http://www.biomedcentral.com/bmcgenomics/ The editor's pick of recent articles published by BMC Genomics 2012-05-04T00:00:00Z Background: Vegetables of the genus Allium are widely consumed but remain poorly understood genetically. Genetic mapping has been conducted in intraspecific crosses of onion (Allium cepa L.), A. fistulosum and interspecific crosses between A. roylei and these two species, but it has not been possible to access genetic maps and underlying data from these studies easily.DescriptionAn online comparative genomics database, AlliumMap, has been developed based on the GMOD CMap tool at http://alliumgenetics.org. It has been populated with curated data linking genetic maps with underlying markers and sequence data from multiple studies. It includes data from multiple onion mapping populations as well as the most closely related species A. roylei and A. fistulosum. Further onion EST-derived markers were evaluated in the A. cepa x A. roylei interspecific population, enabling merging of the AFLP-based maps. In addition, data concerning markers assigned in multiple studies to the Allium physical map using A. cepa-A. fistulosum alien monosomic addition lines have been compiled. The compiled data reveal extensive synteny between onion and A. fistulosum. Conclusions: The database provides the first online resource providing genetic map and marker data from multiple Allium species and populations. The additional markers placed on the interspecific Allium map confirm the value of A. roylei as a valuable bridge between the genetics of onion and A. fistulosum and as a means to conduct efficient mapping of expressed sequence markers in Allium. The data presented suggest that comparative approaches will be valuable for genetic and genomic studies of onion and A. fistulosum. This online resource will provide a valuable means to integrate genetic and sequence-based explorations of Allium genomes. http://www.biomedcentral.com/1471-2164/13/168 John A McCallum Samantha Baldwin Masayoshi Shigyo Yanbo Deng Sjaak van Heusden Meeghan Pither-Joyce Fernand Kenel BMC Genomics 2012, 13:168 2012-05-04T00:00:00Z 10.1186/1471-2164-13-168 Onion comparative genomics comes of age AlliumMap is an online resource for the genetically poorly understood onion genus comprising genetic mapping and marker data from different species and crosses, and integrating these into an Allium comparative consensus map. /content/figures/1471-2164-13-168-toc.gif BMC Genomics 1471-2164 13 168 2012-05-04T00:00:00Z PDF Background: Drosophila albomicans is a unique model organism for studying both sex chromosome and B chromosome evolution. A pair of its autosomes comprising roughly 40% of the whole genome has fused to the ancient X and Y chromosomes only about 0.12 million years ago, thereby creating the youngest and most gene-rich neo-sex system reported to date. This species also possesses recently derived B chromosomes that show non-Mendelian inheritance and significantly influence fertility. Methods: We sequenced male flies with B chromosomes at 124.5-fold genome coverage using next-generation sequencing. To characterize neo-Y specific changes and B chromosome sequences, we also sequenced inbred female flies derived from the same strain but without B's at 28.5-fold. Results: We assembled a female genome and placed 53% of the sequence and 85% of the annotated proteins into specific chromosomes, by comparison with the 12 Drosophila genomes. Despite its very recent origin, the non-recombining neo-Y chromosome shows various signs of degeneration, including a significant enrichment of non-functional genes compared to the neo-X, and an excess of tandem duplications relative to other chromosomes. We also characterized a B-chromosome linked scaffold that contains an actively transcribed unit and shows sequence similarity to the subcentromeric regions of both the ancient X and the neo-X chromosome. Conclusions: Our results provide novel insights into the very early stages of sex chromosome evolution and B chromosome origination, and suggest an unprecedented connection between the births of these two systems in D. albomicans. http://www.biomedcentral.com/1471-2164/13/109 Qi Zhou Hong-mei Zhu Quan-fei Huang Li Zhao Guo-jie Zhang Scott W Roy Beatriz Vicoso Zhao-lin Xuan Jue Ruan Yue Zhang Ruo-ping Zhao Chen Ye Xiu-qing Zhang Jun Wang Wen Wang Doris Bachtrog BMC Genomics 2012, 13:109 2012-03-22T00:00:00Z 10.1186/1471-2164-13-109 Evolutionary analysis of D. albomicans genome Analysis of the genome of Drosophila albomicans, shows the extremely young neo-sex chromosomes already have an accumulation of excess deleterious mutations and the B chromosomes have an origin in sex chromosome-autosome fusion. /content/figures/1471-2164-13-109-toc.gif