De Vega, J. | Search bioRxiv

bioRxiv2025

A haplotype-complete chromosome-level assembly of octoploid Urochloa humidicola cv. Tully reveals multiple genomic compositions and evolutionary histories in the species

We developed a haplotype-resolved, chromosome-scale genome assembly of the Urochloa humidicola (Rendle) Morrone & Zuloaga cultivar Tully, an apomictic C4 forage grass cultivated in the tropics worldwide. We assembled a 4.1 Gb genome into 48 chromosomes (2n = 8x = 48), capturing 99.5% of the BUSCO markers, and annotating 259,254 protein-coding genes. Subgenome assignment revealed an octoploid AABBBBCC structure with three ancestral lineages (A, B, C), and an aneuploid composition of 14A, 22B, and 12C chromosomes. Comparative analyses with related Urochloa species identified U. dictyoneura and U. arrecta as potential progenitors of the B and C subgenomes, respectively. The likely progenitor of the A subgenome remains an unknown wild species from the Humidicola clade. Analysis of LTR-retrotransposons and gene collinearity further indicated a close relationship between A and B ancestries, and a distinct evolutionary path for C. Competitive read mapping across additional U. humidicola accessions supported multiple evolutionary histories in the species, with AABBBB (lacking C ancestry), being the most common. We found that previously described subpopulation structures can be explained by the presence or absence of C ancestry, and that sexual U. humidicola are likely to be autopolyploid from the B ancestry. The genome is available as assembly GCA_965614515.2. This assembly provides the first complete reference for U. humidicola and reveals a multi-ancestral origin and reticulated evolution in U. humidicola. It provides a foundation for studying complex polyploid evolution, regulation of apomixis and biological nitrification inhibition, and molecular breeding strategies.

genomics↗

bioRxiv2024

Whole genome resequencing of a global collection of Napier grass (Cenchrus purpureus) to explore global population structure and QTL governing yield and feed quality traits

Napier grass (Cenchrus purpureus) is a C4 perennial grass species native to Sub-Saharan Africa (SSA), primarily used to feed cattle in SSA. In this study, we sequenced the genomes of 450 Napier grass individuals, sourced from 20 different countries. More than 170 million DNA variants (SNPs and Indels) were detected, of which [~]1% informative SNPs were used to assess genetic diversity in the collection. Our resequencing study provided valuable insights into the genetic diversity across a global Napier grass collection. Furthermore, a genome-wide association study on two independent populations, identified multiple quantitative trait loci (QTL) that were significantly associated with desirable agronomic traits, such as biomass yield, nitrogen and cellulose content. Therefore, our results will serve as a valuable resource in safeguarding and unravelling the patterns of Napier grass genetic diversity, in the face of climate change, and spearhead genomics-based breeding programs to develop high-yielding and drought-tolerant varieties suitable for forage and biofuel production.

plant biology↗