Summary We describe a genetic variation map for the chicken genome containing 2.8 million single nucleotide polymorphisms (SNPs), based on a comparison of the sequences of 3 domestic chickens (broiler, layer, Silkie) to their wild ancestor Red Jungle Fowl (RJF). Subsequent experiments indicate that at least 90% are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about 5 SNP/kb for almost every possible comparison between RJF and domestic lines, between two different domestic lines, and within domestic lines - contrary to the idea that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated prior to domestication, and there is little to no evidence of selective sweeps for adaptive alleles on length scales of greater than 100 kb.

The upcoming next-generation large area radio continuum surveys can expect tens of millions of radio sources, rendering the traditional method for radio morphology classification through visual inspection unfeasible. We present ClaRAN -Classifying Radio sources Automatically with Neural networks -a proof-of-concept radio source morphology classifier based upon the Faster Region-based Convolutional Neutral Networks (Faster R-CNN) method. Specifically, we train and test ClaRAN on the FIRST and WISE images from the Radio Galaxy Zoo Data Release 1 catalogue. ClaRAN provides end users with automated identification of radio source morphology classifications from a simple input of a radio image and a counterpart infrared image of the same region. ClaRAN is the first open-source, end-to-end radio source morphology classifier that is capable of locating and associating discrete and extended components of radio sources in a fast (< 200 milliseconds per image) and accurate (≥ 90%) fashion. Future work will improve ClaRAN's relatively lower success rates in dealing with multi-source fields and will enable ClaRAN to identify sources on much larger fields without loss in classification accuracy.

We study the impact of cluster environment on the morphology of a sample of 4304 extended radio galaxies from Radio Galaxy Zoo. A total of 87% of the sample lies within a projected 15 Mpc of an optically identified cluster. Brightest cluster galaxies (BCGs) are more likely than other cluster members to be radio sources, and are also moderately bent. The surface density as a function of separation from cluster center of non-BCG radio galaxies follows a power law with index 1.10 ± 0.03 out to 10 r 500 (∼ 7 Mpc), which is steeper than the corresponding distribution for optically selected galaxies. Non-BCG radio galaxies are statistically more bent the closer they are to the cluster center. Within the inner 1.5 r 500 (∼ 1 Mpc) of a cluster, non-BCG radio galaxies are statistically more bent in high-mass clusters than in low-mass clusters. Together, we find that non-BCG sources are statistically more bent in environments that exert greater ram pressure. We use the orientation of bent radio galaxies as an indicator of galaxy orbits and find that they are preferentially in radial orbits. Away from clusters, there is a large population of bent radio galaxies, limiting their use as cluster locators; however, they are still located within statistically overdense regions. We investigate the asymmetry in the tail length of sources that have their tails aligned along the radius vector from the cluster center, and find that the length of the inward-pointing tail is weakly suppressed for sources close to the center of the cluster.

We present an analysis of the chicken (Gallus gallus) transcriptome based on the full insert sequences for 19,626 cDNAs, combined with 485,337 EST sequences. The cDNA data set has been functionally annotated and describes a minimum of 11,929 chicken coding genes, including the sequence for 2260 full-length cDNAs together with a collection of noncoding (nc) cDNAs that have been stringently filtered to remove untranslated regions of coding mRNAs. The combined collection of cDNAs and ESTs describe 62,546 clustered transcripts and provide transcriptional evidence for a total of 18,989 chicken genes, including 88% of the annotated Ensembl gene set. Analysis of the ncRNAs reveals a set that is highly conserved in chickens and mammals, including sequences for 14 pri-miRNAs encoding 23 different miRNAs. The data sets described here provide a transcriptome toolkit linked to physical clones for bioinformaticians and experimental biologists who wish to use chicken systems as a low-cost, accessible alternative to mammals for the analysis of vertebrate development, immunology, and cell biology.

Background: Over the last decade, several studies have identified quantitative trait loci (QTL) affecting variation of immune related traits in mammals. Recent studies in humans and mice suggest that part of this variation may be caused by polymorphisms in genes involved in Toll-like receptor (TLR) signalling. In this project, we used a comparative approach to investigate the importance of TLR-related genes in comparison with other immunologically relevant genes for resistance traits in five species by associating their genomic location with previously published immune-related QTL regions.