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  Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds

Wilhelmsson, P. K. I., Chandler, J. O., Fernandez-Pozo, N., Graeber, K., Ullrich, K. K., Arshad, W., et al. (2019). Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds. BMC Genomics, 20: 95. doi:10.1186/s12864-019-5452-4.

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Item Permalink: https://hdl.handle.net/21.11116/0000-0002-F579-2 Version Permalink: https://hdl.handle.net/21.11116/0000-0005-1F51-E
Genre: Journal Article

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 Creators:
Wilhelmsson, Per K. I., Author
Chandler, Jake O., Author
Fernandez-Pozo, Noe, Author
Graeber, Kai, Author
Ullrich, Kristian K.1, Author           
Arshad, Waheed, Author
Khan, Safina, Author
Hofberger, Johannes A., Author
Buchta, Karl, Author
Edger, Patrick P., Author
Pires, J. Chris, Author
Schranz, M. Eric, Author
Leubner-Metzger, Gerhard, Author
Rensing, Stefan A., Author
Affiliations:
1Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445635              

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 Abstract: RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy – producing both a less dormant mucilaginous (M+) seed morph and a more dormant non-mucilaginous (NM) seed morph. Here, we compared de novo and reference-genome based transcriptome assemblies to investigate Ae. arabicum seed dimorphism and to evaluate the reference-free versus -dependent approach for identifying differentially expressed genes (DEGs).

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Language(s): eng - English
 Dates: 2018-05-162019-01-142019-01-302019-01
 Publication Status: Issued
 Pages: -
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 Identifiers: DOI: 10.1186/s12864-019-5452-4
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Project name : Deutsche Forschungsgemeinschaft
Grant ID : RE 1697/8–1
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Project name : Netherlands Organization for Scientific Research
Grant ID : 849.13.004
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Project name : Biotechnology and Biological Sciences Research Council
Grant ID : BB/M00192X/1
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Project name : Biotechnology and Biological Sciences Research Council
Grant ID : BB/M000583/1
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Project name : Natural Environment Research Council (NERC) Doctoral Training Partnership studentship
Grant ID : NE/L002485/1
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Title: BMC Genomics
Source Genre: Journal
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Publ. Info: BioMed Central
Pages: - Volume / Issue: 20 Sequence Number: 95 Start / End Page: - Identifier: ISSN: 1471-2164
CoNE: https://pure.mpg.de/cone/journals/resource/111000136905010