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SignificanceWe performed de novo, full-genome sequence analysis of two Populus species, North American quaking and Eurasian trembling aspen, that contain striking levels of genetic variation. Our results showed that positive and negative selection broadly affects patterns of genomic variation, but to varying degrees across coding and noncoding regions. The strength of selection and rates of sequence divergence were strongly related to differences in gene expression and coexpression network connectivity. These results highlight the importance of both positive and negative selection in shaping genome-wide levels of genetic variation in an obligately outcrossing, perennial plant. The resources we present establish aspens as a powerful study system enabling future studies for understanding the genomic determinants of adaptive evolution.

BackgroundComparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size.ResultsHere we present the Rice TE database (RiTE-db) - a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri. The database consists of more than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive sequences obtained from genome sequencing surveys of 12 species; and (iii) a set of full-length TEs, identified and extracted from 12 whole genome assemblies.ConclusionsThis is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. The database allows sequence browsing, downloading, and similarity searches. Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of Oryza diversity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1762-3) contains supplementary material, which is available to authorized users.

BackgroundNext generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational approaches to evaluate the repetitive component of the genome of sunflower, by using medium/low coverage Illumina or 454 libraries.ResultsBy varying sequencing technology (Illumina or 454), coverage (0.55 x-1.25 x), assemblers and assembly procedures, six different genomic databases were produced. The annotation of these databases showed that they were composed of different proportions of repetitive DNA families. The final assembly of the sequences belonging to the six databases produced a whole genome set of 283,800 contigs. The redundancy of each contig was estimated by mapping the whole genome set with a large Illumina read set and measuring the number of matched Illumina reads. The repetitive component amounted to 81% of the sunflower genome, that is composed mainly of numerous families of Gypsy and Copia retrotransposons. Also many families of non autonomous retrotransposons and DNA transposons (especially of the Helitron superfamily) were identified.ConclusionsThe results substantially matched those previously obtained by using a Sanger-sequenced shotgun library and a standard 454 whole-genome-shotgun approach, indicating the reliability of the proposed procedures also for other species. The repetitive sequences were collected to produce a database, SUNREP, that will be useful for the annotation of the sunflower genome sequence and for studying the genome evolution in dicotyledons.