Haplotype-resolved genomes of octoploid species in Phyllanthaceae family reveal a critical role for polyploidization and hybridization in speciation.

The Phyllanthaceae family comprises a diverse range of plants with medicinal, edible, and ornamental value, extensively cultivated worldwide. Polyploid species commonly occur in Phyllanthaceae. Due to the rather complex genomes and evolutionary histories, their speciation process has been still lacking in research. In this study, we generated chromosome-scale haplotype-resolved genomes of two octoploid species (Phyllanthus emblica and Sauropus spatulifolius) in Phyllanthaceae family. Combined with our previously reported one tetraploid (Sauropus androgynus) and one diploid species (Phyllanthus cochinchinensis) from the same family, we explored their speciation history. The three polyploid species were all identified as allopolyploids with subgenome A/B. Each of their two distinct subgenome groups from various species was uncovered to independently share a common diploid ancestor (Ancestor-AA and Ancestor-BB). Via different evolutionary routes, comprising various scenarios of bifurcating divergence, allopolyploidization (hybrid polyploidization), and autopolyploidization, they finally evolved to the current tetraploid S. androgynus, and octoploid S. spatulifolius and P. emblica, respectively. We further discuss the variations in copy number of alleles and the potential impacts within the two octoploids. In addition, we also investigated the fluctuation of metabolites with medical values and identified the key factor in its biosynthesis process in octoploids species. Our study reconstructed the evolutionary history of these Phyllanthaceae species, highlighting the critical roles of polyploidization and hybridization in their speciation processes. The high-quality genomes of the two octoploid species provide valuable genomic resources for further research of evolution and functional genomics.

Unravelling inversions: Technological advances, challenges, and potential impact on crop breeding.

Inversions, a type of chromosomal structural variation, significantly influence plant adaptation and gene functions by impacting gene expression and recombination rates. However, compared with other structural variations, their roles in functional biology and crop improvement remain largely unexplored. In this review, we highlight technological and methodological advancements that have allowed a comprehensive understanding of inversion variants through the pangenome framework and machine learning algorithms. Genome editing is an efficient method for inducing or reversing inversion mutations in plants, providing an effective mechanism to modify local recombination rates. Given the potential of inversions in crop breeding, we anticipate increasing attention on inversions from the scientific community in future research and breeding applications.

Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication.

BACKGROUND: Gene duplication is a prevalent phenomenon and a major driving force underlying genome evolution. The process leading to the fixation of gene duplicates following duplication is critical to understand how genome evolves but remains fragmentally understood. Most previous studies on gene retention are based on gene duplicate analyses in single reference genome. No population-based comparative gene retention analysis has been performed to date. RESULTS: Taking advantage of recently published genomic data in Triticeae, we dissected a divergent homogentisate phytyltransferase (HPT2) lineage caught in the middle stage of gene fixation following duplication. The presence/absence of HPT2 in barley (diploid), wild emmer (tetraploid), and bread wheat (hexaploid) pangenome lines appears to be associated with gene dosage constraint and environmental adaption. Based on these observations, we adopted a phylogeny-based orthology inference approach and performed comparative gene retention analyses across barley, wild emmer, and bread wheat. This led to the identification of 326 HPT2-pattern-like genes at whole genome scale, representing a pool of gene duplicates in the middle stage of gene fixation. Majority of these HPT2-pattern-like genes were identified as small-scale duplicates, such as dispersed, tandem, and proximal duplications. Natural selection analyses showed that HPT2-pattern-like genes have experienced relaxed selection pressure, which is generally accompanied with partial positive selection and transcriptional divergence. Functional enrichment analyses showed that HPT2-pattern-like genes are over-represented with molecular-binding and defense response functions, supporting the potential role of environmental adaption during gene retention. We also observed that gene duplicates from larger gene family are more likely to be lost, implying a gene dosage constraint effect. Further comparative gene retention analysis in barley and bread wheat pangenome lines revealed combined effects of species-specific selection and gene dosage constraint. CONCLUSIONS: Comparative gene retention analyses at the population level support gene dosage constraint, environmental adaption, and species-specific selection as three factors that may affect gene retention following gene duplication. Our findings shed light on the evolutionary process leading to the retention of newly formed gene duplicates and will greatly improve our understanding on genome evolution via duplication.

Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley.

Divergent selection of populations in contrasting environments leads to functional genomic divergence. However, the genomic architecture underlying heterogeneous genomic differentiation remains poorly understood. Here, we de novo assembled two high-quality wild barley (Hordeum spontaneum K. Koch) genomes and examined genomic differentiation and gene expression patterns under abiotic stress in two populations. These two populations had a shared ancestry and originated in close geographic proximity but experienced different selective pressures due to their contrasting micro-environments. We identified structural variants that may have played significant roles in affecting genes potentially associated with well-differentiated phenotypes such as flowering time and drought response between two wild barley genomes. Among them, a 29-bp insertion into the promoter region formed a cis-regulatory element in the HvWRKY45 gene, which may contribute to enhanced tolerance to drought. A single SNP mutation in the promoter region may influence HvCO5 expression and be putatively linked to local flowering time adaptation. We also revealed significant genomic differentiation between the two populations with ongoing gene flow. Our results indicate that SNPs and small SVs link to genetic differentiation at the gene level through local adaptation and are maintained through divergent selection. In contrast, large chromosome inversions may have shaped the heterogeneous pattern of genomic differentiation along the chromosomes by suppressing chromosome recombination and gene flow. Our research offers novel insights into the genomic basis underlying local adaptation and provides valuable resources for the genetic improvement of cultivated barley.

Genome-wide association mapping combined with gene-based haplotype analysis identify a novel gene for shoot length in rice (Oryza sativa L.).

KEY MESSAGE: Genome-wide association mapping revealed a novel QTL for shoot length across multiple environments. Its causal gene, LOC_Os01g68500, was identified firstly through gene-based haplotype analysis, gene expression and knockout transgenic verification. Strong seedling vigor is an important breeding target for rice varieties used in direct seeding. Shoot length (SL) is one of the important traits associated with seedling vigor characterized by rapid growth of seedling, which enhance seedling emergence. Therefore, mining genes for SL and conducting molecular breeding help to develop varieties for direct seeding. However, few QTLs for SL have been fine mapped or cloned so far. In this study, a genome-wide association study of SL was performed in a diverse rice collection consisting of 391 accessions in two years, using phenotypes generated by different cultivation methods according to the production practice, and a total of twenty-four QTLs for SL were identified. Among them, the novel QTL qSL-1f on chromosome 1 could be stably detected across all three cultivation methods in the whole population and indica subpopulation. Through gene-based haplotype analysis of the annotated genes within the putative region of qSL-1f, and validated by gene expression and knockout transgenic experiments, LOC_Os01g68500 (i.e., Os01g0913100 in RAP-DB) was identified as the causal gene for SL, which has a single-base variation (C-to-A transversion) in its CDS region, resulting in the significant difference in SL of rice. LOC_Os01g68500 encodes a DUF538 (Domain of unknown function) containing protein, and the function of DUF538 protein gene on rice seedling growth is firstly reported in this study. These results provide a new clue for exploring the molecular mechanism regulating SL, and promising gene source for the molecular breeding in rice.

Analysis and experiment of a pneumatic-hydraulic composite support system for in-situ mirror processing and testing.

To address the deformation issues caused by the self-gravity and machining stresses in the process of large-aperture mirror fabrication, this paper proposes an in-situ switchable pneumatic-hydraulic hybrid supporting system that enables the seamless transition between machining and testing. By facilitating in-situ switching, this system not only reduces the machining time of large-aperture mirrors, thereby enhancing production efficiency, but also mitigates the risks associated with traditional switching methods that may result in mirror damage due to human error. Three typical working conditions of the hybrid supporting system, namely hydraulic machining support, air-floating testing support, and three-point rigid support, are investigated in terms of mirror loading through a finite element simulation. Additionally, an experimental platform is constructed to validate the proposed system. The experimental results affirm the feasibility of the designed pneumatic-hydraulic hybrid supporting system. This system will serve as a technological support to advance the rapid development of large-aperture space telescope manufacturing techniques.

