Genomes and Genes
Summary: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.
- Elmer K, Fan S, Gunter H, Jones J, Boekhoff S, Kuraku S, et al. Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes. Mol Ecol. 2010;19 Suppl 1:197-211 pubmed publisher..We conclude that next-generation sequencing technologies allow us to infer natural selection acting to diversify the genomes of young species, such as crater lake cichlids, with much greater scope than previously possible. ..
- Zhang F, Guo H, Zheng H, Zhou T, Zhou Y, Wang S, et al. Massively parallel pyrosequencing-based transcriptome analyses of small brown planthopper (Laodelphax striatellus), a vector insect transmitting rice stripe virus (RSV). BMC Genomics. 2010;11:303 pubmed publisher..To investigate its transcriptome and determine the differences between viruliferous and naïve L. striatellus, we employed 454-FLX high-throughput pyrosequencing to generate EST databases of this insect...
- Dayarian A, Michael T, Sengupta A. SOPRA: Scaffolding algorithm for paired reads via statistical optimization. BMC Bioinformatics. 2010;11:345 pubmed publisher..In general, the methodology presented here will allow better scaffold assemblies of any type of mate pair sequencing data. ..
- Hoskins R, Carlson J, Kennedy C, Acevedo D, Evans Holm M, Frise E, et al. Sequence finishing and mapping of Drosophila melanogaster heterochromatin. Science. 2007;316:1625-8 pubmed..The strategy we describe is also applicable to generating substantially more information about heterochromatin in other species, including humans. ..
- Richter D, Schuster S, Huson D. OSLay: optimal syntenic layout of unfinished assemblies. Bioinformatics. 2007;23:1573-9 pubmed..Related genome sequences can be used to layout contigs in an assembly. OSLay is freely available from: http://www-ab.informatik.unituebingen.de/software/oslay. ..
- Meyer E, Aglyamova G, Wang S, Buchanan Carter J, Abrego D, Colbourne J, et al. Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics. 2009;10:219 pubmed publisher..The characterization of the larval transcriptome for this widely-studied coral will enable research into the biological processes underlying stress responses in corals and evolutionary adaptation to global climate change. ..
- Xu J, Qian X, Wang X, Li R, Cheng X, Yang Y, et al. Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa. BMC Genomics. 2010;11:594 pubmed publisher..This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus, and for comparative analysis of the A genome within Brassica species. ..
- Kerstens H, Crooijmans R, Veenendaal A, Dibbits B, Chin A Woeng T, den Dunnen J, et al. Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey. BMC Genomics. 2009;10:479 pubmed publisher..To illustrate the potential of this technique, we present the results obtained with a randomly sheared, enzymatically generated, 2-3 kbp genome fraction of six pooled Meleagris gallopavo (turkey) individuals...
- Choi J, Kim S, Tang H, Andrews J, Gilbert D, Colbourne J. A machine-learning approach to combined evidence validation of genome assemblies. Bioinformatics. 2008;24:744-50 pubmed publisher..e. greater than 90%). Our combined evidence approach avoids the difficult and often ad hoc selection of many parameters the individual measures require, and significantly improves the overall precisions on the benchmarking data sets. ..
- Chaisson M, Pevzner P. Short read fragment assembly of bacterial genomes. Genome Res. 2008;18:324-30 pubmed
- Wang W, Wang Y, Zhang Q, Qi Y, Guo D. Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing. BMC Genomics. 2009;10:465 pubmed publisher..annua glandular trichomes. Our comprehensive survey of genes expressed in glandular trichome will facilitate new gene discovery and shed light on the regulatory mechanism of artemisinin metabolism and trichome function in A. annua. ..
- Wang S, Peatman E, Abernathy J, Waldbieser G, Lindquist E, Richardson P, et al. Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biol. 2010;11:R8 pubmed publisher..The inter- and intra-specific SNPs identified from all catfish EST dataset assembly will greatly benefit the catfish introgression breeding program and whole genome association studies. ..
- Warren R, Sutton G, Jones S, Holt R. Assembling millions of short DNA sequences using SSAKE. Bioinformatics. 2007;23:500-1 pubmed..SSAKE is designed to help leverage the information from short sequence reads by stringently assembling them into contiguous sequences that can be used to characterize novel sequencing targets. http://www.bcgsc.ca/bioinfo/software/ssake. ..
- von Schalburg K, Yazawa R, de Boer J, Lubieniecki K, Goh B, Straub C, et al. Isolation, characterization and comparison of Atlantic and Chinook salmon growth hormone 1 and 2. BMC Genomics. 2008;9:522 pubmed publisher..The Chinook and other Oncorhynchus GH1s are strikingly different in comparison to the other GHs and this change is not apparent in the surrounding non-coding sequences...
