centromeres of adzuki bean were revealed for the first time and found to be composed of ~ 9-bp minisatellites — a distinct departure from the much longer satellites typically found in other plants. Low sequence conservation between the centromeres of adzuki bean and mung bean further highlights the highly active evolutionary dynamics of centromeric sequences in Vigna species. Whole-genome resequencing of 706 adzuki bean accessions was performed and three major phylogenetic groups were identified. Among these, the Southern China group exhibited the highest genetic diversity and the most rapid linkage disequilibrium (LD) decay. A set of 112 core accessions was selected to represent the global germplasm, and 12 barcode SNPs were identified for DNA fingerprinting. Leveraging high-quality phenotypic data for 39 agronomic traits collected across seven locations over two years, a genome-wide association study (GWAS) identified 9613 significant marker-trait associations (MTAs) and thousands of candidate genes, including 40 MTAs located in the centromere regions. Several genes were experimentally validated, including the flowering-time gene Vigan07G000670, overexpression of which in Arabidopsis led to early flowering phenotype and altered FT/FLC expression. Finally, genomic selection (GS) evaluations demonstrated that even a small set (500 ~ 1000) of trait-associated markers achieved high prediction accuracy (>0.8) for key agronomy traits such as seed weight, flowering date and plant height. The genomic resources and insights generated in this study provide a robust foundation for genetic improvement of adzuki bean and related legume crops.

Whether plant life form influences the long-term persistence of polyploid lineages remains an important unresolved question in plant evolution. Previous studies have suggested that perennial herbaceous plants harbor higher proportions of neo-polyploids, yet comprehensive phylogenetic validation across paleopolyploid lineages using genomic data remains limited. The rapid accumulation of plant genome sequences, particularly from horticultural and agricultural species, provides an unprecedented opportunity to investigate the evolutionary relationships among polyploidization, plant growth form, and plant stature across seed plants. Here, we analyzed 351 seed plant genomes, including major cereals, vegetables, fruits, and their wild relatives, to investigate the long-term evolutionary associations between paleopolyploidization and plant phenotypic diversity. Phylogenetically informed comparative analyses showed that lineages experiencing more paleopolyploidization events were significantly more likely to exhibit herbaceous rather than woody growth forms. We further found that paleopolyploidization frequency was negatively associated with plant height across seed plants after accounting for phylogenetic relatedness. In addition, evolutionary rates, estimated using synonymous substitution rates (Ks), were associated with paleopolyploidization, plant growth form, and species richness. Herbaceous species exhibited higher Ks values than woody and vine species, and plant families with higher evolutionary rates tended to contain more species. Together, these findings provide a phylogenetically informed evidence that paleopolyploidization is closely associated with plant growth form, plant stature, and evolutionary rate, offering new insights into the long-term evolutionary consequences of genome duplication in seed plants.