Recent advances in the genomics of sugarcane (Saccharum).

Complete Chloroplast Genome of Indonesian Sugarcane ( Saccharum ‘Bululawang’): Comparative, Structural, and Evolutionary Analysis of Photosystem I‐Encoding Genes

Sugarcane is one of the most important crops, providing the majority of global sugar production and serving as a major feedstock for bioenergy. Increasing demands for sustainable sugar production under climate and productivity constraint have intensified the need for molecular‐level characterization of elite cultivars. Indonesia, as a country with a long history of sugarcane cultivation, has several superior sugarcane cultivars. The domestic sugarcane ‘Bululawang’ is currently dominant due to its advantageous agronomic parameters. Molecular investigations, particularly genome sequencing and functional analysis of photosystem I, are essential to understand the mechanisms underlying photosynthesis and biomass formation. This study aimed to perform comparative plastome analysis of sugarcane ‘Bululawang’ against other species from Saccharum and Zea ; and specifically characterise the psa genes in terms of gene organization, protein structure and codon usage bias. Methods included sample collection, high molecular weight DNA isolation, library preparation, long‐read sequencing, chloroplast genome assembly and annotation, followed by gene classification and data analysis. The analysis covered comparative chloroplast genome analysis, phylogenetic and selection pressure analysis, gene structure, conserved motifs, protein structure and codon usage bias analysis. The results showed that the plastome of Saccharum ‘Bululawang’ exhibited high conservation across species within Saccharum genus. The concatenated sequences provided sufficient phylogenetic resolution at the genus level. Each of the five photosystem I‐encoding genes feature a single‐exon structure without introns and possess highly conserved functional motifs ( p ‐value 2.29 × 10 −55 to 0.00 × 10 0 ). Protein analysis revealed high stability (ipTM > 0.95) in PsaA and PsaB subunits, with structural similarity nearly identical to the reference (RMSD < 1.0 Å). Codon usage profiling indicated a bias towards TTA (RSCU 3.01) and CGG (RSCU 3.00) codons. In conclusion, sugarcane ‘Bululawang’ possesses a conserved photosystem I structure, warranting further investigation into its functional relevance for photosynthetic efficiency.

Assembly of Silphium interspecific hybrid genomes opens the genus to phylogenomics, ecogenomics, and molecular breeding

Wild perennial plants can be domesticated to make agriculture more diverse and resilient, but many have large genomes that have been recalcitrant to analysis. Here, we report phased genome assemblies for Silphium integrifolium Michx. and S. perfoliatum L., two species native to North America under domestication, and demonstrate the utility of trio-binning for genome assembly using an interspecific hybrid. These genomes have chromosomes reaching 1.8 Gb and a helical structure preserved during interphase with a loop circumference of 43 Mb. A genome-informed low coverage and target sequencing strategy enables the refinement of the genus phylogeny, reveals the spatial distribution and structure of natural populations, and identifies 81 loci associated with environmental and domestication traits. Variants in a MATE transporter, α/β hydrolase, and ortholog of Arabidopsis ACT Domain Repeat (ACR4) protein explain significant variance in floral architecture. These advances in genome assembly and genotyping could expand the range of candidates for de novo crop domestication. Silphium species native to North American prairies show strong drought tolerance. This study presents a haplotype-phased genome of a hybrid between S. integrifolium (oilseed crop) and S. perfoliatum (biomass/fiber crop), identifying loci linked to environmental adaptation and domestication.

Pan-Genomics in Fruit Crops: Current Progress, Challenges and Future Directions

This review synthesizes the concepts, methodological advances, computational tools, and recent progress in plant pan-genomics, with a focused emphasis on tropical and subtropical fruit crops.

Unraveling the complexity of the oilseed rape genome: from sequencing to gene discovery for trait improvement

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.

Leveraging genomic resources for precision breeding and trait improvement in chickpea (Cicer arietinum L.)

An Update on Advancement in Genomics Resources for Spiny Lobster Aquaculture Development

This review synthesises the current state of genomic and transcriptomic resources available for spiny and slipper lobsters (Achelata), contextualising these within the broader decapod framework and proposing future directions integrating genomics, transcriptomics, and functional tools to accelerate sustainable domestication and genetic improvement of lobsters.