- Boetzer M, Henkel C, Jansen H, Butler D, Pirovano W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics. 2011;27:578-9 pubmed publisher..SSPACE shows promising results on both prokaryote and eukaryote genomic testsets where the amount of initial contigs was reduced by at least 75%. ..
- Lin L, Pierce G, Bowers J, Estill J, Compton R, Rainville L, et al. A draft physical map of a D-genome cotton species (Gossypium raimondii). BMC Genomics. 2010;11:395 pubmed publisher..The integrated genetic-physical map is of value both in assembling and validating a planned reference sequence. ..
- Han Y, Gasic K, Marron B, Beever J, Korban S. A BAC-based physical map of the apple genome. Genomics. 2007;89:630-7 pubmed
- Mascher M, Muehlbauer G, Rokhsar D, Chapman J, Schmutz J, Barry K, et al. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J. 2013;76:718-27 pubmed publisher..The method is independent of the need for any prior sequence resources, and will enable rapid and cost-efficient establishment of powerful genomic information for many species...
- Gritsenko A, Nijkamp J, Reinders M, de Ridder D. GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies. Bioinformatics. 2012;28:1429-37 pubmed publisher..They use this limited information to construct scaffolds, often preferring scaffold length over accuracy, when faced with the tradeoff...
- Zhang X, Scheuring C, Tripathy S, Xu Z, Wu C, Ko A, et al. An integrated BAC and genome sequence physical map of Phytophthora sojae. Mol Plant Microbe Interact. 2006;19:1302-10 pubmed..sojae and other Phytophthora spp. In one illustration of this value, we have placed the 350 members of a superfamily of putative pathogenicity effector genes onto the map, revealing extensive clustering of these genes. ..
- Mun J, Kwon S, Yang T, Kim H, Choi B, Baek S, et al. The first generation of a BAC-based physical map of Brassica rapa. BMC Genomics. 2008;9:280 pubmed publisher..The current build of the B. rapa physical map is available at the B. rapa Genome Project website for the user community. ..
- Gu Y, Ma Y, Huo N, Vogel J, You F, Lazo G, et al. A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. BMC Genomics. 2009;10:496 pubmed publisher..A draft of the physical map and its comparisons with rice and wheat are available at http://phymap.ucdavis.edu/brachypodium/. ..
- Aggarwal R, Benatti T, Gill N, Zhao C, Chen M, Fellers J, et al. A BAC-based physical map of the Hessian fly genome anchored to polytene chromosomes. BMC Genomics. 2009;10:293 pubmed publisher..The Hessian fly BAC-clone assembly, and the names and positions of the BAC clones used in the FISH experiments are publically available at (http://genome.purdue.edu/WebAGCoL/Hfly/WebFPC/). ..
- Simpson J, Wong K, Jackman S, Schein J, Jones S, Birol I. ABySS: a parallel assembler for short read sequence data. Genome Res. 2009;19:1117-23 pubmed publisher..Analysis of these contigs identified polymorphic and novel sequences not present in the human reference assembly, which were validated by alignment to alternate human assemblies and to other primate genomes. ..
- Rissman A, Mau B, Biehl B, Darling A, Glasner J, Perna N. Reordering contigs of draft genomes using the Mauve aligner. Bioinformatics. 2009;25:2071-3 pubmed publisher..The software is available for download at http://gel.ahabs.wisc.edu/mauve. ..
- Xu Z, Kohel R, Song G, Cho J, Yu J, Yu S, et al. An integrated genetic and physical map of homoeologous chromosomes 12 and 26 in Upland cotton (G. hirsutum L.). BMC Genomics. 2008;9:108 pubmed publisher..The identification of Gene-rich islands in the integrated map provides a platform for positional cloning of important genes and the targeted sequencing of specific genomic regions. ..
- Vitulo N, Albiero A, Forcato C, Campagna D, Dal Pero F, Bagnaresi P, et al. First survey of the wheat chromosome 5A composition through a next generation sequencing approach. PLoS ONE. 2011;6:e26421 pubmed publisher..From these similarities it was possible to infer the virtual gene order of 392 (5AS) and 1,480 (5AL) genes of chromosome 5A, which was compared to, and found to be largely congruent with the available physical map of this chromosome. ..
- Xu P, Wang S, Liu L, Thorsen J, Kucuktas H, Liu Z. A BAC-based physical map of the channel catfish genome. Genomics. 2007;90:380-8 pubmed..The presented physical map should greatly enhance genome research in the catfish, particularly aiding in the identification of genomic regions containing genes underlying important performance traits...
