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

Recent advances in the genomics of sugarcane (Saccharum).

Sugarcane (Saccharum spp.) is a globally important C4 crop that contributes substantially to sugar production and renewable bioenergy systems. Modern sugarcane cultivars were derived from interspecific hybridization between high-sucrose S. officinarum and stress-resilient wild S. spontaneum, followed by extensive backcrossing and selection. Such breeding trajectory has generated an extremely complex polyploid genome marked by high ploidy, pervasive aneuploidy, mosaic subgenome composition, and a reticulate evolution history. For decades, this complexity has resulted in persistent taxonomic ambiguities, constrained genomic analyses, complicated genetic dissection of agronomic traits, and limited breeding efficiency. The rapid development of third-generation long-read sequencing, haplotype-resolved assembly, and polyploid-aware computational approaches has fundamentally revolutionized sugarcane research. This review synthesizes recent progress in Saccharum taxonomy, polyploid genome architecture and evolution, high-quality genomic resource development, germplasm exploration, and genome-informed breeding strategies. We propose an integrated framework connecting taxonomic refinement, genome biology, and breeding applications. Critical challenges are elaborated, including the taxonomy-genomics disconnect, diploid-centric analytical bias, insufficient haplotype resolution, the lack of polyploid-aware genetic models, and underutilization of wild germplasm. Finally, we outline future priorities toward predictive and design-oriented sugarcane improvement by addressing unresolved core questions. This review provides a comprehensive and forward-looking perspective for accelerating genetic improvement in sugarcane and other highly complex polyploid crops.

Genomics of Tropical Plants: Current Progress, Applications, and Future Opportunities

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

Pan-genomics captures the full spectrum of genetic diversity within plant species and overcomes the limitations of single reference genomes. By integrating core, dispensable, and unique genomic components, pan-genomic approaches enable comprehensive detection of structural variants, presence–absence variations, and lineage-specific genes that underpin phenotypic diversity, domestication, and environmental adaptation. In plant and horticultural crops, particularly tropical and subtropical fruit species characterized by high heterozygosity, polyploidy, and clonal propagation, pangenomics has revealed extensive hidden variation influencing fruit quality, disease resistance, and stress tolerance that was previously inaccessible using traditional genomics.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. We discuss pan-genome construction strategies, graph-based representations, and emerging resources, alongside key applications in trait discovery, evolutionary analysis, and molecular breeding. Current challenges, including limited accession diversity, incomplete functional annotation, and computational complexity, are critically examined. Finally, we highlight future directions toward population-scale, graph-based, and multi-omics–integrated pan-genomes, underscoring their potential to accelerate precision breeding and support the development of climate-resilient, high-quality fruit crop varieties.

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

High‐Throughput Sequencing in Aquaculture Disease Investigations: Challenges and Opportunities for Implementation

The current generation of sequencing technologies can produce terabases of data with exceptional accuracy and speed, at a fraction of the cost of older methods. Despite this unprecedented power, adoption into aquaculture health management presents several challenges, including identifying where such capability may be optimally deployed. Here we synthesise discussions from a structured expert workshop held at the 2025 Aotearoa Aquatic Diseases Symposium in Dunedin, New Zealand, where experts from industry, government and academia explored the challenges and opportunities for adopting high‐throughput sequencing (HTS) to support disease investigations in aquaculture. Workshop participants identified key applications for HTS, including pathogen discovery during unexplained mortality events and source attribution in epidemics, but also noted technical, regulatory and social challenges for widespread adoption. These include the need for standardised sampling and bioinformatic workflows, data sovereignty, equitable access to the technology and uncertainty around interpreting detection of notifiable pathogens. Targeted research and coordinated regulatory frameworks will be essential to guide responsible use of HTS and determine where it adds value relative to existing approaches. Clarifying these opportunities and constraints will guide the responsible adoption of HTS into aquaculture health management to support sustainable growth for the sector.

Integrating Multi-Omics in Aquaculture: From Genetic Gains to Sustainable Aquaculture

This review outlines foundational applications of omics in aquaculture and highlights the characteristics and current applications of distinct omics approaches, and summarizes three core application domains of omics in aquaculture.