http://genomebiology.com/ The latest research articles published by Genome Biology 2010-02-09T00:00:00Z This is an RSS newsfeed from BioMed Central It is intended to be used with an RSS reader. For more information about RSS newsfeeds from BioMed Central, visit http://www.biomedcentral.com/info/about/rss/ Background: Given the availability of full genome sequences, mapping gene gains, duplications, and losses during evolution should theoretically be straightforward. However, this endeavor suffers from overemphasis on detecting conserved genome features, which in turn has lead to sequencing multiple eutherian genomes with low coverage rather than fewer genomes with high-coverage and evener distribution in the phylogeny. Although limitations associated with analysis of low coverage genomes are recognized, they have not been quantified. Results: Here, using recently-developed comparative genomic application systems, we evaluate the impact of low-coverage genomes on inferences pertaining to gene gains and losses when analyzing eukaryote genome evolution through gene duplication. We demonstrate that, when performing inference of genome content evolution, low-coverage genomes generate not only a massive number of false gene losses, but also striking artifacts in gene duplication inference, especially at the most recent common ancestor of low-coverage genomes. We show that the artifactual gains are caused by the low coverage of genome sequence per se rather than by the increased taxon sampling in a biased portion of the species tree. Conclusions: We argue that it will remain difficult to differentiate artifacts from true changes in modes and tempo of genome evolution until there is better homogeneity in both taxon sampling and high-coverage sequencing. This is important for broadening the utility of full genome data to the community of evolutionary biologists, whose interests go well beyond widely-conserved physiologies and developmental patterns as they seek to understand the generative mechanisms underlying biological diversity. http://genomebiology.com/2010/11/2/R16 Michel Milinkovitch Raphael Helaers Eric Depiereux Athanasia Tzika Toni Gabaldon Genome Biology 2010, 11:R16 2010-02-09T00:00:00Z doi:10.1186/gb-2010-11-2-r16 Genome Biology 1465-6906 11 R16 2010-02-09T00:00:00Z PDF We present an automated, high throughput library construction process for 454 technology. Sample handling errors and cross-contamination are minimized via end-to-end barcoding of plasticware, along with molecular DNA barcoding of constructs. Automation-friendly magnetic bead-based size selection and cleanup steps have been devised, eliminating major bottlenecks and significant sources of error. Using this methodology, one technician can create 96 sequence-ready 454 libraries in 2 days, a dramatic improvement over the standard method. http://genomebiology.com/2010/11/2/R15 Niall Lennon Robert Lintner Scott Anderson Pablo Alvarez Andrew Barry William Brockman Riza Daza Rachel Erlich Georgia Giannoukos Lisa Green Andrew Hollinger Cindi Hoover David Jaffe Frank Juhn Danielle McCarthy Danielle Perrin Karen Ponchner Taryn Powers Kamran Rizzolo Dana Robbins Elizabeth Ryan Carsten Russ Todd Sparrow John Stalker Scott Steelman Michael Weiand Andrew Zimmer Matthew Henn Chad Nusbaum Robert Nicol Genome Biology 2010, 11:R15 2010-02-05T00:00:00Z doi:10.1186/gb-2010-11-2-r15 Genome Biology 1465-6906 11 R15 2010-02-05T00:00:00Z PDF We present GOseq, an application for performing Gene Ontology (GO) analysis on RNA-seq data. GO analysis is widely used to reduce complexity and highlight biological processes in genome-wide expression studies, but standard methods give biased results on RNA-seq data due to over-detection of differential expression for long and highly expressed transcripts. Application of GOseq to a prostate cancer data set shows that GOseq dramatically changes the results, highlighting categories more consistent with the known biology. http://genomebiology.com/2010/11/2/R14 Matthew Young Matthew Wakefield Gordon Smyth Alicia Oshlack Genome Biology 2010, 11:R14 2010-02-04T00:00:00Z doi:10.1186/gb-2010-11-2-r14 Genome Biology 1465-6906 11 R14 2010-02-04T00:00:00Z PDF A central goal of biogerontology is to identify robust gene-expression biomarkers of aging. Here we develop a method where the biomarkers are networks of genes selected based on age-dependent activity and a graph-theoretic property called modularity. Tested on Caenorhabditis elegans, our algorithm yields better biomarkers than previous methods -- they are more conserved across studies and better predictors of age. We apply these modular biomarkers to assign novel aging-related functions to poorly characterized longevity genes. http://genomebiology.com/2010/11/2/R13 Kristen Fortney Max Kotlyar Igor Jurisica Genome Biology 2010, 11:R13 2010-02-03T00:00:00Z doi:10.1186/gb-2010-11-2-r13 Genome Biology 1465-6906 11 R13 2010-02-03T00:00:00Z PDF Background: Miscanthus x giganteus (Mxg) is a perennial grass that produces superior biomass yields in temperate environments. The essentially uncharacterized triploid genome (3n = 57, x = 19) of Mxg is likely critical for the rapid growth of this vegetatively-propagated interspecific hybrid. Results: A survey of the complex Mxg genome was conducted using 454 pyrosequencing of genomic DNA and Illumina sequencing-by-synthesis of small RNA. We found that the coding fraction of the Mxg genome has a high level of sequence identity to that of other grasses. Highly repetitive sequences representing the great majority of the Mxg genome were predicted using non-cognate assembly for de novo repeat detection. Twelve abundant families of repeat were observed, with those related to either transposons or centromeric repeats likely to comprise over 95% of the genome. Comparisons of abundant repeat sequences to a small RNA survey of three Mxg organs (leaf, rhizome, inflorescence) revealed that the majority of observed 24-nucleotide small RNAs are derived from these repetitive sequences. We show that high-copy-number repeats match more of the small RNA, even when the amount of the repeat sequence in the genome is accounted for. Conclusions: We show that major repeats are present within the triploid Mxg genome and are actively producing small RNAs. We also confirm the hypothesized origins of Mxg, and suggest that while the repeat content of Mxg differs from sorghum, the sorghum genome is likely to be of utility in the assembly of a gene-space sequence of Mxg. http://genomebiology.com/2010/11/2/R12 Kankshita Swaminathan Magdy Alabady Kranthi Varala Emanuele De Paoli Isaac Ho Dan Rokhsar Aru Arumuganathan Ray Ming Pamela Green Blake Meyers Stephen Moose Matthew Hudson Genome Biology 2010, 11:R12 2010-02-03T00:00:00Z doi:10.1186/gb-2010-11-2-r12 Genome Biology 1465-6906 11 R12 2010-02-03T00:00:00Z PDF Background: Selectively bred alcohol-preferring (P) and alcohol-nonpreferring (NP) rats differ greatly in alcohol preference, in part due to a highly significant quantitative trait locus (QTL) on chromosome 4. Alcohol consumption scores of reciprocal chromosome 4 congenic strains NP.P and P.NP correlated with the introgressed interval. The goal of this study was to identify candidate genes that may influence alcohol consumption by comparing gene expression in 5 brain regions of alcohol-naive inbred alcohol preferring and P.NP congenic rats: amygdala, nucleus accumbens, hippocampus, caudate putamen, and frontal cortex. Results: Within the QTL region, 104 cis-regulated probe sets were differentially expressed in more than one region, and an additional 53 were differentially expressed in a single region. Fewer trans-regulated probe sets were detected, and most differed in only one region. Analysis of the average expression values across the 5 brain regions yielded 141 differentially expressed cis-regulated probe sets and 206 trans-regulated probe sets. Comparing the present results from inbred alcohol-preferring vs. congenic P.NP rats to earlier results from the reciprocal congenic NP.P vs. inbred alcohol-nonpreferring rats demonstrated that 74 cis-regulated probe sets were differentially expressed in the same direction and with a consistent magnitude of difference in at least one brain region. Conclusions: Cis-regulated candidate genes for alcohol consumption that lie within the chromosome 4 QTL were identified and confirmed by consistent results in two independent experiments with reciprocal congenic rats. These genes are strong candidates for affecting alcohol preference in the inbred alcohol-preferring and inbred alcohol-nonpreferring rats. http://genomebiology.com/2010/11/2/R11 Tiebing Liang Mark Kimpel Jeanette McClintick Ashley Skillman Kevin McCall Howard Edenberg Lucinda Carr Genome Biology 2010, 11:R11 2010-02-03T00:00:00Z doi:10.1186/gb-2010-11-2-r11 Genome Biology 1465-6906 11 R11 2010-02-03T00:00:00Z PDF The genome sequence of the giant panda using next- generation sequencing marks a watershed in genome sequencing - in more ways than one. http://genomebiology.com/2010/11/1/102 Genome Biology 2010, 11:102 2010-01-29T00:00:00Z doi:10.1186/gb-2010-11-1-102 Genome Biology 1465-6906 11 102 2010-01-29T00:00:00Z XML Huge advances in the field of genomics along with the continued rise of open access has made the past ten years an exciting time to be a biologist. http://genomebiology.com/2010/11/1/101 Genome Biology 2010, 11:101 2010-01-29T00:00:00Z doi:10.1186/gb-2010-11-1-101 Genome Biology 1465-6906 11 101 2010-01-29T00:00:00Z XML Background: The transmission pattern of the human X chromosome reduces its population size relative to the autosomes, subjects it to disproportionate influence by female demography, and leaves X-linked mutations exposed to selection in males. As a result, the analysis of X-linked genomic variation can provide insights into the influence of demography and selection on the human genome. Here we characterize the genomic variation represented by 16,297 X-linked SNPs genotyped in the CEPH human genome diversity project samples. Results: We found that X chromosomes tend to be more differentiated between human populations than autosomes with several notable exceptions. Comparisons between genetically distant populations also showed an excess of X-linked SNPs with large allele frequency differences. Combining information about these SNPs with results from tests designed to detect selective sweeps, we identified two regions that were clear outliers from the rest of the X chromosome for haplotype structure and allele frequency distribution. We were also able to more precisely define the geographical extent of some previously described X-linked selective sweeps. Conclusions: The relationship between male and female demographic histories is likely to be complex as evidence supporting different conclusions can be found in the same dataset. Although demography may have contributed to the excess of SNPs with large allele frequency differences observed on the X chromosome, we believe that selection is at least partially responsible. Finally, our results reveal the geographical complexities of selective sweeps on the X chromosome and argue for the use of diverse populations in studies of selection. http://genomebiology.com/2010/11/1/R10 Amanda Casto Jun Li Devin Absher Richard Myers Sohini Ramachandran Marcus Feldman Genome Biology 2010, 11:R10 2010-01-28T00:00:00Z doi:10.1186/gb-2010-11-1-r10 Genome Biology 1465-6906 11 R10 2010-01-28T00:00:00Z PDF Gigabase-scale genome assemblies are now feasible using short-read sequencing technology, bringing the cost of such projects below the million-dollar mark. http://genomebiology.com/content/11/1/202 Genome Biology 2010, 11:202 2010-01-28T00:00:00Z doi:10.1186/gb-2010-11-1-202 Genome Biology 1465-6906 11 202 2010-01-28T00:00:00Z XML