VigExp represents an adaptable and updatable resource to support crop improvement in cowpea and other legumes, which are often highly syntenic with respect to genome composition.
Abstract
Legumes include some of the world’s most significant crop species, such as cowpea (Vigna unguiculata), a subsistence crop widely grown in sub-Saharan Africa. Despite their importance, legume crop improvement is hindered by a lack of high-resolution expression data, particularly for reproductive tissues and cell types. Here, we report on VigExp, a tool for visualising cowpea gene expression datasets. We demonstrate its utility across a range of vegetative and reproductive cell types of varieties IT97K-499-35 and IT86D-1010, which exhibit 93.75% protein sequence conservation and are amenable to stable transformation. This includes previously published transcriptomes of vegetative, floral and seed tissues, combined with developmentally staged male and female reproductive tissues. Also integrated are novel transcriptomes of laser-captured cell types covering reproductive development from meiosis to early embryo formation post-fertilisation. Spatial expression patterns and transcript levels can be visualised through an electronic fluorescent pictograph (eFP) browser. Validated by RT-qPCR, in situ hybridisation, transgenic, and CRISPR gene editing analyses, the predictive accuracy of VigExp matches prior cowpea functional study observations. Critical genes for nodule development and regulation were also identified and their expression patterns established in cowpea. Novel reference genes, constitutively expressed gene promoters for visualisation markers/gene-editing, and tissue- and cell-specific gene promoters for targeting these regions, were identified. The A-type cyclin, VuTAM2, was also identified, with a critical role in male meiosis established. Collectively, VigExp represents an adaptable and updatable resource to support crop improvement in cowpea and other legumes, which are often highly syntenic with respect to genome composition.
Evidence on the breeding and omics-based improvement of underutilised legumes is synthesised, identifying a persistent disconnection between genomic resource generation, downstream trait validation, breeding pipeline integration and farmer-level variety release.
Ajesh J. Nair, C. Anjali, M. Nivedhitha et al.· Journal of Advances in Biolo...· 0 citations
This review synthesizes the transformative evolution of rapeseed genomics, traversing from initial fragmented references to the modern era of gap-free Telomere-to-Telomere (T2T) assemblies and graph-based pan-genomes, and underscores the pivotal shift from descriptive genomics to the precision engineering of climate-resilient, high-yielding polyploid crops.
The potato leafhopper, Empoasca fabae (Harris, 1841), is a highly polyphagous, migratory insect pest of eastern North America that feeds on more than 200 herbaceous and woody plant species, causing substantial losses to forage and field crops. Despite its agricultural and ecological importance, no genome has been available for this species. Here, we present the first chromosome-level genome assembly of E. fabae, generated from Oxford Nanopore long reads, Illumina short reads, and Omni-C proximity-ligation data. The final assembly spans 908 Mb across 132 scaffolds, with 99.8% of the assembly captured in ten chromosome-length scaffolds (nine autosomes and an X chromosome) with a scaffold N50 of 96.2 Mb. The assembly is highly complete, recovering 92.4% of conserved hemipteran single-copy orthologs, and is composed of 47.6% repetitive sequence, dominated by long terminal repeat retrotransposons and unclassified elements. Read-depth comparison between male and female individuals supports assignment of a single sex-linked chromosome, consistent with an XO sex-determination system. BRAKER3 gene annotation predicted 31,406 protein-coding genes after retaining the longest isoform per locus. Comparative genome analysis against the two closest related Typhlocybinae species with genomes available, Matsumurasca onukii and Hebata decipiens, revealed extensive chromosome-scale collinearity, while defining a shared core gene repertoire. This reference genome provides a foundation for comparative and population genomic studies and for investigating genetic traits in this economically important crop pest species. SIGNIFICANCE Leafhoppers (Cicadellidae) are among the most diverse families of plant-feeding insects, but chromosome-level genomes remain scarce, particularly for mesophyll-feeding members of the subfamily Typhlocybinae. The potato leafhopper, Empoasca fabae, is an unusually polyphagous crop and migratory pest of major importance across North America. Here, we provide the first chromosome-level genome assembly for this species. This chromosomal reference reveals broad synteny with two related Typhlocybinae relatives. This assembly will serve as a critical resource, enabling further comparative genomics, population genomics, and functional studies of host-plant adaptation in a significant agricultural crop pest species.
Joshua Molligan, Florent Sylvestre, E. Pérez-López· bioRxiv· 0 citations
Ecuador ranks among the world’s leading banana exporters; however, postharvest enzymatic browning, driven by polyphenol oxidases (PPOs), remains an important determinant of fruit quality loss and reduced market value. The genes encoding PPOs in Musa paradisiaca L., a triploid hybrid (AAB) widely cultivated in Ecuador, have not previously been described at the genomic or transcriptional level. The objective of this study was to generate a preliminary de novo draft assembly of Ecuadorian M. paradisiaca, identify PPO-coding loci recovered in this assembly, and compare their relative expression across three field-defined green-fruit developmental stages: early, intermediate, and physiologically mature-green. High-molecular-weight genomic DNA sequencing was performed using the Oxford Nanopore MinION Mk1B platform, and 13,239 contigs were obtained by de novo assembly with Flye v2.9.6. Two intronless PPO-coding loci, designated MpPPO1 and MpPPO2, were identified and deposited in GenBank under accessions PX565008 and PX565009. qRT-PCR showed significantly higher MpPPO1 expression at the physiologically mature-green stage, whereas MpPPO2 showed only a non-significant trend toward higher expression at the intermediate stage. These profiles indicate transcriptional divergence and identify MpPPO1 as a candidate associated with late green-fruit development or physiological maturity. However, because stage classification relied on a qualitative field harvest index and neither controlled postharvest ripening nor quantitative maturity, PPO activity, or browning measurements were performed, the results do not demonstrate ripening-induced activation, functional subfunctionalization, or causality in browning. These findings provide a preliminary molecular basis for future functional and postharvest studies in commercial banana cultivars.
Víctor Huebla-Concha, N. Cruz-Rosero, Jaime Morante-Carriel et al.· Plants· 0 citations
