Population Genomic Analysis Reveals Differential Evolutionary Histories and Patterns of Diversity across Subgenomes and Subpopulations of Brassica napus L.

The allotetraploid species Brassica napus L. is a global crop of major economic importance, providing canola oil (seed) and vegetables for human consumption and fodder and meal for livestock feed. Characterizing the genetic diversity present in the extant germplasm pool of B. napus is fundamental to better conserve, manage and utilize the genetic resources of this species. We used sequence-based genotyping to identify and genotype 30,881 SNPs in a diversity panel of 782 B. napus accessions, representing samples of winter and spring growth habits originating from 33 countries across Europe, Asia and America. We detected strong population structure broadly concordant with growth habit and geography, and identified three major genetic groups: spring (SP), winter Europe (WE), and winter Asia (WA). Subpopulation-specific polymorphism patterns suggest enriched genetic diversity within the WA group and a smaller effective breeding population for the SP group compared to WE. Interestingly, the two subgenomes of B. napus appear to have different geographic origins, with phylogenetic analysis placing WE and WA as basal clades for the other subpopulations in the C and A subgenomes, respectively. Finally, we identified 16 genomic regions where the patterns of diversity differed markedly from the genome-wide average, several of which are suggestive of genomic inversions. The results obtained in this study constitute a valuable resource for worldwide breeding efforts and the genetic dissection and prediction of complex B. napus traits

The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry.

We sequenced and compared the genomes of the Dothideomycete fungal plant pathogensCladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70% of gene content in both genomes are homologs), but differ significantly in size (Cfu \u3e61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2% in Cfu versus 3.2% in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an α-tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation

Computational pan-genomics: Status, promises and challenges

Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different Computational methods and paradigms are needed.We will witness the rapid extension of Computational pan-genomics, a new sub-area of research in Computational biology. In this article, we generalize existing definitions and understand a pangenome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a Computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations

Correction: The Genomes of the Fungal Plant Pathogens <i>Cladosporium fulvum</i> and <i>Dothistroma septosporum</i> Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

<p>Correction: The Genomes of the Fungal Plant Pathogens <i>Cladosporium fulvum</i> and <i>Dothistroma septosporum</i> Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry</p

Genome sequence and analysis of the tuber crop potato.

Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop

Recognition of <i>Dothistroma septosporum</i> effectors by tomato Cf receptors.

<p>A) <i>DsEcp2-1</i>, the <i>D. septosporum</i> ortholog of <i>CfEcp2-1</i>, was cloned into <i>pSfinx</i>. Tomato plants were inoculated with <i>Agrobacterium tumefaciens</i> transformants expressing <i>pSfinx::DsEcp2-1</i>. A hypersensitive response (HR) was induced in the tomato line carrying the <i>Cf-Ecp2</i> resistance gene (MM-Cf-Ecp2). Empty vector was used as a negative control and caused only mosaic symptoms. Pictures were taken at four weeks post inoculation. B) The <i>C. fulvum</i> avirulence gene <i>Avr4</i> (<i>CfAvr4</i>) and its ortholog in <i>D. septosporum (DsAvr4)</i> were heterologously expressed in <i>Cf-4</i> transgenic <i>Nicotiana benthamiana</i> using the <i>A. tumefaciens</i> transient transformation assay (ATTA). Expression of <i>CfAvr4</i> and <i>DsAvr4</i> results in an HR demonstrating that the tomato Cf-4 receptor recognizes DsAvr4. Picture was taken at six days post inoculation.</p

Syntenic and non-syntenic regions between <i>C. fulvum</i> and <i>D. septosporum</i> are unevenly distributed over the <i>C. fulvum</i> scaffolds.

a<p>Number of repeat regions on syntenic vs. non-syntenic scaffolds.</p>b<p>A syntenic scaffold is one that contains at least a single syntenic block, but may not be syntenic along its entire length. Total syntenic scaffold size (37.4-Mb) is therefore larger than total syntenic size in whole genome (22.3-Mb).</p>c<p>Summed repeat length on syntenic <i>versus</i> non-syntenic scaffolds.</p