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Gymnosperms, particularly conifers, exhibit a high abundance of transposable elements (TEs) in their giga-scale genomes. TEs interact both antagonistically and cooperatively with the host genome, promoting structural and genetic innovations across evolutionary lineages. However, how TEs shape the coding space of gymnosperm genomes remains a key unresolved question. Here, we present a high-quality genome assembly for the keystone conifer Platycladus orientalis , with a contig N50 of 57.54 Mb—the highest continuity reported to date—to investigate the role of TEs. Comparative genomics confirms the absence of recent whole-genome duplication and the presence of genome expansion in gymnosperms, revealing complex interactions among recurrent TE proliferation, low DNA removal rates, and DNA methylation-mediated silencing. Computational evidence indicates that TE-mediated gene duplication and pseudogenization provide a genetic basis for adaptive evolution and functional innovation, significantly shaping gene family dynamics and the emergence of species-specific genes. Additionally, TEs capture and duplicate an average of ∼400,000 coding gene fragments per gymnosperm genome, facilitating exon shuffling and triggering epigenetic conflicts between source genes and captured exon fragments. Genes from which fragments are captured (donor genes) show significantly higher levels of exon methylation than genes not captured by TEs (free genes), whereas syntenic donor genes exhibit lower levels of silencing responses than non-syntenic donor genes. This study provides valuable genomic resources and offers insights into the evolutionary patterns and principles underlying the large genome size and complexity of gymnosperms.

BACKGROUND: Sex chromosome turnovers evolve via translocation or duplication of established sex-determining genes, or their replacement by newly evolved ones. Few cases of replacements by new factors have been documented in dioecious plants, but are suspected in Salix, in which both XY and ZW systems occur, with sex-linked regions (SLRs) of different species on various chromosomes. The male-determining genes in XY species' SLRs are partial duplicates of autosomal ARR17-like genes and regulate the expression of downstream genes involved in stamen development by producing small RNAs that suppress the expression of intact copies.

RESULTS: Here we describe phased chromosomal assemblies of three Salix species with a ZW system derived from an XY system, including four lineages of the Salix polyclona complex (six assemblies in total). Their SLRs are within the same repeat-rich pericentromeric region of chromosome 15 as in the willows with XY system. Although these Z- and W- SLRs carry intact and/or partial ARR17 duplicates, few RNA products are detectable in our sampled tissues. However, the W-SLRs include partial duplicates of PISTILLATA (PI), a stamen development gene. These are arranged in inverted repeats and express small interfering RNAs targeting the autosomal intact Salix PI gene, suggesting that they reduce its expression, and therefore act as maleness-suppressing factors.

CONCLUSIONS: The turnover events involving intact ARR17 and partial PI duplications in the 15ZW clade I species involve pericentromeric regions that recombine rarely, making changes possible in these Salix species that would be unlikely in other genome regions.

Hybridization is a driving force in ecological transitions and speciation, yet direct evidence linking it to adaptive differentiation in natural systems remains limited. This study evaluates the role of hybridization in the speciation of Pinus densata, a keystone forest species on the southeastern Tibetan Plateau. By creating artificial interspecific F1s and a long-term common garden experiment on the plateau, we provide in situ assessments on 44 growth and physiological traits across four seasons, along with RNA sequencing. We found significant phenotypic divergence between P. densata and its putative parental species P. tabuliformis and P. yunnanensis, with P. densata demonstrating superior growth and dynamic balance between photosynthesis and photoprotection. The F1s closely resembled P. densata in most traits. Gene expression revealed 19%–10% of 34,000 examined genes as differentially expressed in P. densata and F1s relative to mid-parent expression values. Both additive (4%) and non-additive gene actions (5%–6% in F1s, 10%–12% in P. densata) were common, while transgressive expression occurred more frequently in the stabilized natural hybrids, illustrating transcriptomic reprogramming brought by hybridization and further divergence by natural selection. We provide compelling evidence for hybridization-derived phenotypic divergence at both physiological and gene expression levels that could have contributed to the adaptation of P. densata to high plateau habitat where both parental species have low fitness. The altered physiology and gene expression in hybrids serve both as a substrate for novel ecological adaptation and as a mechanism for the initiation of reproductive isolation.

Effective conservation actions for endangered species rely on a good understanding of the evolutionary forces driving population decline. Detailed genetic analyses, including assessment of demographic history, population structure and diversity, are essential for gaining insights into the species’ adaptive potential and developing strategies of genetic rescue. Salix baileyi is an endemic vulnerable species in China with extremely small population sizes and a limited distribution. The samples of S. baileyi used for whole-genome resequencing cover its whole distribution. The results reveal four distinct genetic lineages within S. baileyi (DBSW, DBSE, TMS, and LXS), with divergence likely driven by paleoclimatic events and geographic barriers. All populations contracted during the Marine Isotope Stage 5 (MIS 5) up to the Last Glacial Maximum (LGM), with most recovering after the LGM, except for LXS lineage that continued to decline. Our results show that climate events, isolation barriers, inbreeding, and population bottlenecks have impacted the genetic status and evolutionary potential of these lineages of S. baileyi. Lineage-specific conservation measures should be applied based on the unique population dynamics of each lineage. This study provides valuable results for studies of vulnerable dioecious plants.

Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers with (Formula presented.) 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited. Using exome capture sequencing and a fossil-calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic. We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species. Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages.

Hybrid genomes usually harbor asymmetrical parental contributions. However, it is challenging to infer the functional significance of asymmetrical retention of parental alleles in hybrid populations of conifer trees. Here we investigated the diversity in the glutathione S-transferase (GST) gene family in a hybrid pine Pinus densata and its parents (Pinus tabuliformis and Pinus yunnanensis). Plant GSTs play major roles in protecting plants against biotic and abiotic stresses. In this study, 19 orthologous groups of GST genes were identified and cloned from these three species. We examined their expression in different tissues, and then purified the corresponding proteins to characterize their enzymatic activities and specificities toward different substrates. We found that among the 19 GST orthologous groups, divergence in gene expression and in enzymatic activities toward different substrates was prevalent. P. densata preferentially retained P. yunnanensis-like GSTs for 17 out of the 19 gene loci. We determined the first GST crystal structure from conifer species at a resolution of 2.19 Å. Based on this structure, we performed site-directed mutagenesis to replace amino acid residuals in different wild-types of GSTs to understand their functional impacts. Reciprocal replacement of amino acid residuals in native GSTs of P. densata and P. tabuliformis demonstrated significant changes in enzyme functions and identified key sites controlling GSTs activities. This study illustrates an approach to evaluating the functional significance of sequence variations in conifer genomes. Our study also sheds light on plausible mechanisms for controlling the selective retention of parental alleles in the P. densata genome.

Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid “84K” (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.

Southeast Asia (SEA) has seen strong climatic oscillations and fluctuations in sea levels during the Quaternary. The impact of past climate changes on the evolution and distribution of local flora in SEA is still poorly understood. Here we aim to infer how the Quaternary climate change affects the evolutionary process and range shifts in two pine species. We investigated the population genetic structure and diversity using cytoplasmic DNA markers, and performed ecological niche modeling to reconstruct the species past distribution and to project range shift under future climates. We found substantial gene flow across the continuous distribution of the subtropical Pinus yunnanensis. In contrast, the tropical Pinus kesiya showed a strong population structure in accordance with its disjunct distribution across montane islands in Indochina and the Philippines. A broad hybrid zone of the two species occurs in southern Yunnan. Asymmetric introgression from the two species was detected in this zone with dominant mitochondrial gene flow from P. yunnanensis and chloroplast gene flow from P. kesiya. The observed population structure suggests a typical postglaciation expansion in P. yunnanensis, and a glacial expansion and interglacial contraction in P. kesiya. Ecological niche modeling supports the inferred demographic history and predicts a decrease in range size for P. kesiya under future climates. Our results suggest that tropical pine species in SEA have undergone evolutionary trajectories different from high latitude species related to their Quaternary climate histories. We also illustrate the need for urgent conservation actions in this fragmented landscape.

Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them.

To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation.

We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients.

The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.

Polyploids recurrently emerge in angiosperms, but most polyploids are likely to go extinct before establishment due to minority cytotype exclusion, which may be specifically a constraint for dioecious plants. Here we test the hypothesis that a stable sex-determination system and spatial/ecological isolation facilitate the establishment of dioecious polyploids. We determined the ploidy levels of 351 individuals from 28 populations of the dioecious species Salix polyclona, and resequenced 190 individuals of S. polyclona and related taxa for genomic diversity analyses. The ploidy survey revealed a frequency 52% of tetraploids in S. polyclona, and genomic k-mer spectra analyses suggested an autopolyploid origin for them. Comparisons of diploid male and female genomes identified a female heterogametic sex-determining factor on chromosome 15, which probably also acts in the dioecious tetraploids. Phylogenetic analyses revealed two diploid clades and a separate clade/grade of tetraploids with a distinct geographic distribution confined to western and central China, where complex mountain systems create higher levels of environmental heterogeneity. Fossil-calibrated phylogenies showed that the polyploids emerged during 7.6–2.3 million years ago, and population demographic histories largely matched the geological and climatic history of the region. Our results suggest that inheritance of the sex-determining system from the diploid progenitor as intrinsic factor and spatial isolation as extrinsic factor may have facilitated the preservation and establishment of polyploid dioecious populations.