Evidence map›Paper›PMID 25637298›Full record

ArticleGenome biology2015

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome.

Jarrod A Chapman, Martin Mascher, Aydın Buluç, Kerrie Barry, Evangelos Georganas, Adam Session, Veronika Strnadova, Jerry Jenkins, Sunish Sehgal, Leonid Oliker and 8 more

Abstract read
In one paragraph

Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 131 papers.

0numbers the graph read from it
0cells of the map it votes in
131citing 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

131 citing papers in PubMed.

  1. Article
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  8. Review
  9. Article
  10. Recent Advances in Assembly of Complex Plant Genomes.Genomics, proteomics & bioinformatics · 2023
    Review
  11. Triticeae crop genome biology: an endless frontier.Frontiers in plant science · 2023
    Review
  12. Article
  13. Article
  14. Article
  15. Integrating Genetic and Chromosome Maps ofInternational journal of molecular sciences · 2022
    Article
  16. Article
  17. Article
  18. Article
  19. Article
  20. Article

71 more citing papers are in PubMed but not listed here.

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

18 authors.

Jarrod A ChapmanDepartment of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. jarrodc@gmail.com.
Martin MascherLeibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany. mascher@ipk-gatersleben.de.
Aydın BuluçComputational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. abuluc@lbl.gov.
Kerrie BarryDepartment of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. kwbarry@lbl.gov.
Evangelos GeorganasComputational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. egeor@eecs.berkeley.edu.
Adam SessionDepartment of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA. adamsession@berkeley.edu.
Veronika StrnadovaDepartment of Computer Science, University of California, Santa Barbara, CA, 93106, USA. veronika@cs.ucsb.edu.
Jerry JenkinsDepartment of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. jjenkins@hudsonalpha.org.
Sunish SehgalDepartment of Plant Pathology, Kansas State University, Manhattan, KS, 65506, USA. sunish.sehgal@sdstate.edu.
Leonid OlikerComputational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. loliker@lbl.gov.
Jeremy SchmutzDepartment of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. jschmutz@hudsonalpha.org.
Katherine A YelickComputational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. yelick@eecs.berkeley.edu.
Uwe ScholzLeibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany. scholz@ipk-gatersleben.de.
Robbie WaughDivision of Plant Sciences, University of Dundee & The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK. Robbie.Waugh@hutton.ac.uk.
Jesse A PolandDepartment of Plant Pathology, Kansas State University, Manhattan, KS, 65506, USA. jpoland@ksu.edu.
Gary J MuehlbauerDepartments of Agronomy and Plant Genetics, and Plant Biology, University of Minnesota, St Paul, MN, 55108, USA. muehl003@umn.edu.
Nils SteinLeibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany. stein@ipk-gatersleben.de.
Daniel S RokhsarDepartment of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. dsrokhsar@gmail.com.

Funding

Biotechnology and Biological Sciences Research Council BB/I00663X/1
6 · The paper itself

Abstract

Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.

Indexed as

BreadGenome, PlantPolyploidyChromosome MappingContig MappingDNA, ComplementaryGenetic LinkageGenetic VariationHomozygoteNucleotidesReproducibility of ResultsSequence Analysis, DNATriticumDNA, ComplementaryNucleotides

Identifiers

PMID25637298
PMCPMC4373400

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.