Sorghum [Sorghum bicolor (L.) Moench] is one of the worlds leading cereal crops, providing food, feed, fiber, fuel, and chemical/biofuels feed-stocks across a range of environments and production systems. Its remarkable ability to produce a crop under adverse conditions, in particular with much less water than most other grain crops, makes sorghum an important failsafe source of food, feed, fiber, and fuel in the global agroecosystem. Sorghum is especially important in areas such as Northeast Africa and the US Southern Plains that often receive too little rainfall for most other grains.. Sorghum is a biofuel crop of growing importance, currently the #2 crop used in US ethanol production. Its lower water demands and market price than alternatives such as maize, versus their similar per-bushel ethanol yields, suggests that sorghum will be of growing importance in meeting US biofuels needs. Progress in understanding the genetic control of perenniality in sorghum makes it promising as a ...
Synteny server Server for Synteny Identification and Analysis of Genome Rearrangement-the Identification of synteny and ... Study of synteny can show how the genome is cut and pasted in the course of evolution. Shared synteny (also known as conserved ... The analysis of synteny in the gene order sense has several applications in genomics. Shared synteny is one of the most ... Patterns of shared synteny or synteny breaks can also be used as characters to infer the phylogenetic relationships among ...
Shared syntenyEdit. Shared synteny (also known as conserved synteny) describes preserved co-localization of genes on ... Synteny server Server for Synteny Identification and Analysis of Genome Rearrangement-the Identification of synteny and ... The analysis of synteny in the gene order sense has several applications in genomics. Shared synteny is one of the most ... Patterns of shared synteny or synteny breaks can also be used as characters to infer the phylogenetic relationships among ...
Chicken-human synteny snippets from Medline:. -- chicken IL2 to be mapped to chromosome 4 with synteny with mouse chromosome 3 ... may be able to provide current information about prion gene synteny in cattle. The conserved synteny expert is Dr Dave Burt. He ... Prion gene synteny relationships. webmaster 16 Dec 98 Lets see if we can locate at least a second copy of the four suspected ... Human-mouse prion gene synteny relationships. Prion gene syntenies in other species. References. Duplications of the prion gene ...
Visible synteny regions can be filtered based on numerical criteria specified for each region in the synteny input file. See ... All visible synteny regions can be filtered according to numerical criteria specified in the synteny input file. See main text ... A web-based multi-genome synteny viewer for customized data.. Revanna KV1, Munro D, Gao A, Chiu CC, Pathak A, Dong Q. ... We have developed a multi-Genome Synteny Viewer (mGSV). Similar to GSV, mGSV is a web-based tool that allows users to upload ...
... Jeffrey L Bennetzen, Purdue University, West Lafayette, Indiana, USA Katrien ... Bennetzen, Jeffrey L, and Devos, Katrien(Jul 2001) Plant Synteny, Colinearity and Genome Evolution. In: eLS. John Wiley & Sons ... large scale duplication followed by selective gene loss creates a network of synteny. Proceedings of the National Academy of ...
Gene disruptions at synteny breaks. The schematic shows the seven genes mapping to the breakpoints (dashed vertical arrow). One ... Sequencing human-gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites.. Girirajan S1, Chen L, ... A) Identification of gibbon BAC clones at the breakpoint of synteny. All BAC clones were experimentally validated by FISH as ... LINE-1 elements, L1PA4 (green block arrows), and L1MA3 (dark green arrows) in the vicinity of human-gibbon synteny breaks are ...
Since evolutionary conserved genes tend to lie within synteny blocks (HSBs) and genes which are not conserved lie within ... D. M. Larkin, G. Pape, R. Donthu, L. Auvil, M. Welge and H. A. Lewin, "Breakpoint Regions and Homologous Synteny Blocks in ... Since evolutionary conserved genes tend to lie within synteny blocks (HSBs) and genes which are not conserved lie within ... P. Giampietro, C. Raggio and R. Blank, "Use of Synteny Conversion in Identification of Candidate Genes for Somitogenesis in ...
... February 25, 2016. , By Dennis Venema on Letters to the Duchess * Tags ... In this post, we explore the concept of "shared synteny" and see how it was used to find vitellogenin gene fragments in the ... Figure 4. Shared synteny between humans and chickens spanning the regions with functional chicken VIT genes. Black bars between ... Genes in closely related organisms can be present in blocks of synteny that are thousands of genes long. Over time, gene order ...
... Multi-genome synteny and gene cross-match analyzer Click to get more info Genes from up to 20 genomes ...
