Background: Fusion transcripts are formed by either fusion genes (DNA level) or trans-splicing events (RNA level). They have been recognized as a promising tool for diagnosing, subtyping and treating cancers. RNA-seq has become a precise and efficient standard for genome-wide screening of such aberration events. Many fusion transcript detection algorithms have been developed for paired-end RNA-seq data but their performance has not been comprehensively evaluated to guide practitioners. In this paper, we evaluated 15 popular algorithms by their precision and recall trade-off, accuracy of supporting reads and computational cost. We further combine top-performing methods for improved ensemble detection.Results: Fifteen fusion transcript detection tools were compared using three synthetic data sets under different coverage, read length, insert size and background noise, and three real data sets with selected experimental validations. No single method dominantly performed the best but SOAPfuse generally performed well, followed by FusionCatcher and JAFFA. We further demonstrated the potential of a meta-caller algorithm by combining top performing methods to re-prioritize candidate fusion transcripts with high confidence that can be followed by experimental validation.Conclusion: Our result provides insightful recommendations when applying individual tool or combining top performers to identify fusion transcript candidates.

BackgroundThe genetic provenance of domesticated plants and the routes along which they were disseminated in prehistory have been a long-standing source of debate. Much of this debate has focused on identifying centers of origins for individual crops. However, many important crops show clear genetic signatures of multiple domestications, inconsistent with geographically circumscribed centers of origin. To better understand the genetic contributions of wild populations to domesticated barley, we compare single nucleotide polymorphism frequencies from 803 barley landraces to 277 accessions from wild populations.ResultsWe find that the genetic contribution of individual wild populations differs across the genome. Despite extensive human movement and admixture of barley landraces since domestication, individual landrace genomes indicate a pattern of shared ancestry with geographically proximate wild barley populations. This results in landraces with a mosaic of ancestry from multiple source populations rather than discrete centers of origin. We rule out recent introgression, suggesting that these contributions are ancient. The over-representation in landraces of genomic segments from local wild populations suggests that wild populations contributed locally adaptive variation to primitive varieties.ConclusionsThis study increases our understanding of the evolutionary process associated with the transition from wild to domesticated barley. Our findings indicate that cultivated barley is comprised of multiple source populations with unequal contributions traceable across the genome. We detect putative adaptive variants and identify the wild progenitor conferring those variants.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0712-3) contains supplementary material, which is available to authorized users.

Chromosomal inversions are thought to play a special role in local adaptation, through dramatic suppression of recombination, which favors the maintenance of locally adapted alleles. However, relatively few inversions have been characterized in population genomic data. On the basis of single-nucleotide polymorphism (SNP) genotyping across a large panel of Zea mays, we have identified an 50-Mb region on the short arm of chromosome 1 where patterns of polymorphism are highly consistent with a polymorphic paracentric inversion that captures .700 genes. Comparison to other taxa in Zea and Tripsacum suggests that the derived, inverted state is present only in the wild Z. mays subspecies parviglumis and mexicana and is completely absent in domesticated maize. Patterns of polymorphism suggest that the inversion is ancient and geographically widespread in parviglumis. Cytological screens find little evidence for inversion loops, suggesting that inversion heterozygotes may suffer few crossover-induced fitness consequences. The inversion polymorphism shows evidence of adaptive evolution, including a strong altitudinal cline, a statistical association with environmental variables and phenotypic traits, and a skewed haplotype frequency spectrum for inverted alleles.T HE evolutionary role of chromosomal inversions has been studied in a wide array of organisms, from insects (Ayala et al. 2011;Stevison et al. 2011) to birds (Huynh et al. 2011) and plants (Hoffmann and Rieseberg 2008; Lowry and Willis 2010). Examination of inversion polymorphism was fundamental to the early study of selection and adaptive diversity, as well as the basis for understanding the maintenance of neutral polymorphism within populations (Dobzhansky 1950;Hoffmann et al. 2004). Homologous pairing of an inverted and a noninverted chromosome in heterozygotes leads to the formation of an inversion loop, and crossing over in an inversion loop can cause the formation of a dicentric chromosome and an acentric fragment at meiosis I, resulting in terminal deletions of the affected chromosome and gamete death at frequencies that correlate with the size of the inversion (Burnham 1962). Because of the difficulty of homologous pairing and the deleterious effects of homologous crossing over in inversions, inversions are typically observed to disrupt recombination in heterozygous individuals, leading to measurable effects on nucleotide sequence polymorphism, including the generation of extended linkage disequilibrium (LD). Inversion-induced LD has been reported in a variety of organisms, including humans (Bansal et al. 2007), Drosophila subobscura (Munte et al. 2005), and several other species (reviewed in Hoffmann and Rieseberg 2008). Strong differentiation between chromosomal arrangements (as measured by F ST ) has also been used as evidence of inversions in Drosophila (Andolfatto et al. 1999;Depaulis et al. 1999;Nóbrega et al. 2008).A variety of circumstances can favor the maintenance or spread of an inversion polymorphism. The inversion may be 2010), ...

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