Biology subjects

Kagale, S.

Publications and source records attributed to Kagale, S..

4 recordsLinked to original sources

bioRxiv2026

Lens species genome assemblies reveal evolutionarily fragile chromosomes associated with pericentric inversions

The genus Lens is comprised of seven diploid species, including the cultivated crop Lentil, and six wild relatives often used in breeding programs for beneficial allele introgression. Lens species are proposed to exhibit considerable levels of genome structural variation both within and between species, which has implications for plant breeding and evolutionary genomics. Plant centromeres are key regions involved in chromosomal stability, where structural changes can be linked to meiotic abnormalities, resulting in inversions, translocations, and deletions of chromosomal segments. Fabeae centromeres are known to be diverse and do not fit the centromere drive model. The origins of this centromere diversity and the evolutionary trends remain unclear, but recent studies suggest that centromere structural variation plays a role in creating new sequence combinations that contribute to the unique centromere evolution patterns observed in legumes. We sequenced, assembled, and performed gene synteny analysis in the genomes of all seven Lens species using long-read sequencing technologies. We also located and characterized the centromeres in these genomes through ChIP-seq experiments to better understand their role in Lens chromosomal stability. Synteny analysis reveals that Lens genomes have undergone extensive rearrangements during evolution, with multiple translocations and inversions identified between species. Specific Lens chromosomes appear more susceptible to rearrangements over time. These same chromosomes also exhibit higher rates of rearrangement throughout Lens speciation. Fragile chromosomes are associated with the occurrence of pericentric inversions, likely disrupting stability. The diversity in satellite sequences in Lens centromeres likely results from structural changes accumulated throughout Lens evolution. These findings suggest that genome and centromere structure play significant roles in generating centromere diversity within this legume genus.

genomics↗

bioRxiv2026

A Large Yield Model for Crop Production and Design in Western Canada

With a changing climate, disease pressure, and other production threats, it is critical to ensure that crop producers are well-positioned to protect and optimize yields. In this work we present LYM-1, the first large-scale, multi-crop model for the prediction of yield performance in the Canadian prairies. This is enabled by a large dataset containing over 4.7 million yield observations across 10 different crop types, distributed over 23 growing years. Leveraging additional data sources for weather and soil properties allows the model to reason about the complex interactions between genetics, environment, and management which underlie yield. The trained model is not only effective at predicting the yield for held-out data, but also reveals scientifically and agronomically relevant effects such as the interaction between solar radiation and nitrogen uptake. We anticipate that large yield models can be used for both the optimization of crop production by producers, as well as by plant breeders and industry for crop design.

bioinformatics↗

bioRxiv2021

Genomic rearrangements have consequences for introgression breeding as revealed by genome assemblies of wild and cultivated lentil species

Understanding the genomic relationship between wild and cultivated genomes would facilitate access to the untapped variability found in crop wild relatives. We developed genome assemblies of a cultivated lentil (Lens culinaris) as well as a wild relative (L. ervoides). Comparative analyses revealed large-scale structural rearrangements and additional repetitive DNA in the cultivated genome, resulting in regions of reduced recombination, segregation distortion and permanent heterozygosity in the offspring of a cross between the two species. These novel findings provide plant breeders with better insight into how best to approach accessing the novel variability available in wild relatives.

plant biology↗

bioRxiv2020

High contiguity long read assembly of Brassica nigra allows localization of active centromeres and provides insights into the ancestral Brassica genome.

High-quality nanopore genome assemblies were generated for two Brassica nigra genotypes (Ni100 and CN115125); a member of the agronomically important Brassica species. The N50 contig length for the two assemblies were 17.1 Mb (58 contigs) and 0.29 Mb (963 contigs), respectively, reflecting recent improvements in the technology. Comparison with a de novo short read assembly for Ni100 corroborated genome integrity and quantified sequence related error rates (0.002%). The contiguity and coverage allowed unprecedented access to low complexity regions of the genome. Pericentromeric regions and coincidence of hypo-methylation enabled localization of active centromeres and identified a novel centromere-associated ALE class I element which appears to have proliferated through relatively recent nested transposition events (<1 million years ago). Computational abstraction was used to define a post-triplication Brassica specific ancestral genome and to calculate the extensive rearrangements that define the genomic distance separating B. nigra from its diploid relatives.

genomics↗