The Tobacco Plant Genome

Abstract

The major global crop Brassica napus L. (rapeseed, oilseed rape, canola, kale, swede, rutabaga; genome AACC, 2n = 4x = 38) is a recent allopoly- ploid species, formed during the past *7500 years by interspecific hybridization between B. rapa (AA, 2n = 2x = 20) and B. oleracea (CC, 2n = 2x = 18). This hybridization is believed to have occurred spontaneously, with at least three independent origins, but most likely under human cultivation as no wild forms of B. napus are known. The diploid progenitors each derived via ancestral hexaploidy from a common origin, but despite relatively close genome homology, evolved into separate species with distinct karyotypes and genome structures. Their hybrid, B. napus, represents the collision of two related, highly duplicated genomes in a single nucleus. As such, B. napus has become an important model for investigation of the consequences of poly- ploidy on duplicated selective forces during crop plant evolution. The availability of assembled B. napus genomes thus provides intriguing insight into the genome restructuring and selection processes associated with poly- ploidization and human selection from agricultural traits. At the time of completion, the B. napus genome was the most highly duplicated plant genome yet sequenced and also the genome with the highest content of annotated genes (more than 100,000). The genome sequence therefore provided a unique opportunity to examine the consequences of large-scale gene duplication, structural and functional crosstalk within and among highly duplicated gene pathways and epigenetic regulation of gene expression and modification. The ability to readily generate and resequence synthetic B. napus forms, derived by embryo rescue from new interspecific crosses between different A-subgenome and C-subgenome diploid progeni- tors, provided an unprecedented view of widespread homeologous exchanges during the allopolyploidization process. Large-scale and small-scale genome restructuring through homeologous exchanges, which was also found to be widespread and prevalent in natural B. napus, appears to have shaped the modern genomes of different B. napus accessions, creating a basis for quantitative trait variation and leading to human selection of ecogeographi- cally and morphologically divergent crop types. As an example, breeding selection for specific genome rearrangements led to loss of glucosinolate genes but expansion of oil biosynthesis genes, providing a genetic basis for a globally important oilseed crop. The availability of high-quality B. napus genome sequence assemblies thus enables novel insights into recenallopolyploid genome evolution and its impact on plant domestication and crop improvement. In contrast to other concerted international plant genome sequencing efforts, many of which have been initiated within the framework of coordi- nated international sequencing consortia, the ultimate completion of the B. napus genome was enabled by informal cooperation between independent genome assembly efforts on different reference genotypes in Europe (winter-type oilseed rape), China (semi-winter-type rapeseed), and Canada (spring-type canola), respectively. The exchange among these programs was facilitated and encouraged by the steering committee of the ‘Multi-national Brassica Genome Project,’ which promotes and coordinates international cooperation in the area of Brassica genomics. The published reference assembly of the European winter-type oilseed rape genotype Darmor-bzh (Chalhoub et al. 2014) represents the result of a highly successful interna- tional research community effort to exchange and share data from competing research programs in the interests of scientific progress. The result was a unique genome assembly, at the time the most complex plant genome to be successfully assembled into a high-quality reference, which provided a hugely valuable resource for research into allopolyploid crop evolution and for breeding and genetics in B. napus and related crops. In this volume, authors from the thriving international B. napus research community present deep insight into genetic and genomic analysis and applications enabled by the B. napus genome. Introductory chapters outlined the importance of B. napus as a crop and as a cytogenetic model for the consequences and importance of polyploidy and introduced the state of the art with regard to mapping of genes and quantitative trait loci for agronomic traits; many of mapping researches were based on the assembled reference genome resource. Five chapters broadly cover genome organization, one of the most interesting and complex features of the B. napus genome, with detailed contributions on genome and gene duplication, organization and evolution of repeat sequences, homeologous exchanges and the influence of these factors on gene expression and epigenetic regulation. Insight into the mitochondrial and chloroplast genomes of B. napus is presented in the context of Brassica evolution and crop differentiation, a topic which is also at the core of gene family differentiation among different Brassica species and forms. The impact of allopolyploidization on selection for important agro- nomic traits is underlined by three chapters which describe the complexities of trait-related gene evolution in relation to oil biosynthesis pathway genes, glucosinolate pathway genes, and resistance genes, respectively. The book closes with an overview of valuable B. napus genomic resources and out- looks on future applications of the B. napus genome for genome-facilitated breeding of oilseed rape and for research on structural, evolutionary, and functional genomics in B. napus. As sequencing technologies and genome assembly strategies become increasingly cost-effective, efficient, and accurate, the first reference genome assembly of B. napus was likely one of the last complex crop genomes to be assembled on a backbone of Titanium Roche 454 and Sanger sequences. Ultra-cheap, ultra-high throughput next-generation sequencing, the ever-increasing accuracy and cost-effectiveness of long-read sequencing technologies, and new assembly procedures including scaffolding and phasing-based chromatin conformation technologies present completely new opportunities to accurately sequence complex crop genomes. As this volume is published, a multitude of new B. napus genomes has already been assembled using new-generation strategies, and many will almost certainly be published in the near future. This will give rise to a new era of crop genome analysis, moving far beyond single reference genome sequences and toward an association of pan-genome variation with agronomic and biolog- ical trait information. Implementing this great magnitude of new information to advance breeding will be one of the great challenges for coming genera- tions of Brassica geneticists and breeders. Even with new possibilities offered by genome editing in association with genomic knowledge, consid- erable challenges still lie ahead: The complex genetics underlying quantita- tive disease resistances, nutrient and water use efficiency and heterosis must be better understood in order to make targeted use of genome diversity in agriculture. A better understanding of chromosome structure, homeologous pairing, recombination, and genome stability will be essential to make best use of available (and de novo) diversity for B. napus improvement, for example, by better control of new interspecific hybridization to exploit the vast diversity present in the diploid progenitors of B. napus. Finally, maxi- mizing the value of genome data in B. napus and other crops will rely in future on coordinated, integrated data management and analysis systems as a basis to navigate between diverse, multidimensional omics datasets from the international research community and implement them to draw biological insight into the complex relationship between genotype and environment. The first B. napus genome has laid an excellent foundation for this quest, and we look forward to working together with future Brassica napus researchers to continue this momentum.