Simen Rød Sandve

Summary: Horizontal gene transfer (HGT) is one of the most intriguing aspects of genome evolution, challenging classical views of vertical inheritance. Growing genome availability across the tree of life offers opportunities to discover HGT, yet recent reanalyses suggest many reported cases may not withstand scrutiny. Detecting ancient transfers is especially difficult, as phylogenetic signal erodes over time and analytical choices strongly shape conclusions. Here we propose 10 practical rules for evaluating HGT in deep plant phylogenies, organised around three themes: genomic foundation, rigorous analytical framework, and biological interpretation. A reliable genomic foundation requires excluding contamination, verifying genomic integration, and avoiding biased taxon sampling. Rigorous phylogenetics is essential, as deep phylogenies are sensitive to alignment parameters, substitution model, rooting strategy, and branch support. We illustrate this with three glycosyl hydrolase families: for GH9 and GH32, analytical choices can eliminate apparent HGT signals entirely, while GH18 shows why complex, multi‐domain families resist confident inference. Finally, HGT signatures demand cautious, biologically plausible interpretation. Recurrent gene duplication, loss, and domain shuffling commonly produce HGT‐like patterns and should always be considered as alternatives. Our rules offer a pragmatic checklist helping authors and reviewers distinguish robust HGT from artefacts, fostering more reliable evidence on HGT in plants.

Whole genome duplication (WGD) events during early vertebrate evolution may have promoted phenotypic innovation by expanding the genetic material for functional diversification. However, their ancient origins obscure how gene regulation evolved during rediploidization, the process that generates duplicate genes and regulatory elements following WGD. Salmonids provide a unique window to these mechanisms, because they experienced a more recent autotetraploid WGD and remain at an earlier stage of rediploidization. Here we generated 771 multiomics datasets spanning embryonic and adult tissues in Atlantic salmon and rainbow trout to investigate the evolution of gene expression and regulatory elements. Our analyses show that regulatory evolution following the salmonid WGD was shaped by developmental and tissue-specific constraints known to act across vertebrate species. We identify a peak of within-genome regulatory constraint at the vertebrate phylotypic period, associated with the functional retention of duplicated enhancer pairs harbouring deeply conserved non-coding elements enriched in motifs for master developmental transcription factors. We further identify roles for enhancers and transposable elements in the expression divergence of duplicated genes. This study advances the understanding of regulatory evolution following WGD and offers an open resource supporting vertebrate comparative genomics and research applications in salmonid aquaculture and conservation.

Comparative genomic studies in birds have revealed that bird genomes are relatively repeat-poor and stable in terms of karyotype, size, and gene synteny/collinearity compared to other vertebrates. One notable exception is the owls, with cytogenetic studies demonstrating large variations in karyotypes and the evolution of unusual centromeric satellite repeats in some species. However, there has so far not been an investigation into genome architecture and repeat landscape of owls. Here, we present a chromosome-level genome assembly for the snowy owl (Bubo scandiacus). We find that the repeat DNA content in the relatively large snowy owl genome (1.6 Gb) is among the highest reported for any bird genome to date (28.34% compared to an average of ~ 10% in other birds). The bulk of the snowy owl genomic repeat landscape consists of extensive centromeric satellite arrays that form large contiguous blocks across multiple chromosomes. These arrays represent one of the largest centromeric satellite expansions reported in birds and are consistent with rapid turnover and amplification of centromeric repeats. Using gene collinearity analyses we show that the position of the centromeres are not homologous with chicken centromeres, and are located in regions with collinearity breaks to other bird genomes due to chromosomal rearrangements. Our results support rapid satellite turnover at lineage-specific centromeres, which could have played a role in centromeric drive, reproductive isolation and speciation of the snowy owl. The extensive centromeric satellite arrays uncovered in this genome highlight centromere evolution as a potentially important driver of genome evolution in owls.