It represents synteny blocks in a hierarchy structure with multiple layers, each of which representing a different granularity ... Sibelia has been designed to work efficiently with a large number of microbial genomes; it finds synteny blocks in 31 S. aureus ... Unlike most other tools, Sibelia can find synteny blocks that are repeated within genomes as well as blocks shared by multiple ... In this paper, we present Sibelia, a tool for finding synteny blocks in multiple closely related microbial genomes using ...
... revealing substantial synteny between lineages diverged over 7 million years - Volume 144 Issue 10 - PETER C. THOMPSON, DANTE S ... Husemann, P. and Stoye, J. (2010). r2cat: synteny plots and comparative assembly. Bioinformatics 26, 570-571. ... Long-read sequencing improves assembly of Trichinella genomes 10-fold, revealing substantial synteny between lineages diverged ... Gene synteny and evolution of genome architecture in trypanosomatids. Molecular and Biochemical Parasitology 134, 183-191. ...
Synteny and conserved gene order between B. mori and H. melpomene:. Recently, a linkage map was reported in a butterfly, H. ... We found significant synteny and conserved gene order between B. mori and a nymphalid butterfly, Heliconius melpomene, in four ... Other candidate loci to confirm synteny were the RpL19, EF-1α, and patched (ptc) genes in LG10 of H. melpomene. Since the ... As described above, all 13 conserved genes in the four LGs of H. melpomene available for a test of synteny were found to be ...
Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Grabherr, Manfred G ...
A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers,
The positions of 100 synteny breakpoints relative to the assembled human genome were determined at a resolution of about 200 kb ... Interestingly, 46% of the gibbon-human synteny breakpoints occur in regions that correspond to segmental duplications in the ... A high-resolution map of synteny disruptions in gibbon and human genomes. In: PLOS Genetics 2(12) , S. 2162-2175 ...
Reconstructed ancestral or extant synteny comes with a support computed from an exhaustive exploration of the solution space. ... DeCo is an algorithm for ancestral synteny reconstruction. It is a dynamic programming scheme on pairs of reconciled gene tree ... Reconstructed ancestral or extant synteny comes with a support computed from an exhaustive exploration of the solution space. ... Efficient gene tree correction guided by species and synteny evolution. 2015, [https://hal.archives-ouvertes.fr/hal-01162963] ...
Comparison with maps of M. truncatula and L. culinaris documented considerable shared synteny and led to the identification of ... Comparison with maps of M. truncatula and L. culinaris documented considerable shared synteny and led to the identification of ... Conserved Synteny between L. ervoides and M. truncatula and C. arietinum. Several research groups have compared the genome ... 2009). A consensus genetic map of cowpea [Vigna unguiculata Walp.] and synteny based on EST-derived SNPs. Proc. Natl. Acad. Sci ...
Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements.. ... Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements. ... Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements., ...
Jung S, Main D, Staton M, Cho I, Zhebentyayeva T, Arús P, Abbott A (2006) Synteny conservation between the Prunus genome and ... Analysis of the markers mapped in more than one rosaceous genus revealed patterns of synteny between genera, while a comparison ...
... we propose to use the notion of spatial synteny which generalises the notion of genomic synteny to the 3D case. ... The breakpoint (A m - B m ) located on the mouse genome is flanked by two synteny blocks, A and B, which are not consecutive on ... we propose to use the notion of spatial synteny which generalises the notion of genomic synteny to the 3D case. ... we propose to use the notion of spatial synteny which generalises the notion of genomic synteny to the 3D case. ...
Homology information implicit in regions of conserved synteny allows quantification of gene origination by complete sequence ... They have ingeniously used micro-synteny to identify the orphan genes created by divergence. They estimate that at most one- ... The authors devised a very neat protocol that detects conserved synteny regions between species and then looks for proteins ... By extrapolating the findings from the conserved synteny regions to the whole genome the authors conclude that divergence ...
COSII genetic maps of two diploid Nicotiana species provide a detailed picture of synteny with tomato and insights into ...
... synteny) with the genomes of six invertebrate outgroups. We show that such synteny comparisons across multiple genomes enhance ... Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison ...
2008 Synteny and candidate gene prediction using an anchored linkage map of Astyanax mexicanus. Proc. Natl. Acad. Sci. U S A ... Using Linkage Maps as a Tool To Determine Patterns of Chromosome Synteny in the Genus Salvelinus. View ORCID ProfileMatthew C. ... Using Linkage Maps as a Tool To Determine Patterns of Chromosome Synteny in the Genus Salvelinus. View ORCID ProfileMatthew C. ... Using Linkage Maps as a Tool To Determine Patterns of Chromosome Synteny in the Genus Salvelinus. View ORCID ProfileMatthew C. ...