- Koop B, von Schalburg K, Leong J, Walker N, Lieph R, Cooper G, et al. A salmonid EST genomic study: genes, duplications, phylogeny and microarrays. BMC Genomics. 2008;9:545 pubmed publisher..A comprehensive gene list and a comparison of genes in some of the different species provide valuable genomic information for one of the most widely studied groups of fish...
- Attardo G, Ribeiro J, Wu Y, Berriman M, Aksoy S. Transcriptome analysis of reproductive tissue and intrauterine developmental stages of the tsetse fly (Glossina morsitans morsitans). BMC Genomics. 2010;11:160 pubmed publisher..This paper identifies 51 putative proteins specific to a tsetse reproductive/immature EST library. 11 of these proteins correspond to hypothetical conserved genes and 7 proteins are tsetse specific. ..
- Xiong Z, Kim J, Pires J. Integration of genetic, physical, and cytogenetic maps for Brassica rapa chromosome A7. Cytogenet Genome Res. 2010;129:190-8 pubmed publisher..napus to demonstrate that this approach can facilitate studies of genome evolution by integrating the genetic, physical, and cytogenetic maps among closely related species of Brassica...
- Jackman S, Birol I. Assembling genomes using short-read sequencing technology. Genome Biol. 2010;11:202 pubmed publisher..Gigabase-scale genome assemblies are now feasible using short-read sequencing technology, bringing the cost of such projects below the million-dollar mark. ..
- Künstner A, Wolf J, Backstrom N, Whitney O, Balakrishnan C, Day L, et al. Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Mol Ecol. 2010;19 Suppl 1:266-76 pubmed publisher..Overall, this study demonstrates the usefulness of next-generation sequencing for obtaining genomic resources for comparative genomic analysis of non-model organisms. ..
- Li Y, Uhm T, Ren C, Wu C, Santos T, Lee M, et al. A plant-transformation-competent BIBAC/BAC-based map of rice for functional analysis and genetic engineering of its genomic sequence. Genome. 2007;50:278-88 pubmed..Because of its plant transformability, the BIBAC/BAC map could provide a platform for functional analysis of the rice genome sequence and effective use of the sequencing results for gene and QTL cloning and molecular breeding. ..
- Crawford J, Guelbeogo W, Sanou A, Traoré A, Vernick K, Sagnon N, et al. De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology. PLoS ONE. 2010;5:e14202 pubmed publisher..Our An. funestus contig set and analytical results provide a valuable resource for future studies in this non-model, but epidemiologically critical, vector insect. ..
- Zimin A, Smith D, Sutton G, Yorke J. Assembly reconciliation. Bioinformatics. 2008;24:42-5 pubmed..genome.umd.edu. The reconciliation software is available for download from http://www.genome.umd.edu/software.htm ..
- Boisvert S, Laviolette F, Corbeil J. Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J Comput Biol. 2010;17:1519-33 pubmed publisher..sf.Net/). For online Supplementary Material , see www.liebertonline.com. ..
- Scaglione D, Acquadro A, Portis E, Tirone M, Knapp S, Lanteri S. RAD tag sequencing as a source of SNP markers in Cynara cardunculus L. BMC Genomics. 2012;13:3 pubmed publisher..Our approach permitted to generate a large and robust SNP datasets by the adoption of optimized filtering criteria. ..
- Raudsepp T, Chowdhary B. The horse pseudoautosomal region (PAR): characterization and comparison with the human, chimp and mouse PARs. Cytogenet Genome Res. 2008;121:102-9 pubmed publisher..Although striking differences like those observed between human and mouse may be rare, variations similar to those seen between horse and human may be prevalent among mammals. ..
- Luo M, Ma Y, You F, Anderson O, Kopecky D, Simkova H, et al. Feasibility of physical map construction from fingerprinted bacterial artificial chromosome libraries of polyploid plant species. BMC Genomics. 2010;11:122 pubmed publisher..It is currently unknown but possible that equally good BAC contigs can be also constructed for polyploid species containing smaller, more gene-rich genomes. ..
- Qin J, Li R, Raes J, Arumugam M, Burgdorf K, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59-65 pubmed publisher..We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively. ..
- van Oeveren J, de Ruiter M, Jesse T, van der Poel H, Tang J, Yalcin F, et al. Sequence-based physical mapping of complex genomes by whole genome profiling. Genome Res. 2011;21:618-25 pubmed publisher..We demonstrate that WGP maps can also be generated for more complex plant genomes and will serve as excellent scaffolds to anchor genetic linkage maps and integrate whole genome sequence data. ..