synteny

Summary

Summary: The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.

Top Publications

  1. Despalins A, Marsit S, Oberto J. Absynte: a web tool to analyze the evolution of orthologous archaeal and bacterial gene clusters. Bioinformatics. 2011;27:2905-6 pubmed publisher
    Absynte (Archaeal and Bacterial Synteny Explorer) is a web-based service designed to display local syntenies in completely sequenced prokaryotic chromosomes...
  2. Ouangraoua A, Tannier E, Chauve C. Reconstructing the architecture of the ancestral amniote genome. Bioinformatics. 2011;27:2664-71 pubmed publisher
    ..Source code, in C++ and Python, is available at http://www.cecm.sfu.ca/~cchauve/SUPP/AMNIOTE2010/ cedric.chauve@sfu.ca Supplementary data are available at Bioinformatics online. ..
  3. Catchen J, Braasch I, Postlethwait J. Conserved synteny and the zebrafish genome. Methods Cell Biol. 2011;104:259-85 pubmed publisher
    ..Conserved synteny analysis provides a method that helps overcome such problems...
  4. Liu S, Rexroad C, Couch C, Cordes J, Reece K, Sullivan C. A microsatellite linkage map of striped bass (Morone saxatilis) reveals conserved synteny with the three-spined stickleback (Gasterosteus aculeatus). Mar Biotechnol (NY). 2012;14:237-44 pubmed publisher
    ..objectives of this study were to construct a microsatellite linkage map of striped bass and to examine conserved synteny between striped bass and three-spined stickleback (Gasterosteus aculeatus)...
  5. Palti Y, Genet C, Gao G, Hu Y, You F, Boussaha M, et al. A second generation integrated map of the rainbow trout (Oncorhynchus mykiss) genome: analysis of conserved synteny with model fish genomes. Mar Biotechnol (NY). 2012;14:343-57 pubmed publisher
    ..Conserved synteny between the rainbow trout genome and model fish genomes was analyzed using 188,443 BAC end sequence (BES) reads...
  6. Galvão V, Nordström K, Lanz C, Sulz P, Mathieu J, Posé D, et al. Synteny-based mapping-by-sequencing enabled by targeted enrichment. Plant J. 2012;71:517-26 pubmed publisher
    ..We have therefore developed a method that exploits synteny with a related genome for genetic mapping...
  7. Fukuoka H, Miyatake K, Nunome T, Negoro S, Shirasawa K, Isobe S, et al. Development of gene-based markers and construction of an integrated linkage map in eggplant by using Solanum orthologous (SOL) gene sets. Theor Appl Genet. 2012;125:47-56 pubmed publisher
    ..The data are available from the DNA marker database of vegetables, VegMarks (http://vegmarks.nivot.affrc.go.jp)...
  8. Galeano C, Fernandez A, Franco Herrera N, Cichy K, McClean P, Vanderleyden J, et al. Saturation of an intra-gene pool linkage map: towards a unified consensus linkage map for fine mapping and synteny analysis in common bean. PLoS ONE. 2011;6:e28135 pubmed publisher
    ..Finally, a synteny analysis was carried out using our highly saturated consensus maps compared with the soybean pseudo-chromosome ..
  9. Pfeifer M, Martis M, Asp T, Mayer K, Lübberstedt T, Byrne S, et al. The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics. Plant Physiol. 2013;161:571-82 pubmed publisher
    ..Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (..

More Information

Publications62

  1. Norman J, Robinson M, Glebe B, Ferguson M, Danzmann R. Genomic arrangement of salinity tolerance QTLs in salmonids: a comparative analysis of Atlantic salmon (Salmo salar) with Arctic charr (Salvelinus alpinus) and rainbow trout (Oncorhynchus mykiss). BMC Genomics. 2012;13:420 pubmed publisher
    ..To facilitate these comparisons, we examined the genomic synteny patterns of key candidate genes in the other model teleost fishes that have experienced three whole-genome ..
  2. Hernandez P, Martis M, Dorado G, Pfeifer M, Gálvez S, Schaaf S, et al. Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. Plant J. 2012;69:377-86 pubmed publisher
    ..much reduced template and the consequent avoidance of the problem of sequence duplication, in conjunction with synteny-based comparisons with other grass genomes, have facilitated construction of an ordered gene map of chromosome 4A,..
