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. 2021 May 20;22(3):bbaa136.
doi: 10.1093/bib/bbaa136.

Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook

Hartmut Foerster  1 , James N D Battey  2 , Nicolas Sierro  2 , Nikolai V Ivanov  2 , Lukas A Mueller  1
Affiliations

Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook

Hartmut Foerster et al. Brief Bioinform. .

Abstract

Manually curated metabolic databases residing at the Sol Genomics Network comprise two taxon-specific databases for the Solanaceae family, i.e. SolanaCyc and the genus Nicotiana, i.e. NicotianaCyc as well as six species-specific databases for Nicotiana tabacum TN90, N. tabacum K326, Nicotiana benthamiana, N. sylvestris, N. tomentosiformis and N. attenuata. New pathways were created through the extraction, examination and verification of related data from the literature and the aid of external database guided by an expert-led curation process. Here we describe the curation progress that has been achieved in these databases since the first release version 1.0 in 2016, the curation flow and the curation process using the example metabolic pathway for cholesterol in plants. The current content of our databases comprises 266 pathways and 36 superpathways in SolanaCyc and 143 pathways plus 21 superpathways in NicotianaCyc, manually curated and validated specifically for the Solanaceae family and Nicotiana genus, respectively. The curated data have been propagated to the respective Nicotiana-specific databases, which resulted in the enrichment and more accurate presentation of their metabolic networks. The quality and coverage in those databases have been compared with related external databases and discussed in terms of literature support and metabolic content.

Keywords: data quality; database development; literature coverage; manual curation; taxon-specific databases.

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Figures

Figure 1
Figure 1
Flow chart of the curation process in the manually curated taxon-specific databases SolanaCyc and NicotianaCyc. External resources used for curation have been highlighted and referenced in the text.
Figure 2
Figure 2
Number of pathways and curated enzymes in the taxon-specific databases SolanaCyc and NicotianaCyc. Square icons represent pathways (filled) and enzymes (empty) of the family-specific SolanaCyc database and round icons represent pathways (filled) and enzymes (empty) in the genus-specific NicotianaCyc database. Note that transporters and enzyme complexes have been excluded from the protein count.
Figure 3
Figure 3
Curation progress in Nicotiana-specific databases over time. Filled icons represent the number of pathways present at the time of the respective release version. Empty icons mark the release version of the blacklist application referenced in the text. formula imageN. tabacum (TN90) formula imageN. tabacum (K326) formula imageN. benthamianaformula imageN. sylvestrisformula imageN. attenuataformula imageN. tomentosiformis.
Figure 4a
Figure 4a
Curation progress made between 2016 (A) and 2019 (B) on the cholesterol biosynthetic pathway in solanaceous plant species.
Figure 4b
Figure 4b
Figure 5
Figure 5
Nicotiana-specific pathway network Venn diagram. Crossover of pathway networks between N. tabacum (K326), N. sylvestris, N. tomentosiformis, N. benthamiana and N. attenuata. The numbers for shared and unique pathways are shown in each intersection.
See this image and copyright information in PMC

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