Plants with amphitropical distributions have closely related populations in both Northern and Southern Hemispheres, but are absent from the intervening tropics. They provide a unique opportunity to study the constraints shaping the distribution of temperate lineages through time. Using grasses from the ecologically diverse supertribe Melicodae, an emerging study system with species distributed throughout the temperate regions, we test the hypothesis that geography and/or environmental niche constrain which lineages successfully cross the tropics to establish in the opposite hemisphere. Biogeographic and evolutionary modelling was conducted on well resolved plastid and nuclear phylogenies constructed from whole-genome sequencing of 178 accessions of 103 Melicodae species. Results show that species from cold regions are much less likely to successfully cross the tropics, with successful lineages all sharing warmer niches that evolved prior to their establishment in the opposite hemisphere. Evidence suggests that this result is explained both by the greater distances that high-latitude, cold-origin lineages must disperse to cross the tropics, and inherent limitations associated with colder thermal niches. In particular, our results suggest that traits allowing species to cope with cold winters, rather than an inability to cope with warm summers, limit their ability to establish in the opposite hemisphere, hinting at important trade-offs between cold-tolerance and biogeographic potential. These results provide insight into the drivers of the distribution and diversity of plants, and the challenges facing cold-origin lineages in a rapidly warming world. If cold-origin species occupy a smaller proportion of their potential range, and are unlikely to establish in new areas with suitable climates, their ability to track preferred habitat as climates warm may be worse than currently expected.

We describe a chromosome-level genome assembly from an individual male plant of the cloudberry (Rubus chamaemorus). The haplotype-resolved assemblies contain 1 pseudo-haplotype spanning 1,198 megabases and 1 pseudo-haplotype spanning 1161 megabases. Most of these 2 assemblies, 93.57% and 96.55% respectively, are each scaffolded into 28 pseudo-chromosomes. Both assemblies show high completeness, with the same Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 99.2%. Most BUSCO genes are duplicated in both pseudo-haplotypes, in line with the polyploid nature of the cloudberry genome. The assemblies contain 74,132 and 70,692 predicted protein-coding genes, respectively. Analysis of repetitive sequences classified ~60% of each haplotype as repeats. Comparative synteny with red raspberry (Rubus idaeus) reveals a 4:1 chromosome correspondence, supporting an octoploid origin. Across k-mer composition, synonymous divergence, and genome-wide gene-tree analyses, 1 set of 7 chromosomes is consistently distinct (β), while the remaining 21 (3 × 7) chromosomes form an α set with no resolvable internal subdivision. These results are consistent with a complex polyploid origin of the cloudberry genome, involving a combination of allopolyploid and autopolyploid processes. Significance statement Cloudberry cultivation has lagged due to limited genomic resources and an unresolved polyploid history. We present a haplotype-resolved, chromosome-scale assembly that resolves 4 homologs per ancestral chromosome into 28 pseudo-chromosomes per haplotype and shows a 4:1 correspondence with red raspberry (Rubus idaeus). Genome-wide analyses support an octoploid architecture with 1 distinct 7-chromosome set (β) and a remaining α-set of 21 chromosomes with no resolvable internal subdivision. This reference provides a foundation for future work on polyploid origin, trait discovery, and breeding.

Early vertebrate autotetraploidization events may have enabled major innovations by expanding the genetic material for functional diversification, yet their ancient timing obscures how genome doubling reshaped gene regulatory evolution. Salmonids provide a unique window to these mechanisms, because they experienced a comparatively recent autotetraploidization and are earlier in the rediploidization process - which creates new genes and regulatory elements during evolution. Here, using large-scale multiomics spanning embryonic and adult tissues in two salmonids, we investigate gene regulatory evolution following genome doubling and rediploidization, which we show is governed by developmental and tissue-specific context, with a period of maximal constraint at advanced stages of embryogenesis. This work advances understanding of vertebrate genome evolution, while providing an open resource supporting salmonid aquaculture and conservation.

Whole-genome duplication (WGD) through autopolyploidization has played a role in genome evolution across eukaryotes. A major consequence of WGD is the rewiring of gene regulatory networks, partly driven by selection on dosage balance. In multicellular organisms, evidence for dosage balance selection has relied on comparative patterns of duplicate gene retention and expression, with few studies directly examining regulatory architecture after WGD. Here, we analysed a large-scale eQTL dataset from Atlantic salmon (Salmo salar), which experienced a WGD 100 million years ago. We found that trans-regulatory connections were enriched between duplicated regions, indicating long-term conservation of ancestral interchromosomal regulatory interactions. Overall, 230 duplicated genes (5%) shared eQTLs, suggesting conserved regulatory control. Moreover, 16 gene pairs showed compensatory expression effects mediated by a common regulator, consistent with predictions of the dosage balance hypothesis. These gene pairs were significantly enriched in recently rediploidized regions. Our results indicate long-term maintenance of dosage balance after WGD. Teaser: Genetic regulation in Atlantic salmon shows that duplicated genes can remain dosage-balanced across 100 million years of evolution.