  3. Saxena R, Penmetsa R, Upadhyaya H, Kumar A, Carrasquilla Garcia N, Schlueter J, et al. Large-scale development of cost-effective single-nucleotide polymorphism marker assays for genetic mapping in pigeonpea and comparative mapping in legumes. DNA Res. 2012;19:449-61 pubmed publisher
    ..21 cM was constructed. Mapped PKAMs showed a higher degree of synteny with the genome of Glycine max followed by Medicago truncatula and Lotus japonicus and least with Vigna ..
  4. Varshney R, Chen W, Li Y, Bharti A, Saxena R, Schlueter J, et al. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol. 2011;30:83-9 pubmed publisher
  5. Dos Santos S, Mazan S, Venkatesh B, Cohen Tannoudji J, Qu rat B. Emergence and evolution of the glycoprotein hormone and neurotrophin gene families in vertebrates. BMC Evol Biol. 2011;11:332 pubmed publisher
  6. Nagy E, Guo Y, Tang S, Bowers J, Okashah R, Taylor C, et al. A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut. BMC Genomics. 2012;13:469 pubmed publisher
    ..b>Synteny analysis between A...
  7. Osugi T, Ohtaki N, Sunakawa Y, Son Y, Ohkubo M, Iigo M, et al. Molecular evolution of kiss2 genes and peptides in vertebrates. Endocrinology. 2013;154:4270-80 pubmed publisher
    ..The present study suggests that the kiss2 gene may have mutated in primates and crocodilians and been lost in birds during the course of evolution. In contrast, the kiss2 gene and mature kiss2 peptide are present in turtles and fish. ..
  8. Čejková D, Zobaníková M, Chen L, Pospíšilová P, Strouhal M, Qin X, et al. Whole genome sequences of three Treponema pallidum ssp. pertenue strains: yaws and syphilis treponemes differ in less than 0.2% of the genome sequence. PLoS Negl Trop Dis. 2012;6:e1471 pubmed publisher
    ..pallidum (TPA). Both yaws and syphilis are distinguished on the basis of epidemiological characteristics, clinical symptoms, and several genetic signatures of the corresponding causative agents...
  9. Irwin J, Lister C, Soumpourou E, Zhang Y, Howell E, Teakle G, et al. Functional alleles of the flowering time regulator FRIGIDA in the Brassica oleracea genome. BMC Plant Biol. 2012;12:21 pubmed publisher
    ..thaliana FRI due to an ancient recombination event. This has complicated previous association analyses of FRI with variation in life history strategy in the Brassica genus. ..
  10. Zuriaga E, Molina L, Badenes M, Romero C. Physical mapping of a pollen modifier locus controlling self-incompatibility in apricot and synteny analysis within the Rosaceae. Plant Mol Biol. 2012;79:229-42 pubmed publisher
    ..cv. 'Canino'. Fine-mapping of this mutated modifier gene (M-locus) and the synteny analysis of the M-locus within the Rosaceae are here reported...
  11. Pottorff M, Ehlers J, Fatokun C, Roberts P, Close T. Leaf morphology in Cowpea [Vigna unguiculata (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species. BMC Genomics. 2012;13:234 pubmed publisher
  12. Oliver R, Tinker N, Lazo G, Chao S, Jellen E, Carson M, et al. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species. PLoS ONE. 2013;8:e58068 pubmed publisher
    ..These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources. ..
  13. Amselem J, Cuomo C, van Kan J, Viaud M, Benito E, Couloux A, et al. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet. 2011;7:e1002230 pubmed publisher
    ..This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops...
  14. Souza R, Lima F, Barros R, Cortez D, Santos M, Cordero E, et al. Genome size, karyotype polymorphism and chromosomal evolution in Trypanosoma cruzi. PLoS ONE. 2011;6:e23042 pubmed publisher
    ..Mapping of the syntenic regions on T. cruzi chromosomal bands provides evidence for the occurrence of fusion and split events involving T. brucei and T. cruzi chromosomes. ..
  15. Kim B, Yu H, Park S, Shin J, Oh M, Kim N, et al. Identification and profiling of novel microRNAs in the Brassica rapa genome based on small RNA deep sequencing. BMC Plant Biol. 2012;12:218 pubmed publisher
    ..In this study, we sought to provide a more comprehensive prediction of B. rapa miRNAs based on high throughput small RNA deep sequencing...
  16. Burt C, Nicholson P. Exploiting co-linearity among grass species to map the Aegilops ventricosa-derived Pch1 eyespot resistance in wheat and establish its relationship to Pch2. Theor Appl Genet. 2011;123:1387-400 pubmed publisher
    ..This would assist the mapping of genes of interest and the breaking of deleterious linkages to enable greater use of these introgressions in commercial varieties...
