Evidence map›Paper›PMID 26252423›Full record

ArticleThe Plant journal : for cell and molecular biology2015

Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome.

María Muñoz-Amatriaín, Stefano Lonardi, MingCheng Luo, Kavitha Madishetty, Jan T Svensson, Matthew J Moscou, Steve Wanamaker, Tao Jiang, Andris Kleinhofs, Gary J Muehlbauer and 39 more

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Article in The Plant journal : for cell and molecular biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.

0numbers the graph read from it
0cells of the map it votes in
18citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

18 citing papers in PubMed.

  1. High-Resolution Mapping ofFrontiers in plant science · 2022
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  4. The Dark Matter of Large Cereal Genomes: Long Tandem Repeats.International journal of molecular sciences · 2019
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  6. Article
  7. A single nucleotide polymorphism in the "Fra" gene results in fractured starch granules in barley.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018
    Article
  8. Article
  9. Copy number variation and disease resistance in plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017
    Review
  10. Article
  11. MISA-web: a web server for microsatellite prediction.Bioinformatics (Oxford, England) · 2017
    Article
  12. Article
  13. Article
  14. Article
  15. Article
  16. Fine mapping of barley locus Rps6 conferring resistance to wheat stripe rust.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2016
    Article
  17. Article
  18. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

49 authors.

María Muñoz-AmatriaínDepartment of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
Stefano LonardiDepartment of Computer Science, University of California, Riverside, CA, 92521, USA.
MingCheng LuoDepartment of Plant Sciences, University of California, Davis, CA, 95616, USA.
Kavitha MadishettyDepartment of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
Jan T SvenssonDepartment of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
Matthew J MoscouDepartment of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
Steve WanamakerDepartment of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
Tao JiangDepartment of Computer Science, University of California, Riverside, CA, 92521, USA.
Andris KleinhofsDepartment of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
Gary J MuehlbauerDepartment of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
Roger P WiseCorn Insects and Crop Genetics Research, USDA-Agricultural Research Service & Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011-1020, USA.
Nils SteinLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany.
Yaqin MaDepartment of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
Edmundo RodriguezDepartment of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
Dave KudrnaArizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA.
Prasanna R BhatDepartment of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
Shiaoman ChaoUSDA-ARS Biosciences Research Lab, Fargo, ND, 58105, USA.
Pascal CondamineDepartment of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
Shane HeinenDepartment of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
Josh ResnikDepartment of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
Rod WingArizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA.
Heather N WittDepartment of Plant Sciences, University of California, Davis, CA, 95616, USA.
Matthew AlpertDepartment of Computer Science, University of California, Riverside, CA, 92521, USA.
Marco BeccutiDepartment of Computer Science, University of California, Riverside, CA, 92521, USA.
Serdar BozdagDepartment of Computer Science, University of California, Riverside, CA, 92521, USA.
Francesca CorderoDepartment of Computer Science, University of California, Riverside, CA, 92521, USA.
Hamid MirebrahimDepartment of Computer Science, University of California, Riverside, CA, 92521, USA.
Rachid OunitDepartment of Computer Science, University of California, Riverside, CA, 92521, USA.
Yonghui WuDepartment of Computer Science, University of California, Riverside, CA, 92521, USA.
Frank YouUSDA-ARS, Albany, CA, 94710, USA.
Jie ZhengDepartment of Computer Science, University of California, Riverside, CA, 92521, USA.
Hana SimkováCentre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic.
Jaroslav DolezelCentre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic.
Jane GrimwoodHudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA.
Jeremy SchmutzHudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA.
Denisa DumaDepartment of Computer Science, University of California, Riverside, CA, 92521, USA.
Lothar AltschmiedLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany.
Tom BlakeDepartment of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA.
Phil BregitzerUSDA-ARS, Aberdeen, ID, 83210, USA.
Laurel CooperDepartment of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA.
Muharrem DilbirligiDepartment of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
Anders FalkSwedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden.
Leila FeizDepartment of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA.
Andreas GranerLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany.
Perry GustafsonUSDA, University of Missouri, Columbia, MO, 65211, USA.
Patrick M HayesDepartment of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA.
Peggy LemauxDepartment of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
Jafar MammadovDepartment of Crop & Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
Timothy J CloseDepartment of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.

Indexed as

Chromosomes, Artificial, BacterialGenome, PlantHordeumMolecular Sequence DataAegilops tauschiiBAC sequencingBarleycentromere BACsgene distributionHarvEST:BarleyHordeum vulgare L.recombination frequencysynteny

Identifiers

PMID26252423
PMCPMC5014227

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