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9 recordsLinked to original sources
PubMed2025

The T2T genome assembly of watershield (Brasenia schreberi) unveils genomic insights into aquatic adaptation.

Watershield (Brasenia schreberi), belonging to Cabombaceae within the order Nymphaeales, represents one of the early-diverged angiosperm lineages. This perennial floating leaf freshwater aquatic plant features submerged juvenile leaves enveloped in a thick layer of transparent gelatinous mucilage, aiding in its resistance to aquatic stress. However, the evolutionary history of the mechanisms underlying its specific phenotype remains unclear. In this study, we present the telomere-to-telomere level genome of B. schreberi, unveiling that it underwent two rounds of whole-genome duplications (WGDs) and a recent whole-genome triplication, with the most ancient WGD being shared by Nymphaeaceae. WGD and dispersed duplication significantly contributed to the expansion of gene families, which are primarily associated with environmental adaptation. Additionally, we discovered that mature leaves primarily conduct photosynthesis and may transport nutrients to underwater juvenile leaves for polysaccharide synthesis. We also identified an ancestral broad expression pattern of ABC genes, and the similar expression of anthocyanin biosynthesis genes across all flower organs resulted in entirely purple flowers. Our findings deepen the understanding of the evolution of this specific aquatic plant phenotypes.

Genome, Plant↗
PubMed2025

Discovery of additional ancient genome duplications in yeasts.

Whole genome duplication (WGD) has had profound macroevolutionary impacts on diverse lineages1,2, preceding adaptive radiations in vertebrates3-5, teleost fish6,7, and angiosperms8,9. In contrast to the many known ancient WGDs in animals10,11 and especially plants12-14, we are aware of evidence for only four in fungi15,16. The oldest of these occurred ~100 million years ago (mya) and is shared by ~60 extant Saccharomycetales species17,18, including the baker's yeast Saccharomyces cerevisiae (Fig. 1). Notably, this is the only known ancient WGD in the yeast subphylum Saccharomycotina. The dearth of ancient WGD events in fungi remains a mystery15. Some studies have suggested that fungal lineages that experience chromosome19 and genome15 duplication quickly go extinct, leaving no trace in the genomic record, while others contend that the lack of known WGD is due to an absence of data15,16. Under the second hypothesis, additional sampling and deeper sequencing of fungal genomes should lead to the discovery of more WGD events. Coupling hundreds of recently published genomes from nearly every described Saccharomycotina species with three additional long-read assemblies, we discovered three novel WGD events. While the functions of retained duplicate genes originating from these events are broad, they bear many similarities to the well-known WGD that occurred in the Saccharomycetales17. Our results suggest that WGD may be a more common evolutionary force in fungi than previously believed.

Convergent Evolution↗
PubMed2026

Ancient polyploidization waves as evolutionary shields for angiosperms.

Chen et al. identified 132 whole-genome duplications (WGDs) clustered around environmental crises. We highlight how, over longer evolutionary timescales, ancient WGDs convergently retained MADS-box, MYB, WRKY and HSF transcription factors, building stress-adaptation networks. These insights guide climate-resilient crop improvement through comparative genomics and CRISPR engineering.

MADS-box↗
PubMed2006

Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes.

Many Saccharomyces cerevisiae duplicate genes that were derived from an ancient whole-genome duplication (WGD) unexpectedly show a small synonymous divergence (K(S)), a higher sequence similarity to each other than to orthologues in Saccharomyces bayanus, or slow evolution compared with the orthologue in Kluyveromyces waltii, a non-WGD species. This decelerated evolution was attributed to gene conversion between duplicates. Using approximately 300 WGD gene pairs in four species and their orthologues in non-WGD species, we show that codon-usage bias and protein-sequence conservation are two important causes for decelerated evolution of duplicate genes, whereas gene conversion is effective only in the presence of strong codon-usage bias or protein-sequence conservation. Furthermore, we find that change in mutation pattern or in tDNA copy number changed codon-usage bias and increased the K(S) distance between K. waltii and S. cerevisiae. Intriguingly, some proteins showed fast evolution before the radiation of WGD species but little or no sequence divergence between orthologues and paralogues thereafter, indicating that functional conservation after the radiation may also be responsible for decelerated evolution in duplicates.

Codon↗
PubMed2006

Reorganization of adjacent gene relationships in yeast genomes by whole-genome duplication and gene deletion.

In Saccharomyces, an ancient whole-genome duplication (WGD) and widespread duplicate gene deletion resulted in extensive reorganization of adjacent gene relationships. We have studied the evolution of adjacent gene pairs' identity, orientation, and spacing following whole-genome duplication and deletion (WGD-D) using comparative genomic analyses and simulations. Surveying adjacent gene organization across the Saccharomyces species complex, we find a genome-wide bias toward divergently and convergently transcribed gene pairs in all species but a reduction in this bias in the species that underwent WGD-D. Among neutral models of WGD-D, only single-gene deletion can produce the appropriate reduction in orientation bias and recapitulate the pattern of short, highly dispersed deletions we observe in Saccharomyces cerevisiae. To characterize the dynamics of WGD-D, we trace the conservation and creation of adjacent gene pairs along the S. cerevisiae lineage. We find that newly created adjacencies have a tandem orientation bias, while adjacencies conserved from prior to WGD-D have the same divergent-convergent bias as found in the species that diverged before WGD. We also find that adjacent gene pairs produced by WGD-D gained greater intergenic spacing but that this is reduced in the older adjacencies. Given this, and the preponderance of short deleted blocks, we argue that the deletion phase of WGD-D occurred primarily by small inactivating mutations followed by numerous small deletions. Newly created adjacent gene pairs also have an initial increase in mean log2 expression ratios and maximal expression levels, suggesting that increased intergenic spacing caused a genome-wide reduction in transcriptional interference.