  17. Ka S, Markljung E, Ring H, Albert F, Harun Or Rashid M, Wahlberg P, et al. Expression of carnitine palmitoyl-CoA transferase-1B is influenced by a cis-acting eQTL in two chicken lines selected for high and low body weight. Physiol Genomics. 2013;45:367-76 pubmed publisher
    ..Based on molecular phylogeny and gene synteny we suggest that chicken CPT1B is pro-orthologous of the mammalian CPT1c...
  18. Ocampo Daza D, Sundstrom G, Bergqvist C, Larhammar D. The evolution of vertebrate somatostatin receptors and their gene regions involves extensive chromosomal rearrangements. BMC Evol Biol. 2012;12:231 pubmed publisher
    ..To resolve their evolution in vertebrates we have investigated the SSTR genes and a large number of adjacent gene families by phylogeny and conserved synteny analyses in a broad range of vertebrate species.
  19. Georgi L, Johnson Cicalese J, Honig J, Das S, Rajah V, Bhattacharya D, et al. The first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci. Theor Appl Genet. 2013;126:673-92 pubmed publisher
    ..Regions of the cranberry map were identified that showed conservation of synteny with Vitis vinifera and Arabidopsis thaliana...
  20. Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, et al. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature. 2011;477:587-91 pubmed publisher
    ..Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations...
  21. Marquioni V, Bertollo L, Diniz D, Cioffi M. Comparative chromosomal mapping in Triportheus fish species. Analysis of synteny between ribosomal genes. Micron. 2013;45:129-35 pubmed publisher
    ..The double-FISH experiments have showed that the synteny of the 18S and 5S rDNA genes is not a synapomorphy for the genus, since it is not present in all the species ..
  22. Oberto J. SyntTax: a web server linking synteny to prokaryotic taxonomy. BMC Bioinformatics. 2013;14:4 pubmed publisher
    The study of the conservation of gene order or synteny constitutes a powerful methodology to assess the orthology of genomic regions and to predict functional relationships between genes...
  23. Decatur W, Hall J, Smith J, Li W, Sower S. Insight from the lamprey genome: glimpsing early vertebrate development via neuroendocrine-associated genes and shared synteny of gonadotropin-releasing hormone (GnRH). Gen Comp Endocrinol. 2013;192:237-45 pubmed publisher
    ..Furthermore, paralogous type 3 genes (lGnRH-I/III and GnRH3) evolved divergent structure/function in lamprey and gnathostome lineages. ..
  24. Yamaguchi Y, Kaiya H, Konno N, Iwata E, Miyazato M, Uchiyama M, et al. The fifth neurohypophysial hormone receptor is structurally related to the V2-type receptor but functionally similar to V1-type receptors. Gen Comp Endocrinol. 2012;178:519-28 pubmed publisher
    ..Analysis suggested that the mammalian V2bR may have lost its function. Based on molecular phylogenetic, synteny and functional analyses, we propose a new evolutionary history for the neurohypophysial hormone receptors in ..
  25. Clarke S, Vandermeer J, Wenger A, Schaar B, Ahituv N, Bejerano G. Human developmental enhancers conserved between deuterostomes and protostomes. PLoS Genet. 2012;8:e1002852 pubmed publisher
    ..Bicores show conservation of sequence and gene synteny. Sequence conservation of Bicores reflects conserved patterns of transcription factor binding sites...
  26. Srikulnath K, Uno Y, Nishida C, Matsuda Y. Karyotype evolution in monitor lizards: cross-species chromosome mapping of cDNA reveals highly conserved synteny and gene order in the Toxicofera clade. Chromosome Res. 2013;21:805-19 pubmed publisher
    ..salvator macromaculatus and V. exanthematicus. Morphologic differences in chromosomes 6-8 between the two species could have resulted from pericentric inversion or centromere repositioning...
  27. Thole S, Kalhoefer D, Voget S, Berger M, Engelhardt T, Liesegang H, et al. Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life. ISME J. 2012;6:2229-44 pubmed publisher
    ..sites from the two different hemispheres, the genome comparison demonstrated a surprisingly high level of synteny (only 3% nucleotide dissimilarity and 88% and 93% shared genes)...
  28. Revanna K, Munro D, Gao A, Chiu C, Pathak A, Dong Q. A web-based multi-genome synteny viewer for customized data. BMC Bioinformatics. 2012;13:190 pubmed publisher
    Web-based synteny visualization tools are important for sharing data and revealing patterns of complicated genome conservation and rearrangements. Such tools should allow biologists to upload genomic data for their own analysis...
