Evidence for suppression of immunity as a driver for genomic introgressions and host range expansion in races of Albugo candida, a generalist parasite

How generalist parasites with wide host ranges can evolve is a central question in parasite evolution. Albugo candida is an obligate biotrophic parasite that consists of many physiological races that each specialize on distinct Brassicaceae host species. By analyzing genome sequence assemblies of five isolates, we show they represent three races that are genetically diverged by ∼1%. Despite this divergence, their genomes are mosaic-like, with ∼25% being introgressed from other races. Sequential infection experiments show that infection by adapted races enables subsequent infection of hosts by normally non-infecting races. This facilitates introgression and the exchange of effector repertoires, and may enable the evolution of novel races that can undergo clonal population expansion on new hosts. We discuss recent studies on hybridization in other eukaryotes such as yeast, Heliconius butterflies, Darwin’s finches, sunflowers and cichlid fishes, and the implications of introgression for pathogen evolution in an agro-ecological environment

26th Fungal Genetics Conference at Asilomar

Program and abstracts from the 26th Fungal Genetics Conference, March 15-20, 2011

Aeronautical Engineering: A Continuing Bibliography with Indexes (supplement 194)

This bibliography lists 369 reports, articles and other documents introduced into the NASA scientific and technical information system in November 1985

The genomic and evolutionary analysis of floral heteromorphy in Primula

The genetic basis and evolutionary significance of floral heteromorphy in Primula has been debated for over 150 years. Charles Darwin was the first to explain the importance of the two heterostylous floral morphs, pin and thrum, suggesting that their reciprocal anther and stigma heights facilitate cross-pollination, and showing that only between morph crosses are fully compatible. This key innovation is an archetypal example of convergent evolution that serves to physically promote insect-mediated outcrossing, having evolved in over 28 angiosperm families . Darwin’s findings laid the foundation for an extensive number of studies into heterostyly that contributed to the establishment of modern genetic theory. The widely accepted genetic model portrays the Primula S locus, which controls heterostyly and self-incompatibility, as a coadapted group of tightly-linked genes, or supergene. It is predicted that self-fertile homostyle flowers, with anthers and stigma at the same height, arise via rare recombination events between dominant and recessive alleles in heterozygous thrums. These observations have underpinned over 60 years of research into the genetics and evolution of heterostyly. The Primula vulgaris genome assembly and associated transcriptomic and comparative sequence analyses have facilitated the assembly and characterisation of the complete S locus in this species. Here it is revealed that thrums are hemizygous not heterozygous: the S locus contains five thrum-specific genes which are completely absent in pins, which means recombination cannot be the cause of homostyles as previously believed. The studies also reveal candidate genes in Primula veris and other species, and have facilitated an estimation for the assembly of the S locus supergene at 51.7 MYA. These findings challenge established theory, and reveal novel insight into the structure and origin of the Primula S locus, providing the foundation for understanding the evolution and breakdown of insect-mediated outcrossing in Primula and other heterostylous species

De novo sequencing, annotation, and characterization of the genome of Lavandula angustifolia (Lavender)

Lavender (Lavandula angustifolia) is a perennial plant native to the Mediterranean region, best known for its essential oil (EOs) that have numerous applications in the pharmaceutical, cosmetic and perfume industries. We performed sequencing of the L. angustifolia genome and report a detailed analysis of the assembled genome, focusing on genome size, ploidy, and repeat content. The lavender genome was estimated to be around 870 Mbp (1C=0.96 pg) using a quantitative PCR method. Genome size was further validated through analysis of raw genome sequences using Kmergenie, providing a conclusive end to the lavender genome size dispute. The repeat element composition of the genome was analyzed using de novo (RepeatModeler) and library-based methods (RepeatMasker) and was estimated to be around 45% of the full genome or ~57% of the non-gap genome sequences. Further characterization revealed Long Terminal Repeat (LTRs) retrotransposons as the major repeat type, which contribute to ~18% of the genome, followed by DNA transposons at ~8.5% of the genome. Interestingly, unlike most other plant genomes, the lavender genome has many more Copia than Gypsy elements, both showing a trend of recent increasing activity. Furthermore, these LTRs, especially Copia elements, have shown active participation in gene function including genes for essential oil production, with Copia elements contributing to ~30 % of the coding DNA sequence (CDS) regions, in addition to promoter, intron and untranslated (UTR) regions. The lavender genome also has an unusually high number of miniature inverted-repeat transposable elements (MITEs) compared to other model plant genomes, with the number being ~88,000, which is close to that (~90,000) of the much larger maize genome. Analysis also revealed the lavender genome with a high proportion at polyploidy level, which is strongly biased towards regions containing essential oil genes, with polyploidization events in the lavender genome occurred between 16 to 41 Mya. In conclusion, our results reveal the lavender genome to be highly duplicated and with past and ongoing active retrotransposition, making the genome optimized for EO production

Comparative genomic analysis of 31 Phytophthora genomes reveal genome plasticity and horizontal gene transfer

Phytophthora species are oomycete plant pathogens that cause great economic and ecological impacts. The Phytophthora genus includes over 180 known species, infecting a wide range of plant hosts including crops, trees, and ornamentals. We sequenced 31 individual Phytophthora species genomes and 24 individual transcriptomes to study genetic relationships across the genus. De novo genome assemblies revealed variation in genome sizes, numbers of predicted genes, and in repetitive element content across the Phytophthora genus. A genus-wide comparison evaluated orthologous groups of genes. Predicted effector gene counts varied across Phytophthora species by effector family, genome size, as well as plant host range. Predicted numbers of apoplastic effectors increased as the host range of Phytophthora species increased. Predicted numbers of cytoplasmic effectors also increased with host range but leveled off or decreased in Phytophthora species that have enormous host ranges. With extensive sequencing across the Phytophthora genus we now have the genomic resources to evaluate horizontal gene transfer events across the oomycetes. Using a machine learning approach to identify horizontally transferred genes with bacterial or fungal origin we identified 44 candidates over 36 Phytophthora species genomes. Phylogenetic reconstruction indicates that the transfers of most of these 44 candidates happened in parallel to major advances in the evolution of the oomycetes and Phytophthoras. We conclude that the 31 genomes presented here are essential for investigating genus-wide genomic associations in Phytophthora

Proceedings of the 7th Sound and Music Computing Conference

Proceedings of the SMC2010 - 7th Sound and Music Computing Conference, July 21st - July 24th 2010

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