The Chicken Pan-Genome Reveals Gene Content Variation and a Promoter Region Deletion in IGF2BP1 Affecting Body Size.

Domestication and breeding have reshaped the genomic architecture of chicken, but the retention and loss of genomic elements during these evolutionary processes remain unclear. We present the first chicken pan-genome constructed using 664 individuals, which identified an additional approximately 66.5-Mb sequences that are absent from the reference genome (GRCg6a). The constructed pan-genome encoded 20,491 predicated protein-coding genes, of which higher expression levels are observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated that gene PAV in chicken was shaped by selection, genetic drift, and hybridization. PAV-based genome-wide association studies identified numerous candidate mutations related to growth, carcass composition, meat quality, or physiological traits. Among them, a deletion in the promoter region of IGF2BP1 affecting chicken body size is reported, which is supported by functional studies and extra samples. This is the first time to report the causal variant of chicken body size quantitative trait locus located at chromosome 27 which was repeatedly reported. Therefore, the chicken pan-genome is a useful resource for biological discovery and breeding. It improves our understanding of chicken genome diversity and provides materials to unveil the evolution history of chicken domestication.

Machine learning models outperform deep learning models, provide interpretation and facilitate feature selection for soybean trait prediction.

Recent growth in crop genomic and trait data have opened opportunities for the application of novel approaches to accelerate crop improvement. Machine learning and deep learning are at the forefront of prediction-based data analysis. However, few approaches for genotype to phenotype prediction compare machine learning with deep learning and further interpret the models that support the predictions. This study uses genome wide molecular markers and traits across 1110 soybean individuals to develop accurate prediction models. For 13/14 sets of predictions, XGBoost or random forest outperformed deep learning models in prediction performance. Top ranked SNPs by F-score were identified from XGBoost, and with further investigation found overlap with significantly associated loci identified from GWAS and previous literature. Feature importance rankings were used to reduce marker input by up to 90%, and subsequent models maintained or improved their prediction performance. These findings support interpretable machine learning as an approach for genomic based prediction of traits in soybean and other crops.

Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003.

KEY MESSAGE: The major soy protein QTL, cqProt-003, was analysed for haplotype diversity and global distribution, and results indicate 304 bp deletion and variable tandem repeats in protein coding regions are likely causal candidates. Here, we present association and linkage analysis of 985 wild, landrace and cultivar soybean accessions in a pan genomic dataset to characterize the major high-protein/low-oil associated locus cqProt-003 located on chromosome 20. A significant trait-associated region within a 173 kb linkage block was identified, and variants in the region were characterized, identifying 34 high confidence SNPs, 4 insertions, 1 deletion and a larger 304 bp structural variant in the high-protein haplotype. Trinucleotide tandem repeats of variable length present in the second exon of gene Glyma.20G085100 are strongly correlated with the high-protein phenotype and likely represent causal variation. Structural variation has previously been found in the same gene, for which we report the global distribution of the 304 bp deletion and have identified additional nested variation present in high-protein individuals. Mapping variation at the cqProt-003 locus across demographic groups suggests that the high-protein haplotype is common in wild accessions (94.7%), rare in landraces (10.6%) and near absent in cultivated breeding pools (4.1%), suggesting its decrease in frequency primarily correlates with domestication and continued during subsequent improvement. However, the variation that has persisted in under-utilized wild and landrace populations holds high breeding potential for breeders willing to forego seed oil to maximize protein content. The results of this study include the identification of distinct haplotype structures within the high-protein population, and a broad characterization of the genomic context and linkage patterns of cqProt-003 across global populations, supporting future functional characterization and modification.

Stress-induced deformation of the coating on large lightweight freeform optics.

Large aperture, lightweight optics are frequently utilized in modern optical systems. However, despite the use of advanced techniques for developing their materials, fabrication, and mechanical structure, the coatings placed on the substrates induce slight lattice mismatches and increase the thin film stress on polished surfaces. This significantly distorts nano-accuracy optical surfaces, especially on lightweight freeform surfaces. In this study, we construct a finite element model (FEM) and a ray tracing model to estimate the impact of the stress-induced deformation of the coating on a 1.5m class lightweight silicon carbine (SiC) mirror with a freeform surface. Our simulation results are within 10% deviation from the experimental results, and the deformation texture map matches these results as well. We discuss several possible strategies to overcome stress-induced deformation, including fabrication pre-compensation, lightweight structure redesign, and an inverse print-through effect.

Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics.

KEY MESSAGE: Safeguarding crop yields in a changing climate requires bioinformatics advances in harnessing data from vast phenomics and genomics datasets to translate research findings into climate smart crops in the field. Climate change and an additional 3 billion mouths to feed by 2050 raise serious concerns over global food security. Crop breeding and land management strategies will need to evolve to maximize the utilization of finite resources in coming years. High-throughput phenotyping and genomics technologies are providing researchers with the information required to guide and inform the breeding of climate smart crops adapted to the environment. Bioinformatics has a fundamental role to play in integrating and exploiting this fast accumulating wealth of data, through association studies to detect genomic targets underlying key adaptive climate-resilient traits. These data provide tools for breeders to tailor crops to their environment and can be introduced using advanced selection or genome editing methods. To effectively translate research into the field, genomic and phenomic information will need to be integrated into comprehensive clade-specific databases and platforms alongside accessible tools that can be used by breeders to inform the selection of climate adaptive traits. Here we discuss the role of bioinformatics in extracting, analysing, integrating and managing genomic and phenomic data to improve climate resilience in crops, including current, emerging and potential approaches, applications and bottlenecks in the research and breeding pipeline.

Geometric layout optimization of a large aperture thin elliptical mirror's axial and lateral support.

For passive support of large aperture telescopes, geometric layout optimization of the support structure is one of the most critical tasks because it determines the deformation of the mirror under gravity, which affects the wavefront aberration and image quality of the system. Due to a lack of symmetry, the optimization of an elliptical mirror support can be much more complex compared with circular mirrors. We optimize the geometric layout of axial and lateral support for the tertiary mirror of the Thirty Meter Telescope (TMT). Based on a theoretical analysis of the whiffletree principle, a parametric model of axial support is established based on the multi-point constraint equation. The mirror deformation SlopeRMS of the tertiary mirror under vertical gravity is used as the optimization target of the support points. The axial support point position is optimized by means of a simulated annealing algorithm and a mirror-deformed post-processing script written in Python. The TMT tertiary mirror lateral support also uses the whiffletree structure, and its in-plane layout affects the system's resonant modal frequency and the maximum load at each point. According to the dynamic equation and the static principle, the lateral support optimization model is established. The first-order resonant frequency and maximum load of the support point are the objective function. Through optimization of the axial and lateral support, the overall mirror distortion of the system is improved.

Construction and comparison of three reference-quality genome assemblies for soybean.

We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.

Equivalent thin-plate method for stressed mirror polishing of an off-axis aspheric silicon carbide lightweight mirror.

No physical model of stressed mirror polishing, based on the small deflection and deformation of elastic thin plates, has been applied in processing lightweight mirrors. We propose an equivalent thin-plate method for the stressed loading of lightweight mirrors for the first time. Stressed loading and polishing of an aspheric lightweight mirror are simulated using the small-deflection deformation theory of an elastic thin plate. We simulate off-axis aspheric silicon carbide (SiC) lightweight mirrors with three different structures, determining the corresponding equivalent thickness plate in a lightweight structure with a nearly uniform surface density distribution and isotropic bending properties. We then establish a residual removal model of a stressed polishing surface, design the stressed loading equipment, and propose an iterative method for stressed polishing of an off-axis aspheric SiC lightweight mirror. The results demonstrate that it is feasible to choose a lightweight structure that performs full-aperture stressed polishing on off-axis aspheric lightweight mirrors consisting of SiC or other materials.

Comprehensive study of the rapid stressed mirror polishing method for off-axis aspheric SiC thin-plate mirrors.