  29. Gaur R, Azam S, Jeena G, Khan A, Choudhary S, Jain M, et al. High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Res. 2012;19:357-73 pubmed publisher
    ..70 cM, thereby representing one of the most advanced maps of chickpea. The map was used for the synteny analysis of chickpea, which revealed a higher degree of synteny with the phylogenetically close Medicago than ..
  30. Pasquier J, Lafont A, Jeng S, Morini M, Dirks R, van den Thillart G, et al. Multiple kisspeptin receptors in early osteichthyans provide new insights into the evolution of this receptor family. PLoS ONE. 2012;7:e48931 pubmed publisher
    ..Due to gene loss there was no impact of the teleost-specific whole genome duplication (3R) on the number of Kissr paralogs in current teleosts. ..
  31. Proux Wera E, Armisén D, Byrne K, Wolfe K. A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach. BMC Bioinformatics. 2012;13:237 pubmed publisher
    ..YGAP does automatic de novo annotation, exploiting homology and synteny information from other yeast species stored in the Yeast Gene Order Browser (YGOB) database...
  32. Nomiyama H, Osada N, Yoshie O. Systematic classification of vertebrate chemokines based on conserved synteny and evolutionary history. Genes Cells. 2013;18:1-16 pubmed publisher
    ..Our study reveals an interesting evolutionary history that gave origin and diversification to the vertebrate chemokine superfamily. ..
  33. Hiremath P, Kumar A, Penmetsa R, Farmer A, Schlueter J, Chamarthi S, et al. Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes. Plant Biotechnol J. 2012;10:716-32 pubmed publisher
    ..Detailed analyses of 1064 mapped loci of this second-generation chickpea genetic map showed a higher degree of synteny with genome of Medicago truncatula, followed by Glycine max, Lotus japonicus and least with Vigna unguiculata...
  34. Star B, Nederbragt A, Jentoft S, Grimholt U, Malmstrøm M, Gregers T, et al. The genome sequence of Atlantic cod reveals a unique immune system. Nature. 2011;477:207-10 pubmed publisher
    ..These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates. ..
  35. Bu L, Bergthorsson U, Katju V. Local synteny and codon usage contribute to asymmetric sequence divergence of Saccharomyces cerevisiae gene duplicates. BMC Evol Biol. 2011;11:279 pubmed publisher
    ..In this study we investigated the effect of local synteny (gene-neighborhood conservation) and codon usage on the sequence evolution of gene duplicates in the S...
  36. Yelton A, Thomas B, Simmons S, Wilmes P, Zemla A, Thelen M, et al. A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes. PLoS Comput Biol. 2011;7:e1002230 pubmed publisher
    ..If the relationship between synteny and sequence divergence can be modeled, gene clusters in genomes of distantly related organisms exhibiting ..
  37. Young N, Debellé F, Oldroyd G, Geurts R, Cannon S, Udvardi M, et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature. 2011;480:520-4 pubmed publisher
    ..As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox...
  38. Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van de Peer Y, et al. i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets. Nucleic Acids Res. 2012;40:e11 pubmed publisher
    ..The different algorithmical improvements ensure that i-ADHoRe 3.0 will remain a powerful tool to study genome evolution. ..
  39. Wang Y, Tang H, DeBarry J, Tan X, Li J, Wang X, et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012;40:e49 pubmed publisher
    ..The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of ..
  40. Kuraku S, Meyer A. Detection and phylogenetic assessment of conserved synteny derived from whole genome duplications. Methods Mol Biol. 2012;855:385-95 pubmed publisher
    ..In this chapter, we summarize current understanding of phylogenetic distribution and evolutionary impact of WGDs, introduce basic procedures to detect conserved synteny, and discuss typical pitfalls, as well as biological insights.
  41. Guyomard R, Boussaha M, Krieg F, Hervet C, Quillet E. A synthetic rainbow trout linkage map provides new insights into the salmonid whole genome duplication and the conservation of synteny among teleosts. BMC Genet. 2012;13:15 pubmed publisher
  42. Guyot R, Lefebvre Pautigny F, Tranchant Dubreuil C, Rigoreau M, Hamon P, Leroy T, et al. Ancestral synteny shared between distantly-related plant species from the asterid (Coffea canephora and Solanum Sp.) and rosid (Vitis vinifera) clades. BMC Genomics. 2012;13:103 pubmed publisher
    ..We report the first multiple comparison between species from Asterid and Rosid clades, to examine both macro-and microsynteny relationships...
