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Proteogenomic Analy...
Proteogenomic Analysis Greatly Expands the Identification of Proteins Related to Reproduction in the Apogamous Fern Dryopteris affinis ssp affinis
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- Grossmann, Jonas (författare)
- Funct Genom Ctr Zurich, Zurich, Switzerland.
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- Fernández, Helena (författare)
- Univ Oviedo, Dept Organisms & Syst Biol BOS, Area Plant Physiol, Oviedo, Spain.
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- Chaubey, Pururawa M. (författare)
- Univ Zurich, Inst Plant & Microbial Biol, Zurich Basel Plant Sci Ctr, Zurich, Switzerland.;Hadron Finsys GmbH, Pharma & Life Sci, Cham, Switzerland.
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- Valdés, Ana E. (författare)
- Uppsala universitet,Stockholms universitet,Institutionen för ekologi, miljö och botanik,Linnean Centre for Plant Biology, Sweden,Fysiologisk botanik,Linnean Ctr Plant Biol, Uppsala, Sweden.; Stockholm Univ, Dept Ecol Environm & Plant Sci, Stockholm, Sweden.
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- Gagliardini, Valeria (författare)
- Univ Zurich, Inst Plant & Microbial Biol, Zurich Basel Plant Sci Ctr, Zurich, Switzerland.
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- Cañal, María J. (författare)
- Univ Oviedo, Dept Organisms & Syst Biol BOS, Area Plant Physiol, Oviedo, Spain.
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- Russo, Giancarlo (författare)
- Funct Genom Ctr Zurich, Zurich, Switzerland.
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- Grossniklaus, Ueli (författare)
- Univ Zurich, Inst Plant & Microbial Biol, Zurich Basel Plant Sci Ctr, Zurich, Switzerland.
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Funct Genom Ctr Zurich, Zurich, Switzerland Univ Oviedo, Dept Organisms & Syst Biol BOS, Area Plant Physiol, Oviedo, Spain. (creator_code:org_t)
- 2017-03-22
- 2017
- Engelska.
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 8
- Relaterad länk:
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https://doi.org/10.3...
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https://doi.org/10.3...
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https://urn.kb.se/re...
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https://doi.org/10.3...
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https://urn.kb.se/re...
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Abstract
Ämnesord
Stäng
- Performing proteomic studies on non-model organisms with little or no genomic information is still difficult. However, many specific processes and biochemical pathways occur only in species that are poorly characterized at the genomic level. For example, many plants can reproduce both sexually and asexually, the first one allowing the generation of new genotypes and the latter their fixation. Thus, both modes of reproduction are of great agronomic value. However, the molecular basis of asexual reproduction is not well understood in any plant. In ferns, it combines the production of unreduced spores (diplospory) and the formation of sporophytes from somatic cells (apogamy). To set the basis to study these processes, we performed transcriptomics by next-generation sequencing (NGS) and shotgun proteomics by tandem mass spectrometry in the apogamous fern D. affinis ssp. affinis. For protein identification we used the public viridiplantae database (VPDB) to identify orthologous proteins from other plant species and new transcriptomics data to generate a species-specific transcriptome database (SSTDB). In total 1,397 protein clusters with 5,865 unique peptide sequences were identified (13 decoy proteins out of 1,410, protFDR 0.93% on protein cluster level). We show that using the SSTDB for protein identification increases the number of identified peptides almost four times compared to using only the publically available VPDB. We identified homologs of proteins involved in reproduction of higher plants, including proteins with a potential role in apogamy. With the increasing availability of genomic data from non -model species, similar proteogenomics approaches will improve the sensitivity in protein identification for species only distantly related to models.
Ämnesord
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
- NATURVETENSKAP -- Biologi -- Botanik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Botany (hsv//eng)
Nyckelord
- apogamy
- apomixis
- Dryopteris affinis ssp affinis
- fern
- gametophyte
- proteogenomics
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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