Details
| Original language | English |
|---|---|
| Article number | 1193122 |
| Journal | Frontiers in Plant Science |
| Volume | 14 |
| Publication status | Published - 26 Jun 2023 |
Abstract
Keywords
- complex I, Complexome profiling, database development, Illumina sequencing, mitochondria, oxidative phosphorylation (OXPHOS), PacBio sequencing, supercomplex
ASJC Scopus subject areas
- Agricultural and Biological Sciences(all)
- Plant Science
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In: Frontiers in Plant Science, Vol. 14, 1193122, 26.06.2023.
Research output: Contribution to journal › Article › Research › peer review
}
TY - JOUR
T1 - The Viscum album Gene Space database
AU - Schröder, Lucie
AU - Rupp, Oliver
AU - Senkler, Michael
AU - Rugen, Nils
AU - Hohnjec, Natalija
AU - Goesmann, Alexander
AU - Küster, Helge
AU - Braun, Hans-Peter
N1 - This research has been supported by the Deutsche Forschungsgemeinschaft, grant BR 1829/16-1, to HPB. The publication of this article was funded by the Open Access Fund of Leibniz Universität Hannover.
PY - 2023/6/26
Y1 - 2023/6/26
N2 - The hemiparasitic flowering plant Viscum album (European mistletoe) is known for its very special life cycle, extraordinary biochemical properties, and extremely large genome. The size of its genome is estimated to be 30 times larger than the human genome and 600 times larger than the genome of the model plant Arabidopsis thaliana. To achieve insights into the Gene Space of the genome, which is defined as the space including and surrounding protein-coding regions, a transcriptome project based on PacBio sequencing has recently been conducted. A database resulting from this project contains sequences of 39,092 different open reading frames encoding 32,064 distinct proteins. Based on ‘Benchmarking Universal Single-Copy Orthologs’ (BUSCO) analysis, the completeness of the database was estimated to be in the range of 78%. To further develop this database, we performed a transcriptome project of V. album organs harvested in summer and winter based on Illumina sequencing. Data from both sequencing strategies were combined. The new V. album Gene Space database II (VaGs II) contains 90,039 sequences and has a completeness of 93% as revealed by BUSCO analysis. Sequences from other organisms, particularly fungi, which are known to colonize mistletoe leaves, have been removed. To evaluate the quality of the new database, proteome data of a mitochondrial fraction of V. album were re-analyzed. Compared to the original evaluation published five years ago, nearly 1000 additional proteins could be identified in the mitochondrial fraction, providing new insights into the Oxidative Phosphorylation System of V. album. The VaGs II database is available at https://viscumalbum.pflanzenproteomik.de/. Furthermore, all V. album sequences have been uploaded at the European Nucleotide Archive (ENA).
AB - The hemiparasitic flowering plant Viscum album (European mistletoe) is known for its very special life cycle, extraordinary biochemical properties, and extremely large genome. The size of its genome is estimated to be 30 times larger than the human genome and 600 times larger than the genome of the model plant Arabidopsis thaliana. To achieve insights into the Gene Space of the genome, which is defined as the space including and surrounding protein-coding regions, a transcriptome project based on PacBio sequencing has recently been conducted. A database resulting from this project contains sequences of 39,092 different open reading frames encoding 32,064 distinct proteins. Based on ‘Benchmarking Universal Single-Copy Orthologs’ (BUSCO) analysis, the completeness of the database was estimated to be in the range of 78%. To further develop this database, we performed a transcriptome project of V. album organs harvested in summer and winter based on Illumina sequencing. Data from both sequencing strategies were combined. The new V. album Gene Space database II (VaGs II) contains 90,039 sequences and has a completeness of 93% as revealed by BUSCO analysis. Sequences from other organisms, particularly fungi, which are known to colonize mistletoe leaves, have been removed. To evaluate the quality of the new database, proteome data of a mitochondrial fraction of V. album were re-analyzed. Compared to the original evaluation published five years ago, nearly 1000 additional proteins could be identified in the mitochondrial fraction, providing new insights into the Oxidative Phosphorylation System of V. album. The VaGs II database is available at https://viscumalbum.pflanzenproteomik.de/. Furthermore, all V. album sequences have been uploaded at the European Nucleotide Archive (ENA).
KW - complex I
KW - Complexome profiling
KW - database development
KW - Illumina sequencing
KW - mitochondria
KW - oxidative phosphorylation (OXPHOS)
KW - PacBio sequencing
KW - supercomplex
UR - http://www.scopus.com/inward/record.url?scp=85165306873&partnerID=8YFLogxK
U2 - 10.3389/fpls.2023.1193122
DO - 10.3389/fpls.2023.1193122
M3 - Article
VL - 14
JO - Frontiers in Plant Science
JF - Frontiers in Plant Science
SN - 1664-462X
M1 - 1193122
ER -