  43. Henkel C, Dirks R, Jansen H, Forlenza M, Wiegertjes G, Howe K, et al. Comparison of the exomes of common carp (Cyprinus carpio) and zebrafish (Danio rerio). Zebrafish. 2012;9:59-67 pubmed publisher
    ..of the scaffolding was confirmed by comparisons with RNA deep sequencing data sets and a manual analysis for synteny with the zebrafish, especially the Hox gene clusters...
  44. Revanna K, Chiu C, Bierschank E, Dong Q. GSV: a web-based genome synteny viewer for customized data. BMC Bioinformatics. 2011;12:316 pubmed publisher
    The analysis of genome synteny is a common practice in comparative genomics. With the advent of DNA sequencing technologies, individual biologists can rapidly produce their genomic sequences of interest...
  45. Timusk E, Ferguson M, Moghadam H, Norman J, Wilson C, Danzmann R. Genome evolution in the fish family salmonidae: generation of a brook charr genetic map and comparisons among charrs (Arctic charr and brook charr) with rainbow trout. BMC Genet. 2011;12:68 pubmed publisher
    ..The formation of quadrivalents during meiosis leads to pseudolinkage. This phenomenon is more prevalent within 5 of the 12 ancestral teleost linkage groups in salmonids...
  46. DeBarry J, Kissinger J. Jumbled genomes: missing Apicomplexan synteny. Mol Biol Evol. 2011;28:2855-71 pubmed publisher
    ..We have developed an in silico protein-encoding gene based pipeline to investigate synteny across 12 apicomplexan species from six genera. Genome rearrangement between lineages is extensive...
  47. Quraishi U, Abrouk M, Murat F, Pont C, Foucrier S, Desmaizieres G, et al. Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution. Plant J. 2011;65:745-56 pubmed publisher
    ..We propose an evolutionary model for the NUE locus in cereals from a common ancestral region, involving species specific shuffling events such as gene deletion, inversion, transposition and the invasion of repetitive elements. ..
  48. Leidenroth A, Hewitt J. A family history of DUX4: phylogenetic analysis of DUXA, B, C and Duxbl reveals the ancestral DUX gene. BMC Evol Biol. 2010;10:364 pubmed publisher
    ..Their relationships should be considered when interpreting the relevance of functional data from DUX4 homologues such as Dux and Duxbl to FSHD. ..
  49. González V, Rodriguez Moreno L, Centeno E, Benjak A, Garcia Mas J, Puigdomenech P, et al. Genome-wide BAC-end sequencing of Cucumis melo using two BAC libraries. BMC Genomics. 2010;11:618 pubmed publisher
    ..We therefore sequenced BAC-ends representing a total of 33,024 clones, half of them from a previously described melon BAC library generated with restriction endonucleases and the remainder from a new random-shear BAC library...
  50. Göpel Y, Lüttmann D, Heroven A, Reichenbach B, Dersch P, Görke B. Common and divergent features in transcriptional control of the homologous small RNAs GlmY and GlmZ in Enterobacteriaceae. Nucleic Acids Res. 2011;39:1294-309 pubmed publisher
    ..coli glmY requires binding of the integration host factor to sites upstream of the promoter. Finally, evidence is provided that phosphorylation of GlrR increases its activity and thereby sRNA expression. ..
  51. Drader T, Kleinhofs A. A synteny map and disease resistance gene comparison between barley and the model monocot Brachypodium distachyon. Genome. 2010;53:406-17 pubmed publisher
    ..Here, we present a synteny map between the crop species Hordeum vulgare and the recently sequenced Brachypodium distachyon genome, focusing ..
  52. Martin J, Yoshimoto M, Ludkovski O, Thorner P, Zielenska M, Squire J, et al. Analysis of segmental duplications, mouse genome synteny and recurrent cancer-associated amplicons in human chromosome 6p21-p12. Cytogenet Genome Res. 2010;128:199-213 pubmed publisher
    ..This process may involve homology-dependent DNA recombination and/or repair, which may also contribute towards the overall plasticity of the human genome. ..
  53. Fujii S, Kazama T, Yamada M, Toriyama K. Discovery of global genomic re-organization based on comparison of two newly sequenced rice mitochondrial genomes with cytoplasmic male sterility-related genes. BMC Genomics. 2010;11:209 pubmed publisher
    ..Genomic rearrangements were dynamic in the CMS lines in comparison with those of rice cultivars, suggesting that 'death' and possible 'birth' processes of the CMS genes occurred during the breeding history of rice. ..