A unified VCF data set from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize.

Efforts to capture and analyze maize nucleotide diversity have ranged widely in scope, but differences in reference genome version and software algorithms used in these efforts inhibit comparison, and these data are generally not available in an easy-to-use visualization platform for quick access and analysis. To address these issues, The Maize Genetics and Genomics Database has collaborated with maize researchers to offer variant data from a diverse set of 1,498 inbred lines, traditional varieties, and teosintes through a standardized variant-calling pipeline against version 5 of the B73 reference genome. The output was filtered for mapping quality, completeness, and linkage disequilibrium, and annotated based on variant effects relative to the B73 RefGen_v5 gene annotations.

Tools and Resources at the Maize Genetics and Genomics Database (MaizeGDB).

The Maize Genetics and Genomics Database (MaizeGDB) is the community resource for maize researchers, offering a suite of tools, informatics resources, and curated data sets to support maize genetics, genomics, and breeding research. Here, we provide an overview of the key resources available at MaizeGDB, including maize genomes, comparative genomics, and pan-genomics tools. This review aims to familiarize users with the range of options available for maize research and highlights the importance of MaizeGDB as a central hub for the maize research community.

Testing the Hard to Test: A Pilot Study Examining the Role of Questionnaires in Eliciting Visual Behaviours in Children with Autistic Spectrum Disorder.

Purpose: There is a higher prevalence of visual problems in children with Autistic Spectrum Disorder (ASD) compared with the neuro-typical population. Issues relating to visual perception can be evident as atypical visual behaviours (ViBes). The aim of the study was to compare findings of parents and eye health professionals using questionnaires to describe visual function in young children with ASD.

Functional annotation and meta-analysis of maize transcriptomes reveal genes involved in biotic and abiotic stress.

Background: Environmental stress factors, such as biotic and abiotic stress, are becoming more common due to climate variability, significantly affecting global maize yield. Transcriptome profiling studies provide insights into the molecular mechanisms underlying stress response in maize, though the functions of many genes are still unknown. To enhance the functional annotation of maize-specific genes, MaizeGDB has outlined a data-driven approach with an emphasis on identifying genes and traits related to biotic and abiotic stress.

Enhanced pan-genomic resources at the maize genetics and genomics database.

Pan-genomes, encompassing the entirety of genetic sequences found in a collection of genomes within a clade, are more useful than single reference genomes for studying species diversity. This is especially true for a species like Zea mays, which has a particularly diverse and complex genome. Presenting pan-genome data, analyses, and visualization is challenging, especially for a diverse species, but more so when pan-genomic data is linked to extensive gene model and gene data, including classical gene information, markers, insertions, expression and proteomic data, and protein structures as is the case at MaizeGDB.

Ciliary muscle and anterior segment characteristics in pre-presbyopic adults with Down syndrome.

Purpose: Previous research has shown that accommodation deficits are common in individuals with Down syndrome (DS), but the origin and mechanisms behind these deficits are still unknown. The aim of this study was to investigate the characteristics of different ocular structures involved in accommodation, in particular the ciliary muscle (CM), in a population of individuals with DS to further understand this deficit and its mechanisms.

Methods: Thirty-two volunteer participants of pre-presbyopic age with (n = 16) and without DS (n = 16) were recruited.

PanEffect: a pan-genome visualization tool for variant effects in maize.

Summary: Understanding the effects of genetic variants is crucial for accurately predicting traits and functional outcomes. Recent approaches have utilized artificial intelligence and protein language models to score all possible missense variant effects at the proteome level for a single genome, but a reliable tool is needed to explore these effects at the pan-genome level. To address this gap, we introduce a new tool called PanEffect.

Maize Feature Store: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications.

The big-data analysis of complex data associated with maize genomes accelerates genetic research and improves agronomic traits. As a result, efforts have increased to integrate diverse datasets and extract meaning from these measurements. Machine learning models are a powerful tool for gaining knowledge from large and complex datasets.

Maize protein structure resources at the maize genetics and genomics database.

Protein structures play an important role in bioinformatics, such as in predicting gene function or validating gene model annotation. However, determining protein structure was, until now, costly and time-consuming, which resulted in a structural biology bottleneck. With the release of such programs AlphaFold and ESMFold, this bottleneck has been reduced by several orders of magnitude, permitting protein structural comparisons of entire genomes within reasonable timeframes.

Association mapping across a multitude of traits collected in diverse environments in maize.

Classical genetic studies have identified many cases of pleiotropy where mutations in individual genes alter many different phenotypes. Quantitative genetic studies of natural genetic variants frequently examine one or a few traits, limiting their potential to identify pleiotropic effects of natural genetic variants. Widely adopted community association panels have been employed by plant genetics communities to study the genetic basis of naturally occurring phenotypic variation in a wide range of traits.

Voluntary Flutter Presenting During Ophthalmoscopy: A Case Report.

Voluntary flutter (sometimes known as "voluntary nystagmus") is a conjugate saccadic oscillation of the eyes that occurs in some healthy individuals. It has no relation to pathological nystagmus, which can manifest in infancy or become acquired later in life. This report presents an unusual case of voluntary flutter that presented in a 20-year-old male with autism spectrum disorder during ocular examination via direct ophthalmoscopy.

Visual and Refractive Status of Children With Down's Syndrome and Nystagmus.

