The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome

Background: Brassica carinata (Ethiopian mustard) is an ancient crop from the Ethiopian highlands with remarkable heat and drought tolerance that has potential as a sustainable oil source for biofuel production. The resilience of this species might be due to hybrid vigor, as B. carinata is a species derived from a hybridization between Brassica nigra (black mustard) and Brassica oleracea (kale, broccoli, etc.). Thus, the B. carinata genome is allotetraploid with two parental genomes, or subgenomes, merged in one nucleus. We present a high-quality, chromosome-scale reference assembly of the B. carinata genome, which is the last of six genomes comprising the classic Triangle of U model used to study hybridization and polyploid evolution. Question: Here, we compare B. carinata to the other Triangle of U genomes for insight into the remarkable heat and drought tolerance of this crop. We investigate the evolutionary trajectory of the B. carinata genome as it returns to the diploid state to elucidate the mechanisms that act on duplicated genes, such as functional divergence of gene families and the biased fractionation of one subgenome. Findings: The B. carinata genome is the largest among the Triangle of U with notable expansions in repetitive DNA sequences and gene families related to transcriptional regulation and stress tolerance. We characterized patterns of subgenome bias, finding that the subgenome derived from B. nigra is likely dominant over the subgenome from B. oleracea. Furthermore, we comprehensively characterize subgenomic bias in homoeologous exchanges, or meiotic crossover between subgenomes, in the Triangle of U allotetraploids. Next steps: The presented B. carinata genome is a crucial resource for its expanded use as a biofuel feedstock and insight into polyploid evolution. Unraveling the genomic basis of the stress resilience of B. carinata provides an opportunity to introgress these traits to other cruciferous vegetables, which are used worldwide as vegetable and oil sources.Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. Brassica carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid species (AABB, AACC, and BBCC). Of the genomes of these species, that of B. carinata is the least understood. Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical theory of the evolutionary relationships among these six species. Our assembly provides insights into the hybridization event that led to the current B. carinata genome and the genomic features that gave rise to the superior agronomic traits of B. carinata. Notably, we identified an expansion of transcription factor networks and agronomically important gene families. Completion of the Triangle of U comparative genomics platform has allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in the domestication and continuing agronomic improvement of B. carinata and other Brassica species.We gratefully acknowledge the support of the Nevada Agricultural Experiment Station (Grant No. NEV00384) and VPRI research funding (University of Nevada, Reno).The Pires lab is funded by the National Science Foundation (NSF IOS 1339156) and the Department of Energy Defense Threat Reduction Agency (HDTRA 1-16-1-0048). The Edger lab is funded by the National Science Foundation (NSF IOS 2029959). The Mason lab is partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC 2070 - 390732324). The Alvarez-Ponce lab is funded by the National Science Foundation (NSF MCB 1818288)

A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster

Homologous chromosomes in the diploid genome are thought to contain equivalent genetic information, but this common concept has not been fully verified in animal genomes with high heterozygosity. Here we report a near-complete, haplotype-phased, genome assembly of the pearl oyster, Pinctada fucata, using hi-fidelity (HiFi) long reads and chromosome conformation capture data. This assembly includes 14 pairs of long scaffolds (>38 Mb) corresponding to chromosomes (2n = 28). The accuracy of the assembly, as measured by an analysis of k-mers, is estimated to be 99.99997%. Moreover, the haplotypes contain 95.2% and 95.9%, respectively, complete and single-copy BUSCO genes, demonstrating the high quality of the assembly. Transposons comprise 53.3% of the assembly and are a major contributor to structural variations. Despite overall collinearity between haplotypes, one of the chromosomal scaffolds contains megabase-scale non-syntenic regions, which necessarily have never been detected and resolved in conventional haplotype-merged assemblies. These regions encode expanded gene families of NACHT, DZIP3/hRUL138-like HEPN, and immunoglobulin domains, multiplying the immunity gene repertoire, which we hypothesize is important for the innate immune capability of pearl oysters. The pearl oyster genome provides insight into remarkable haplotype diversity in animals

Model Plants and Crop Improvement

Within the past decade, there has been an explosion of research in both the public and private sectors regarding the use of plant genetic models to improve crop yield. Bringing together experts from across the globe, Model Plants and Crop Improvement provides a critical assessment of the potential of model plant species for crop improvement. The first comprehensive summary of the use of model plant systems, the book delineates the model species' contribution to understanding the genomes of crop species. The book provides an in-depth examination of the achievements and limitations of the model paradigm. It explores how continued research in models can contribute to the goal of delivering the outputs of molecular biology to crops. Covering the major genetic models such as Arabidopsis thaliana, Lotus japonicus, and Medigago, the book goes on to discuss applications to food plants of global importance including rice, canola, and legumes. The book introduces the evolutionary, genetic, genomic, and morphological attributes of B. distachyon that make it such an attractive new model plant system. As the post-genomic era dawns, a key question to address is how this growing body of genetic and biological information can be extended beyond the model to the modeled species. This book takes you one step closer to applying modeling results to crops in the field

28th Fungal Genetics Conference

Full abstracts from the 28th Fungal Genetics Conference Asilomar, March 17-22, 2015

Evolutionary genomics : statistical and computational methods

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Evolutionary Genomics

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Abstracts from the 11th European Conference on Fungal Genetics

Programs and Abstracts from the 11th European Conference on Fungal Genetic

Phenotypic and meiotic differences between diploid and polyploid plants

Polyploidy is present in a large number of crop plants and is considered as one of the driving forces in the evolution of angiosperms. Unlocking genetic variation in various autopolyploid crop plants is highly relevant to crop breeders. Homologous recombination, a tightly controlled cell process during the production of gametes in meiosis, is responsible for creation of genetic variation. Owing to the presence of more than two homologous chromosomes, polyploid meiosis faces a variety of challenges, such as multivalent formation and mis-segregation. Using a plant trial with more than 300 diploid and tetraploid Arabidopsis thaliana F2 individuals, significant differences were found in various traits between the two populations. Cytological analysis using FISH on diploid and tetraploid plants revealed an overall increase in meiotic recombination in tetraploids, although the per bivalent frequency was reduced. The process of meiotic recombination was further explored in potato (Solanum tuberosum), a globally important autotetraploid crop. Chiasma frequency and multivalent frequency for chromosomes 1 and 2 varied according to variety, where the diploid variety showed a reduced chiasma frequency compared with tetraploid varieties. Immunolocalisation of the axis and synaptonemal complex proteins, ASY1 and ZYP1, demonstrated the complexities that may arise during meiosis in an autotetraploid plant