Evolution, Molecular↗
PubMed2024

Genome evolution of the ancient hexaploid Platanus × acerifolia (London planetree).

Whole-genome duplication (WGD; i.e., polyploidy) and chromosomal rearrangement (i.e., genome shuffling) significantly influence genome structure and organization. Many polyploids show extensive genome shuffling relative to their pre-WGD ancestors. No reference genome is currently available for Platanaceae (Proteales), one of the sister groups to the core eudicots. Moreover, Platanus × acerifolia (London planetree; Platanaceae) is a widely used street tree. Given the pivotal phylogenetic position of Platanus and its 2-y flowering transition, understanding its flowering-time regulatory mechanism has significant evolutionary implications; however, the impact of Platanus genome evolution on flowering-time genes remains unknown. Here, we assembled a high-quality, chromosome-level reference genome for P. × acerifolia using a phylogeny-based subgenome phasing method. Comparative genomic analyses revealed that P. × acerifolia (2n = 42) is an ancient hexaploid with three subgenomes resulting from two sequential WGD events; Platanus does not seem to share any WGD with other Proteales or with core eudicots. Each P. × acerifolia subgenome is highly similar in structure and content to the reconstructed pre-WGD ancestral eudicot genome without chromosomal rearrangements. The P. × acerifolia genome exhibits karyotypic stasis and gene sub-/neo-functionalization and lacks subgenome dominance. The copy number of flowering-time genes in P. × acerifolia has undergone an expansion compared to other noncore eudicots, mainly via the WGD events. Sub-/neo-functionalization of duplicated genes provided the genetic basis underlying the unique flowering-time regulation in P. × acerifolia. The P. × acerifolia reference genome will greatly expand understanding of the evolution of genome organization, genetic diversity, and flowering-time regulation in angiosperms.

Polyploidy↗
PubMed2007

Rearrangement rate following the whole-genome duplication in teleosts.

It is now clear that a whole-genome duplication (WGD) occurred at the base of the teleost fish lineage. Like the other anciently polyploid genomes investigated so far, teleost genomes now behave like diploids with chromosomes forming pairs at meiosis. The diploidization process is currently poorly understood. It is associated with many gene deletions, such that one of the duplicates is lost at most loci and has also been proposed to coincide with an increase in genomic instability. Here we ask whether WGD is a determinant of the genomic rearrangement rate in teleosts. We study variability of the rates of rearrangement along a vertebrate phylogenetic tree, composed of 3 tetrapods (human, chicken, and mouse) and 3 teleost fishes (zebrafish, Tetraodon, and Takifugu), whose complete genome sequences are available. We devise a simple parsimony method for counting rearrangements, which takes into account various methodological complications caused by the WGD and the subsequent gene losses. We show that there does appear to be an increase in rearrangement rate after WGD, but that there is also a great deal of additional variability in rearrangement rates across species.

Animals↗
PubMed2005

Evidence for an ancient whole-genome duplication event in rice and other cereals.

Gene duplication has been proposed as an accelerator of evolution. Ancient genome duplication events have been identified in diverse organisms, such as yeast, vertebrates, and Arabidopsis. Here, we have identified a whole genome duplication event (WGD) in the rice genome, which took place prior to the divergence of grasses about 70 million years ago (mya). A total of 117 duplicated blocks were detected, which are distributed on all 12 chromosomes and cover about 60% of the rice genome. About 20% genes on these duplicated segments are retained as duplicate pairs. In contrast, 60% of the transcription factor genes are retained as duplicates. The identification of a WGD in the ancestral grass genome will impact the study of grass genome evolution, and suggest that polyploidization and subsequent gene losses and chromosomal rearrangements have played an important role in the diversification of grasses.

Edible Grain↗
PubMed2026

Genus-Wide Pan-Genome Analysis of Populus bZIP Transcription Factors with Reanalysis of Public Salt-Stress Transcriptomes.

Basic leucine zipper (bZIP) transcription factors regulate plant development and stress responses, but their genus-wide diversity in Populus remains unclear. We analyzed 19 Populus genomes and retained 1764 bZIP proteins, including 21 independent new loci and four annotation corrections. Of these, 1762 were assigned to 79 orthologous gene groups (OGGs), comprising 43 core, 20 soft-core, 15 shell and one cloud OGG, of which 59 showed copy-number variation. Phylogenetic analysis assigned 74 representative pangenes to 13 subfamilies, with five remaining unclassified and motif patterns differing among subfamilies. Whole-genome duplication (WGD)/segmental duplication accounted for 81.0% of OGG-assigned proteins and contributed predominantly to the conserved component. Although 72.2% of bZIP proteins overlapped a transposable element within the gene body or 2-kb flanks, this proportion was modestly lower than in matched non-bZIP genes, and copy-number-variable OGGs showed no greater TE coverage than invariant OGGs. Among retained homologous comparisons, 97.6% had Ka/Ks ≤ 1, supporting predominant purifying selection. Across the heterogeneous public salt-stress RNA-seq datasets analyzed, no OGG showed a significant, directionally concordant response in at least two Populus taxa. These results reveal a conserved bZIP framework shaped mainly by ancient duplication alongside variable genomic contexts and transcriptional responses.

Populus↗