In this study, the stressed mirror polishing technique is used to perform off-axis aspheric silicon carbide (SiC) mirror full-aperture polishing for the first time. Mechanical and optical parameter analysis methods have been proposed. A medium-diameter off-axis aspheric SiC thin-plate mirror is used as a scaling model for an optical system mirror. A full diameter polishing simulation was completed, and a conceptual design for stress loading equipment is presented. An initial aspheric surface method for stressed mirror polishing of an off-axis aspheric SiC thin-plate mirror, providing a reference for rapid stress mirror polishing of SiC mirrors, is also proposed.

Designing a hydraulic support system for large monolithic mirror's precise in-situ testing-polishing iteration.

In order to improve the fabrication efficiency and testing accuracy of meter-scale, large monolithic mirrors, hydraulic support units (HSUs) are commonly used. However, the challenges to reduce the disparity of the HSUs' stiffness and keep the stability of the mirrors' altitude are hard to resolve, especially for large-scale mirrors. In this paper, we found the air ratio of the working fluid for HSUs is a key factor for designing the HSUs to resolve the challenges from the analytical solution that we derived for supporting large mirrors. Here we designed, tested and fabricated dozens of HSUs and used a four-meter SiC mirror, the world's largest monolithic SiC reported in public, as a study case. It shows that the stiffness values of grouped HSUs vary within ± 3%, and the mirror's reference surface PV is less than 20 µm in 10 days, producing a mirror tip/tilt angle less than 1.5″. The surface error of the supported mirror is about 20 nm, which is very close to the ideal case where uniform stiffness exists, for randomly distributed stiffness values. The repeatability of the in-situ interferometric test with 0.019 λ RMS of the mirror surface demonstrates the supporting system in a high precision. With such a supporting system, the fabrication process of this mirror was estimated to be sped up by 47% compared to the typical fabricating iteration. With minor modifications and easy extensions, such a novel supporting system could be used widely for many in-situ, high-quality fabricating-testing processes.

Economic fabrication of a novel hybrid planar Grating/Fresnel lens for miniature spectrometers.

We propose a new technique to fabricate a highly specialized optical element, a hybrid planar Grating/Fresnel lens (G-Fresnel), which is particularly useful to improve or enable more-affordable miniature/portable spectrometers. Both the Fresnel and the grating surface are fabricated simultaneously by sandwiching soft PDMS between a hard grating and a pre-replicated negative Fresnel surface. Several adhesion reduction techniques are also investigated that help improve both fabrication and cost efficiency (by reducing the solidification time) as well as the lifetime of the mold. Alignment errors are systematically analyzed, and their effects on the G-Fresnel lens evaluated. A compact fabrication platform was built, which is smaller than a volume of 160☓140☓106 mm3 to fit into a conventional vacuum drying oven, for the fabrication of a G-Fresnel lens with a diameter of 25.4 mm, an equivalent focal length of 25 mm, and a blazed grating pattern with 600 lines/mm spacing. The solidification time was reduced to 2 hours thanks to the improved adhesion reduction technique that permits a PDMS drying-temperature as high as 65 °C. The fabricated G-Fresnel lens was evaluated with regard to both geometrical fabrication precision and optical performance. The measured results, using a step gauge and atomic force microscopy, confirm that this replication technique produces high-quality replicates of the master surface-profile. Furthermore, a prototype spectrometer that uses a G-Fresnel lens was built and evaluated. The spectrometer fits within a volume of about 100 mm☓50 mm☓30 mm, and it operates across a wide wavelength spectrum (450 nm to 650 nm). Both the calculation based on the optical software ZEMAX and the experimental measurements are consistent and confirm that the spectrometer with the G-Fresnel lens can provide a spectral resolution of better than 1.2nm.

Technological Development and Advances for Constructing and Analyzing Plant Pangenomes.

A pangenome captures the genomic diversity for a species, derived from a collection of genetic sequences of diverse populations. Advances in sequencing technologies have given rise to three primary methods for pangenome construction and analysis: de novo assembly and comparison, reference genome-based iterative assembly, and graph-based pangenome construction. Each method presents advantages and challenges in processing varying amounts and structures of DNA sequencing data. With the emergence of high-quality genome assemblies and advanced bioinformatic tools, the graph-based pangenome is emerging as an advanced reference for exploring the biological and functional implications of genetic variations.