Haplotype-resolved genome assembly of Populus tremula × P. alba reveals aspen-specific megabase satellite DNA

Overexpression of plasma membrane SUT1 in poplar alters lateral sucrose partitioning in stem and promotes leaf necrosis

In Populus and many other tree species, photoassimilate sucrose diffuses down a concentration gradient via symplastically connected mesophyll cells to minor vein phloem for long-distance transport. There is no evidence for apoplastic phloem-loading in Populus. However, plasma membrane sucrose transporters (SUT1 and SUT3) orthologous to those associated with apoplastic phloem loading are expressed in vascular tissues of poplar. While SUT3 functions in sucrose import into developing xylem, the role of SUT1 remains unclear. Here, we overexpressed PtaSUT1 in Populus tremula x P. alba to examine the effects on sucrose partitioning in transgenic plants. Overall leaf sucrose levels were similar between wild type and transgenic lines. Stem sucrose levels were not changed in bark but were significantly reduced in the adjacent xylem, suggesting hindered intercellular sucrose trafficking from the phloem to the developing xylem. Fully expanded leaves of transgenic plants deteriorated prematurely with declining photosynthesis prior to severe necrotic spotting. Necrotic spotting advanced most rapidly in the distal portion of mature leaves and was accompanied by sharp hexose increases and sharp sucrose decreases there. Leaf transcriptome profiling and network inference revealed the down-regulation of copper proteins and elevated expression of copper microRNAs prior to noticeable leaf injury. Our results suggest ectopic expression of PtaSUT1 altered sucrose partitioning in stems with systemic effects on leaf health and copper homeostasis mediated in part by sucrose-sensitive copper miRNAs.

The Current Status and Prospects of the Application of Omics Technology in the Study of Ulmus

Elm (Ulmus) species are important components of forest resources with significant ecological and economic value. As tall hardwood trees that are drought-resistant, poor-soil-tolerant, and highly adaptable, Ulmus species are an excellent choice for ecologically protected forests and urban landscaping. Additionally, the bioactive substances identified in the fruits, leaves, bark, and roots of Ulmus have potential applications in the food and medical fields and as raw materials in industrial and cosmetic applications. However, the survival of Ulmus species in the natural environment has been threatened by recurrent outbreaks of Dutch elm disease, which have led to the death of large numbers of Ulmus trees. In addition, severe damage to the natural habitats of some Ulmus species is driving their populations to extinction. Omics technology has become an important tool for the collection, protection, and biological characteristic analysis of Ulmus species and their resources due to its recent advances. This article summarizes the current research and application status of omics technology in Ulmus. The remaining problems are noted, and future research directions are proposed. Our review is aimed at providing a reference for resource conservation of Ulmus and for scientific research into this genus.

Molecular Mechanisms of Heterosis and Its Applications in Tree Breeding: Progress and Perspectives

Heterosis, or hybrid vigor, refers to the phenomenon where hybrid progenies outperform their parents in traits such as yield and resistance. This phenomenon has been widely applied in plant breeding. Recent advances in high-throughput genomics have significantly advanced our understanding of heterosis. This review systematically summarizes the genetic, molecular, and epigenetic mechanisms underlying heterosis. Furthermore, we discuss recent advances in predictive methods for heterosis and their applications in improving growth rate, resistance to abiotic stresses, and wood yield in tree species. We also explore the role of tree genomics in unraveling the mechanisms underlying heterosis, emphasizing the potential of integrating high-resolution genomics, single-cell sequencing, and spatial transcriptomics to achieve a comprehensive understanding of heterosis from the molecular to spatial levels. Building on this, CRISPR-based gene-editing technologies can be employed to precisely edit heterotic loci, enabling the study of allele function. Additionally, molecular marker-assisted selection (MAS) can be utilized to identify heterotic loci in parental lines, facilitating the selection of optimal hybrid combinations and significantly reducing the labor and time costs of hybrid breeding. Finally, we review the utilization of heterosis in tree breeding and provide a forward-looking perspective on future research directions, highlighting the potential of integrating multi-omics approaches and emerging gene-editing tools to revolutionize tree hybrid breeding.

Exploring the complexity of genome size reduction in angiosperms

The genome sizes of angiosperms decreased significantly more than the genome sizes of their ancestors (pteridophytes and gymnosperms). Decreases in genome size involve a highly complex process, with remnants of the genome size reduction scattered across the genome and not directly linked to specific genomic structures. This is because the associated mechanisms operate on a much smaller scale than the mechanisms mediating increases in genome size. This review thoroughly summarizes the available literature regarding the molecular mechanisms underlying genome size reductions and introduces Utricularia gibba and Arabidopsis thaliana as model species for the examination of the effects of these molecular mechanisms. Additionally, we propose that phosphorus deficiency and drought stress are the major external factors contributing to decreases in genome size. Considering these factors affect almost all land plants, angiosperms likely gained the mechanisms for genome size reductions. These environmental factors may affect the retention rates of deletions, while also influencing the mutation rates of deletions via the functional diversification of the proteins facilitating double-strand break repair. The biased retention and mutation rates of deletions may have synergistic effects that enhance deletions in intergenic regions, introns, transposable elements, duplicates, and repeats, leading to a rapid decrease in genome size. We suggest that these selection pressures and associated molecular mechanisms may drive key changes in angiosperms during recurrent cycles of genome size decreases and increases.

