BackgroundAureobasidium pullulans is a black-yeast-like fungus used for production of the polysaccharide pullulan and the antimycotic aureobasidin A, and as a biocontrol agent in agriculture. It can cause opportunistic human infections, and it inhabits various extreme environments. To promote the understanding of these traits, we performed de-novo genome sequencing of the four varieties of A. pullulans.ResultsThe 25.43-29.62 Mb genomes of these four varieties of A. pullulans encode between 10266 and 11866 predicted proteins. Their genomes encode most of the enzyme families involved in degradation of plant material and many sugar transporters, and they have genes possibly associated with degradation of plastic and aromatic compounds. Proteins believed to be involved in the synthesis of pullulan and siderophores, but not of aureobasidin A, are predicted. Putative stress-tolerance genes include several aquaporins and aquaglyceroporins, large numbers of alkali-metal cation transporters, genes for the synthesis of compatible solutes and melanin, all of the components of the high-osmolarity glycerol pathway, and bacteriorhodopsin-like proteins. All of these genomes contain a homothallic mating-type locus.ConclusionsThe differences between these four varieties of A. pullulans are large enough to justify their redefinition as separate species: A. pullulans, A. melanogenum, A. subglaciale and A. namibiae. The redundancy observed in several gene families can be linked to the nutritional versatility of these species and their particular stress tolerance. The availability of the genome sequences of the four Aureobasidium species should improve their biotechnological exploitation and promote our understanding of their stress-tolerance mechanisms, diverse lifestyles, and pathogenic potential.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-549) contains supplementary material, which is available to authorized users.

Background: Sex chromosomes have arisen independently in a wide variety of species, yet they share common characteristics, including the presence of suppressed recombination surrounding sex determination loci. Mammalian sex chromosomes contain multiple palindromic repeats across the non-recombining region that show sequence conservation through gene conversion and contain genes that are crucial for sexual reproduction. In plants, it is not clear if palindromic repeats play a role in maintaining sequence conservation in the absence of homologous recombination. Results: Here we present the first evidence of large palindromic structures in a plant sex chromosome, based on a highly contiguous assembly of the W chromosome of the dioecious shrub Salix purpurea. The W chromosome has an expanded number of genes due to transpositions from autosomes. It also contains two consecutive palindromes that span a region of 200 kb, with conspicuous 20-kb stretches of highly conserved sequences among the four arms that show evidence of gene conversion. Four genes in the palindrome are homologous to genes in the sex determination regions of the closely related genus Populus, which is located on a different chromosome. These genes show distinct, floral-biased expression patterns compared to paralogous copies on autosomes. Conclusion: The presence of palindromes in sex chromosomes of mammals and plants highlights the intrinsic importance of these features in adaptive evolution in the absence of recombination. Convergent evolution is driving both the independent establishment of sex chromosomes as well as their fine-scale sequence structure.

Local adaptation is the process by which natural selection drives adaptive phenotypic divergence across environmental gradients. Theory suggests that local adaptation results from genetic trade-offs at individual genetic loci, where adaptation to one set of environmental conditions results in a cost to fitness in alternative environments. However, the degree to which there are costs associated with local adaptation is poorly understood because most of these experiments rely on two-site reciprocal transplant experiments. Here, we quantify the benefits and costs of locally adaptive loci across 17° of latitude in a four-grandparent outbred mapping population in outcrossing switchgrass (Panicum virgatumL.), an emerging biofuel crop and dominant tallgrass species. We conducted quantitative trait locus (QTL) mapping across 10 sites, ranging from Texas to South Dakota. This analysis revealed that beneficial biomass (fitness) QTL generally incur minimal costs when transplanted to other field sites distributed over a large climatic gradient over the 2 y of our study. Therefore, locally advantageous alleles could potentially be combined across multiple loci through breeding to create high-yielding regionally adapted cultivars.

Background Genomic variation is widespread, and both neutral and selective processes can generate similar patterns in the genome. These processes are not mutually exclusive, so it is difficult to infer the evolutionary mechanisms that govern population and species divergence. Boechera stricta is a perennial relative of Arabidopsis thaliana native to largely undisturbed habitats with two geographic and ecologically divergent subspecies. Here, we delineate the evolutionary processes driving the genetic diversity and population differentiation in this species. Results Using whole-genome re-sequencing data from 517 B. stricta accessions, we identify four genetic groups that diverged around 30–180 thousand years ago, with long-term small effective population sizes and recent population expansion after the Last Glacial Maximum. We find three genomic regions with elevated nucleotide diversity, totaling about 10% of the genome. These three regions of elevated nucleotide diversity show excess of intermediate-frequency alleles, higher absolute divergence ( d XY ), and lower relative divergence ( F ST ) than genomic background, and significant enrichment in immune-related genes, reflecting long-term balancing selection. Scattered across the genome, we also find regions with both high F ST and d XY among the groups, termed F ST - islands. Population genetic signatures indicate that F ST - islands with elevated divergence, which have experienced directional selection, are derived from divergent sorting of ancient polymorphisms. Conclusions Our results suggest that long-term balancing selection on disease resistance genes may have maintained ancestral haplotypes across different geographical lineages, and unequal sorting of balanced polymorphisms may have generated genomic regions with elevated divergence. This study highlights the importance of ancestral balanced polymorphisms as crucial components of genome-wide variation. Electronic supplementary material The online version of this article (10.1186/s13059-019-1729-9) contains supplementary material, which is available to authorized users.

1 Background 2 Sex chromosomes in a wide variety of species share common characteristics, including the 3 presence of suppressed recombination surrounding sex determination loci. They have arisen 4 independently in numerous lineages, providing a conclusive example of convergent evolution. 5Mammalian sex chromosomes contain multiple palindromic repeats across the non-recombining 6 region that facilitate sequence conservation through gene conversion, and contain genes that are 7 crucial for sexual reproduction. Plant sex chromosomes are less well understood, and in 8 particular it is not clear how coding sequence conservation is maintained in the absence of 9 homologous recombination. 10 Results 11 Here we present the first evidence of large palindromic structures in a plant sex chromosome, 12 based on a highly contiguous assembly of the W chromosome of the dioecious shrub Salix 13 purpurea. Two consecutive palindromes span over a region of 200 kb, with conspicuous 20 kb 14 stretches of highly conserved sequences among the four arms. The closely-related species S. 15 suchowensis also has two copies of a portion of the palindrome arm and provides strong 16 evidence for gene conversion. Four genes in the palindrome are homologous to genes in the SDR 17 of the closely-related genus Populus, which is located on a different chromosome. These genes 18 show distinct, floral-biased expression patterns compared to paralogous copies on autosomes.19 Conclusion 20The presence of palindromic structures in sex chromosomes of mammals and plants highlights 21 the intrinsic importance of these features in adaptive evolution in the absence of recombination. 22Convergent evolution is driving both the independent establishment of sex chromosomes as well 23 as their fine-scale sequence structure. 24 26 103 297 kb in length lacked mapped markers and could not be placed unambiguously. 104Location of the SDR 105 We repeated sex association analysis with our new assembly with Chr15Z removed. 106Among 54,959 tested SNPs, all 105 significantly sex-associated SNPs were present only on 107 Chr15W (Fig. 1a; Additional File 2: Figure S2a-c), and markers from PARs and other scaffolds 108 in the main genome did not show any sex association (Additional File 2: Figure S2a). The eight 109 top-ranking sex-associated markers were distributed from 7.66 Mb to 8.66 Mb. Sex-associated 110 markers were primarily heterozygous in females and homozygous in males, confirming our 111 previously-reported observation of ZW sex determination in S. purpurea [18].