Supplementary data are available at Bioinformatics online.

Multi-wavelength observations provide a complementary view of the formation of young, directly imaged planetmass companions. We report the ALMA 1.3 mm and Magellan adaptive optics Hα, ¢ i , ¢ z , and Y S observations of the GQ Lup system, a classical T Tauri star with a -M 10 40 Jup substellar companion at ∼110 au projected separation. We estimate the accretion rates for both components from the observed Hα fluxes. In our ∼0 05 resolution ALMA map, we resolve GQ Lup A's disk in thedust continuum, but no signal is found from the companion. The disk is compact, with a radius of ∼22 au, a dust mass of ∼6 M ⊕ , an inclination angle of ∼56°, and a very flat surface density profile indicative of a radial variation in dust grain sizes. No gaps or inner cavity are found in the disk, so there is unlikely a massive inner companion to scatter GQ Lup B outward. Thus, GQ Lup B might have formed in situ via disk fragmentation or prestellar core collapse. We also show that GQ Lup A's disk is misaligned with its spin axis, and possibly with GQ Lup B's orbit. Our analysis on the tidal truncation radius of GQ Lup A's disk suggests that GQ Lup B's orbit might have a low eccentricity.

Long intergenic non-coding RNAs (lincRNAs) are an abundant and functionally diverse class of eukaryotic transcripts. Reported lincRNA repertoires in mammals vary, but are commonly in the thousands to tens of thousands of transcripts, covering ~90% of the genome. In addition to elucidating function, there is particular interest in understanding the origin and evolution of lincRNAs. Aside from mammals, lincRNA populations have been sparsely sampled, precluding evolutionary analyses focused on their emergence and persistence. Here we present Evolinc, a two-module pipeline designed to facilitate lincRNA discovery and characterize aspects of lincRNA evolution. The first module (Evolinc-I) is a lincRNA identification workflow that also facilitates downstream differential expression analysis and genome browser visualization of identified lincRNAs. The second module (Evolinc-II) is a genomic and transcriptomic comparative analysis workflow that determines the phylogenetic depth to which a lincRNA locus is conserved within a user-defined group of related species. Here we validate lincRNA catalogs generated with Evolinc-I against previously annotated Arabidopsis and human lincRNA data. Evolinc-I recapitulated earlier findings and uncovered an additional 70 Arabidopsis and 43 human lincRNAs. We demonstrate the usefulness of Evolinc-II by examining the evolutionary histories of a public dataset of 5,361 Arabidopsis lincRNAs. We used Evolinc-II to winnow this dataset to 40 lincRNAs conserved across species in Brassicaceae. Finally, we show how Evolinc-II can be used to recover the evolutionary history of a known lincRNA, the human telomerase RNA (TERC). These latter analyses revealed unexpected duplication events as well as the loss and subsequent acquisition of a novel TERC locus in the lineage leading to mice and rats. The Evolinc pipeline is currently integrated in CyVerse's Discovery Environment and is free for use by researchers.

SummaryThe EPIC-CoGe browser is a web-based genome visualization utility that integrates the GMOD JBrowse genome browser with the extensive CoGe genome database (currently containing over 30 000 genomes). In addition, the EPIC-CoGe browser boasts many additional features over basic JBrowse, including enhanced search capability and on-the-fly analyses for comparisons and analyses between all types of functional and diversity genomics data. There is no installation required and data (genome, annotation, functional genomic and diversity data) can be loaded by following a simple point and click wizard, or using a REST API, making the browser widely accessible and easy to use by researchers of all computational skill levels. In addition, EPIC-CoGe and data tracks are easily embedded in other websites and JBrowse instances.Availability and implementationEPIC-CoGe Browser is freely available for use online through CoGe (https://genomevolution.org). Source code (MIT open source) is available: https://github.com/LyonsLab/coge.Supplementary information Supplementary data are available at Bioinformatics online.

Summary: Following polyploidy events, genomes undergo massive reduction in gene content through a process known as fractionation. Importantly, the fractionation process is not always random, and a bias as to which homeologous chromosome retains or loses more genes can be observed in some species. The process of characterizing whole genome fractionation requires identifying syntenic regions across genomes followed by post-processing of those syntenic datasets to identify and plot gene retention patterns. We have developed a tool, FractBias, to calculate and visualize gene retention and fractionation patterns across whole genomes. Through integration with SynMap and its parent platform CoGe, assembled genomes are pre-loaded and available for analysis, as well as letting researchers integrate their own data with security options to keep them private or make them publicly available. Availability and implementation: FractBias is freely available as a web application at https://genomevolution.org/CoGe/SynMap.pl. The software is open source (MIT license) and executable with Python 2.7 or iPython notebook, and available on GitHub (https://goo.gl/PaAtqy).