Rare but diverse off-target and somatic mutations found in field and greenhouse grown trees expressing CRISPR/Cas9

Introduction: CRISPR gene editing, while highly efficient in creating desired mutations, also has the potential to cause off-target mutations. This risk is especially high in clonally propagated plants, where editing reagents may remain in the genome for long periods of time or in perpetuity. We studied a diverse population of Populus and Eucalyptus trees that had CRISPR/Cas9-containing transgenes that targeted one or two types of floral development genes, homologs of LEAFY and AGAMOUS. Methods: Using a targeted sequence approach, we studied approximately 20,000 genomic sites with degenerate sequence homology of up to five base pairs relative to guide RNA (gRNA) target sites. We analyzed those sites in 96 individual tree samples that represented 37 independent insertion events containing one or multiples of six unique gRNAs. Results: We found low rates of off-target mutations, with rates of 1.2 × 10-9 in poplar and 3.1 × 10-10 in eucalypts, respectively, comparable to that expected due to sexual reproduction. The rates of mutation were highly idiosyncratic among sites and not predicted by sequence similarity to the target sites; a subset of two gRNAs showed off-target editing of four unique genomic sites with up to five mismatches relative to the true target sites, reaching fixation in some gene insertion events and clonal ramets. The location of off-target mutations relative to the PAM site were essentially identical to that seen with on-target CRISPR mutations. Discussion: The low rates observed support many other studies in plants that suggest that the rates of off-target mutagenesis from CRISPR/Cas9 transgenes are negligible; our study extends this conclusion to trees and other long-lived plants where CRISPR/Cas9 transgenes were present in the genome for approximately four years.

High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar

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.

Haplotype-resolved genome assembly of poplar line NL895 provides a valuable tree genomic resource

Poplar line NL895 can potentially become a model plant for poplar study as it is a widely cultivated elite line. However, the lack of genome resources hindered the use of NL895 as the major plant material in poplar. In this study, we provided a high-quality genome assembly for poplar line NL895 with PacBio single molecule real-time (SMRT) sequencing and High-throughput chromosome conformation capture (Hi-C) technology. The raw assembly of NL895 for the diploid genome included 606 contigs with a total size of ~815 Mb, and the monoploid genome included 246 contigs with a total size of ~412 Mb. The haplotype-resolved chromosomes in the diploid genomes were also generated. All the monoploid, diploid, and haplotype-resolved genomes showed more than 97% completeness and they can largely improve the mapping efficiency in RNA-Seq analysis. By comprehensively comparing the two haplotype genomes we found the heterozygosity of NL895 is much higher than other poplar lines. We also found that NL895 harbors more genomic variants and more gene diversity. The haplotype-specific genes showed higher variable gene expression patterns. These characters would be attributed to the high heterosis of poplar line NL895. The allele-specific expression (ASE) was also investigated and lots of alleles showed biased expressions in different tissues or environmental conditions. Taken together, the genome sequence for NL895 is a valuable tree genomic resource and it would greatly facilitate studies in poplar.

The structure, function, and evolution of plant centromeres

Centromeres are essential regions of eukaryotic chromosomes responsible for the formation of kinetochore complexes, which connect to spindle microtubules during cell division. Notably, although centromeres maintain a conserved function in chromosome segregation, the underlying DNA sequences are diverse both within and between species and are predominantly repetitive in nature. The repeat content of centromeres includes high-copy tandem repeats (satellites), and/or specific families of transposons. The functional region of the centromere is defined by loading of a specific histone 3 variant (CENH3), which nucleates the kinetochore and shows dynamic regulation. In many plants, the centromeres are composed of satellite repeat arrays that are densely DNA methylated and invaded by centrophilic retrotransposons. In some cases, the retrotransposons become the sites of CENH3 loading. We review the structure of plant centromeres, including monocentric, holocentric, and metapolycentric architectures, which vary in the number and distribution of kinetochore attachment sites along chromosomes. We discuss how variation in CENH3 loading can drive genome elimination during early cell divisions of plant embryogenesis. We review how epigenetic state may influence centromere identity and discuss evolutionary models that seek to explain the paradoxically rapid change of centromere sequences observed across species, including the potential roles of recombination. We outline putative modes of selection that could act within the centromeres, as well as the role of repeats in driving cycles of centromere evolution. Although our primary focus is on plant genomes, we draw comparisons with animal and fungal centromeres to derive a eukaryote-wide perspective of centromere structure and function.