RESUMO
Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.
Assuntos
Produtos Agrícolas , Diploide , Variação Genética , Genoma de Planta , Genômica , Melhoramento Vegetal , Proteínas de Plantas , Vicia faba , Cromossomos de Plantas/genética , Produtos Agrícolas/genética , Produtos Agrícolas/metabolismo , Variações do Número de Cópias de DNA/genética , DNA Satélite/genética , Amplificação de Genes/genética , Genes de Plantas/genética , Variação Genética/genética , Genoma de Planta/genética , Estudo de Associação Genômica Ampla , Geografia , Melhoramento Vegetal/métodos , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Recombinação Genética , Retroelementos/genética , Sementes/anatomia & histologia , Sementes/genética , Vicia faba/anatomia & histologia , Vicia faba/genética , Vicia faba/metabolismoRESUMO
During the last two decades, whole-genome sequencing has revolutionized genetic research in all kingdoms, including fungi. More than 1000 fungal genomes have been submitted to sequence databases, mostly obtained through second generation short-read DNA sequencing. As a result, highly fragmented genome drafts have typically been obtained. However, with the emergence of third generation long-read DNA sequencing, the assembly challenge can be overcome and highly contiguous assemblies obtained. Such attractive results, however, are extremely dependent on the ability to extract highly purified high molecular weight (HMW) DNA. Extraction of such DNA is currently a significant challenge for all species with cell walls, not least fungi. In this study, four isolates of filamentous ascomycetes (Apiospora pterospermum, Aspergillus sp. (subgen. Cremei), Aspergillus westerdijkiae, and Penicillium aurantiogriseum) were used to develop extraction and purification methods that result in HMW DNA suitable for third generation sequencing. We have tested and propose two straightforward extraction methods based on treatment with either a commercial kit or traditional phenol-chloroform extraction both in combination with a single commercial purification method that result in high quality HMW DNA from filamentous ascomycetes. Our results demonstrated that using these DNA extraction methods and coverage, above 75 x of our haploid filamentous ascomycete fungal genomes result in complete and contiguous assemblies.
Assuntos
Ascomicetos , Sequenciamento por Nanoporos , Ascomicetos/genética , DNA , Genoma Fúngico , Peso MolecularRESUMO
The phylogenetic relationship of the Arthrinium genus has changed throughout the years. For many years, the Arthrinium genus included the Apiospora genus as well. New evidence has now showed that these two genera in fact are phylogenetically different and belong to two different clades. Here, we present the first genome draft within the Arthrinium genus. This genome was sequenced using the MinION platform from Oxford Nanopore Technologies and the assembly was contiguous. The assembly comprises ten contigs totaling 39.8 Mb with an N50 length of 7.9. In the assembly, 11,602 genes were predicted whereof 10,784 were functionally annotated. A total of 37 rRNA genes were observed in the assembly and repeat elements spanning 7.39% of the genome were found. A total of 99 secondary metabolite gene clusters were predicted, showing a high potential of novel secondary metabolites. This genome sequence will not only be useful for further investigation of the Arthrinium clade, but also for discovery of novel secondary metabolite compounds that could be of high interest for the food, agricultural, or pharmaceutical industry.