BMC Genomics 1471-2164 13 109 2012-03-22T00:00:00Z XML Background: The catalog of genetic variants in the horse genome originates from a few select animals, the majority originating from the Thoroughbred mare used for the equine genome sequencing project. The purpose of this study was to identify genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs) in the genome of an individual Quarter Horse mare sequenced by next-generation sequencing. Results: Using massively parallel paired-end sequencing, we generated 59.6 Gb of DNA sequence from a Quarter Horse mare resulting in an average of 24.7X sequence coverage. Reads were mapped to approximately 97% of the reference Thoroughbred genome. Unmapped reads were de novo assembled resulting in 19.1 Mb of new genomic sequence in the horse. Using a stringent filtering method, we identified 3.1 million SNPs, 193 thousand INDELs, and 282 CNVs. Genetic variants were annotated to determine their impact on gene structure and function. Additionally, we genotyped this Quarter Horse for mutations of known diseases and for variants associated with particular traits. Functional clustering analysis of genetic variants revealed that most of the genetic variation in the horse's genome was enriched in sensory perception, signal transduction, and immunity and defense pathways. Conclusions: This is the first sequencing of a horse genome by next-generation sequencing and the first genomic sequence of an individual Quarter Horse mare. We have increased the catalog of genetic variants for use in equine genomics by the addition of novel SNPs, INDELs, and CNVs. The genetic variants described here will be a useful resource for future studies of genetic variation regulating performance traits and diseases in equids. http://www.biomedcentral.com/1471-2164/13/78 Ryan Doan Noah D Cohen Jason Sawyer Noushin Ghaffari Charles D Johnson Scott V Dindot BMC Genomics 2012, 13:78 2012-02-17T00:00:00Z 10.1186/1471-2164-13-78 Quarter horse genetic link to agility Whole genome sequencing of the American Quarter Horse breed has revealed genetic differences from the Thoroughbred horse in genes linked to traits responsible for its renowned fast and nimble performance, and with characteristic diseases. /content/figures/1471-2164-13-78-toc.gif BMC Genomics 1471-2164 13 78 2012-02-17T00:00:00Z XML Background: Many biological systems respond to the presence or absence of gravity. Since experiments performed in space are expensive and can only be undertaken infrequently, Earth-based simulation techniques are used to investigate the biological response to weightlessness. A high gradient magnetic field can be used to levitate a biological organism so that its net weight is zero. Results: We have used a superconducting magnet to assess the effect of diamagnetic levitation on the fruit fly D. melanogaster in levitation experiments that proceeded for up to 22 consecutive days. We have compared the results with those of similar experiments performed in another paradigm for microgravity simulation, the Random Positioning Machine (RPM). We observed a delay in the development of the fruit flies from embryo to adult. Microarray analysis indicated changes in overall gene expression of imagoes that developed from larvae under diamagnetic levitation, and also under simulated hypergravity conditions. Significant changes were observed in the expression of immune-, stress-, and temperature-response genes. For example, several heat shock proteins were affected. We also found that a strong magnetic field, of 16.5 Tesla, had a significant effect on the expression of these genes, independent of the effects associated with magnetically-induced levitation and hypergravity. Conclusions: Diamagnetic levitation can be used to simulate an altered effective gravity environment in which gene expression is tuned differentially in diverse Drosophila melanogaster populations including those of different age and gender. Exposure to the magnetic field per se induced similar, but weaker, changes in gene expression. http://www.biomedcentral.com/1471-2164/13/52 Raul Herranz Oliver J Larkin Camelia E Dijkstra Richard JA Hill Paul Anthony Michael R Davey Laurence Eaves Jack JWA van Loon F Javier Medina Roberto Marco BMC Genomics 2012, 13:52 2012-02-01T00:00:00Z 10.1186/1471-2164-13-52 Fruitfly genes in zero-g Drosophila melanogaster fruit flies raised in a zero-gravity environment created by a superconducting magnet show substantial changes in the expression of many essential genes, suggesting that extended weightlessness during space flight could also potentially have negative effects on cellular processes. /content/figures/1471-2164-13-52-toc.gif BMC Genomics 1471-2164 13 52 2012-02-01T00:00:00Z XML