Fungi are pivotal in transitioning to a bio-based, circular economy due to their ability to transform organic material into valuable products such as organic acids, enzymes, and drugs. Mucor circinelloides is a model organism for studying lipogenesis and is particularly promising for its metabolic capabilities in producing oils like TAGs and carotenoids, influenced by environmental factors such as nutrient availability. Notably, strains VI04473 and FRR5020 have been identified for their potential in producing single-cell oils and carotenoids, respectively. Calcium starvation has previously been shown to have strain-specific effects, with VI04473 accumulating more lipids and FRR5020 producing more carotenoids. Here, we used genome sequencing, comparative genomics, transcriptomics, and metabolite phenotyping to explore the genetic basis of lipid and carotenoid production under calcium starvation in these strains. We found extensive genomic rearrangements between these strains, as well as low conservation of gene regulatory responses to calcium depletion. This lack of conservation also applies to genes involved in lipid and carotenoid production, ie the lipidome. Crucially, we identified several metabolic pathways with distinct transcriptional responses to calcium depletion, suggesting the existence of a previously unrecognized, strain-dependent mechanism by which calcium signaling modulates metabolite production. This points to a potentially novel regulatory pathway linking calcium homeostasis to secondary metabolism in fungi, which may be linked to the complex gene family evolution of several lipidome-genes. Our study sheds light on the complexity of the evolution of metabolic networks in M. circinelloides. Understanding these genetic underpinnings can optimize the industrial use of M. circinelloides, enhancing lipid productivity and stress tolerance, and tailoring metabolic profiles for specific applications.

We describe a chromosome-level genome assembly from an individual male plant of the cloudberry ( Rubus chamaemorus ). The haplotype-resolved assemblies contain one pseudo-haplotype spanning 1198 megabases and one pseudo-haplotype spanning 1161 megabases. Most of these two assemblies, 93.57% and 96.55% respectively, are each scaffolded into 28 pseudo-chromosomes. Both assemblies show high completeness, with the same BUSCO completeness score of 99.2%. Most BUSCO genes are duplicated in both pseudo-haplotypes, in line with the polyploid nature of the cloudberry genome. The assemblies contain 74,132 and 70,692 predicted protein-coding genes, respectively. Analysis of repetitive sequences classified ∼60% of each haplotype as repeats. Comparative synteny with red raspberry ( Rubus idaeus ) reveals a 4:1 chromosome correspondence, supporting an octoploid origin. Ks distributions and k-mer clustering indicate a fairly recent polyploidization involving one divergent (β) and three closely related (α) subgenomes. Low coverage targeted sequencing data mapped to our assembly link the β-subgenome to a relative of R. pedatus or R. lasiococcus, while the α-subgenomes might derive from a putative auto-allohexaploid within the main Rubus clade. In conclusion, these results indicate that the cloudberry genome arose through multiple hybridization events, including recurrent allopolyploidy and possibly autopolyploidy. Significance statement: Cloudberry cultivation has lagged due to unclear origin and genome structure. We present a haplotype-resolved, chromosome-scale assembly that resolves four homologs per ancestral chromosome into 28 pseudo-chromosomes per haplotype and shows a 4:1 correspondence with red raspberry ( Rubus idaeus ). Genomic analyses indicate a recent polyploidization in which three closely related subgenomes likely derive from a putative hexaploid within the main Rubus clade, associated with R. arcticus (Arctic raspberry), whereas the fourth, more divergent subgenome is linked to relatives of R. pedatus (strawberryleaf raspberry) and R. lasiococcus (dwarf bramble). These results clarify cloudberry’s formation and provide a foundation for trait discovery and accelerated breeding.