The abundance of high-throughput DNA sequence data has revolutionised our understanding of biology. For example, genome analyses are supported by bioinformatics methods and algorithms to understand how DNA sequence information is associated with observable physical and functional characteristics. The study of whole genome sequences offers the potential to relate sequence variation to complex molecular interactions. In plant bioinformatics, computational methods provide the advantage of screening plant genetic resources for sustainable agriculture in a shorter time than traditional plant breeding. Brassica juncea, also known as Indian mustard or Chinese mustard, is a species with increasing agricultural and economic importance. This crop is cultivated for the production of leafy vegetables and oil for human consumption or industrial purposes, including biodiesel and animal feed. The oilseed varieties of B. juncea are of particular importance due to their adaptation to hot and low rainfall areas. Hence, the crop is grown in drier regions where it has an advantage over other oilseed Brassicas. This thesis describes a bioinformatics approach to order assembled genome contigs utilising genetic patterns inherited through a population. This method has been applied to produce newly ordered genome references of B. nigra and B. juncea. The subsequent analysis includes genome annotation of the new genome reference of B. juncea. This is followed by two analyses of whole genome variation: inter-variety and inter-species. The inter-variety analysis includes the discovery of single nucleotide polymorphisms (SNPs), and gene variation studies within a diversity set of B. juncea varieties. These results represent the first genomic characterisation of these B. juncea varieties. The inter-species analysis presents a comparison of whole genome sequences of B. juncea with its closely related species B. rapa, B. nigra and A. thaliana. The B. juncea sequence information was also compared to the Ancestral Crucifer Karyotype (ACK) blocks, to define conserved genomic regions between B. juncea and the ACK blocks. In summary, new insights associated with the genomic content of a particular diversity set of B. juncea are presented. Studies of overlooked species such as B. juncea leverage the potential of underutilised species, enabling breeding programs to produce more sustainable commercial varieties with essential agronomic traits. In addition, the methods presented here are suitable to investigate other agronomically important crops.