Purpose: Children with Down's syndrome (DS) are known to have poorer visual acuity than neurotypical children. One report has shown that children with DS and nystagmus also have poor acuity when compared to typical children with nystagmus. What has not been established is the extent of any acuity deficit due to nystagmus and whether nystagmus affects refractive error within a population with DS.

A pan-genomic approach to genome databases using maize as a model system.

Research in the past decade has demonstrated that a single reference genome is not representative of a species' diversity. MaizeGDB introduces a pan-genomic approach to hosting genomic data, leveraging the large number of diverse maize genomes and their associated datasets to quickly and efficiently connect genomes, gene models, expression, epigenome, sequence variation, structural variation, transposable elements, and diversity data across genomes so that researchers can easily track the structural and functional differences of a locus and its orthologs across maize. We believe our framework is unique and provides a template for any genomic database poised to host large-scale pan-genomic data.

qTeller: a tool for comparative multi-genomic gene expression analysis.

Motivation: Over the last decade, RNA-Seq whole-genome sequencing has become a widely used method for measuring and understanding transcriptome-level changes in gene expression. Since RNA-Seq is relatively inexpensive, it can be used on multiple genomes to evaluate gene expression across many different conditions, tissues and cell types. Although many tools exist to map and compare RNA-Seq at the genomics level, few web-based tools are dedicated to making data generated for individual genomic analysis accessible and reusable at a gene-level scale for comparative analysis between genes, across different genomes and meta-analyses.

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes.

We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day.

Behavioural Features of Cerebral Visual Impairment Are Common in Children With Down Syndrome.

It is widely recognised that children with Down syndrome have a broad range and a high prevalence of visual deficits and it has been suggested that those with Down syndrome are more likely to exhibit visual perception deficits indicative of cerebral visual impairment. This exploratory study aims to determine the prevalence of behavioural features suggestive of cerebral visual impairment (CVI) occurring with Down syndrome and whether the visual problems can be ascribed to optometric factors. A cohort of 226 families of children with Down syndrome (trisomy 21), aged 4-17, were invited to participate in a validated question inventory, to recognise visual perception issues.

FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences.

Background: Gene annotation in eukaryotes is a non-trivial task that requires meticulous analysis of accumulated transcript data. Challenges include transcriptionally active regions of the genome that contain overlapping genes, genes that produce numerous transcripts, transposable elements and numerous diverse sequence repeats. Currently available gene annotation software applications depend on pre-constructed full-length gene sequence assemblies which are not guaranteed to be error-free.

Spatial transcriptional signatures define margin morphogenesis along the proximal-distal and medio-lateral axes in tomato (Solanum lycopersicum) leaves.

Leaf morphogenesis involves cell division, expansion, and differentiation in the developing leaf, which take place at different rates and at different positions along the medio-lateral and proximal-distal leaf axes. The gene expression changes that control cell fate along these axes remain elusive due to difficulties in precisely isolating tissues. Here, we combined rigorous early leaf characterization, laser capture microdissection, and transcriptomic sequencing to ask how gene expression patterns regulate early leaf morphogenesis in wild-type tomato (Solanum lycopersicum) and the leaf morphogenesis mutant trifoliate.

In-vivo anterior segment OCT imaging provides unique insight into cerulean blue-dot opacities and cataracts in Down syndrome.

Down syndrome (DS) is frequently associated with cataract, but there remains scant information about DS cataract morphology. Supra-nuclear cataracts in DS have been proposed as indicative of beta-amyloid (Aβ) aggregation and thus potential biomarkers for Alzheimer's (AD). This study employed anterior segment OCT (AS-OCT) and slit-lamp (SL) photography to image the crystalline lens in DS, compared with adult controls.

Gapless assembly of maize chromosomes using long-read technologies.

Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We use two independent assemblies and an optical map-based merging pipeline to produce a maize genome (B73-Ab10) composed of 63 contigs and a contig N50 of 162 Mb. This genome includes gapless assemblies of chromosome 3 (236 Mb) and chromosome 9 (162 Mb), and 53 Mb of the Ab10 meiotic drive haplotype.

GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations.

Background: Genome assemblies are foundational for understanding the biology of a species. They provide a physical framework for mapping additional sequences, thereby enabling characterization of, for example, genomic diversity and differences in gene expression across individuals and tissue types. Quality metrics for genome assemblies gauge both the completeness and contiguity of an assembly and help provide confidence in downstream biological insights.

Tissue-specific gene expression and protein abundance patterns are associated with fractionation bias in maize.

Background: Maize experienced a whole-genome duplication event approximately 5 to 12 million years ago. Because this event occurred after speciation from sorghum, the pre-duplication subgenomes can be partially reconstructed by mapping syntenic regions to the sorghum chromosomes. During evolution, maize has had uneven gene loss between each ancient subgenome.

Evolutionary flexibility in flooding response circuitry in angiosperms.

Flooding due to extreme weather threatens crops and ecosystems. To understand variation in gene regulatory networks activated by submergence, we conducted a high-resolution analysis of chromatin accessibility and gene expression at three scales of transcript control in four angiosperms, ranging from a dryland-adapted wild species to a wetland crop. The data define a cohort of conserved submergence-activated genes with signatures of overlapping cis regulation by four transcription factor families.