Molecular diversity in the genus Nicotiana as revealed by randomly amplified polymorphic DNA

Raju, K. Kanaka; Sheshumadhav, M.; Murthy, T. G. K.

doi:10.1007/s12298-008-0037-8

Cited by 8 publications

(6 citation statements)

References 9 publications

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“…27 (∼40%) pathways, was classified under the specialized metabolite category. The divergence in some metabolic divisions in cultivated and wild tobacco species is certainly also due to the observed high molecular diversity in the genus Nicotiana , where the high degree of genetic polymorphism results in gaining or losing the ability to biosynthesize a range of metabolites ( 64 ).…”

Section: Resultsmentioning

confidence: 99%

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks inSolanumandNicotianaspecific databases

et al. 2018

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SolCyc is the entry portal to pathway/genome databases (PGDBs) for major species of the Solanaceae family hosted at the Sol Genomics Network. Currently, SolCyc comprises six organism-specific PGDBs for tomato, potato, pepper, petunia, tobacco and one Rubiaceae, coffee. The metabolic networks of those PGDBs have been computationally predicted by the pathologic component of the pathway tools software using the manually curated multi-domain database MetaCyc (http://www.metacyc.org/) as reference. SolCyc has been recently extended by taxon-specific databases, i.e. the family-specific SolanaCyc database, containing only curated data pertinent to species of the nightshade family, and NicotianaCyc, a genus-specific database that stores all relevant metabolic data of the Nicotiana genus. Through manual curation of the published literature, new metabolic pathways have been created in those databases, which are complemented by the continuously updated, relevant species-specific pathways from MetaCyc. At present, SolanaCyc comprises 199 pathways and 29 superpathways and NicotianaCyc accounts for 72 pathways and 13 superpathways. Curator-maintained, taxon-specific databases such as SolanaCyc and NicotianaCyc are characterized by an enrichment of data specific to these taxa and free of falsely predicted pathways. Both databases have been used to update recently created Nicotiana-specific databases for Nicotiana tabacum, Nicotiana benthamiana, Nicotiana sylvestris and Nicotiana tomentosiformis by propagating verifiable data into those PGDBs. In addition, in-depth curation of the pathways in N.tabacum has been carried out which resulted in the elimination of 156 pathways from the 569 pathways predicted by pathway tools. Together, in-depth curation of the predicted pathway network and the supplementation with curated data from taxon-specific databases has substantially improved the curation status of the species–specific N.tabacum PGDB. The implementation of this strategy will significantly advance the curation status of all organism-specific databases in SolCyc resulting in the improvement on database accuracy, data analysis and visualization of biochemical networks in those species.Database URL https://solgenomics.net/tools/solcyc/

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Section: Resultsmentioning

confidence: 99%

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks inSolanumandNicotianaspecific databases

et al. 2018

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“…However, a certain amount of divergence for some metabolic categories in domesticated and wild tobacco species is to be expected. The genus Nicotiana is known for its high molecular diversity due to the polymorphic variability of its species, often resulting in either gaining or losing biosynthetic flexibility [ 96 ].…”

Section: Resultsmentioning

confidence: 99%

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

Foerster¹,

Battey

Sierro

et al. 2020

Briefings in Bioinformatics

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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.

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“…The majority of disease resistance genes in plants contain a nucleotide-binding site and leucine-rich repeat (NBS-LRR) domain [ 36 , 37 ], which confers resistance to fungi, bacteria, viruses, and nematodes. In plants, based on the presence or absence of a TIR homology region at the N-terminus, the NBS-LRR genes can be subdivided into two main groups: TIR-NBS-LRR and non-TIR-NBS-LRR.…”

Section: Resultsmentioning

confidence: 99%

Sequencing and characterization of leaf transcriptomes of six diploid Nicotiana species

Long

Ren

Xiang

et al. 2016

J of Biol Res-Thessaloniki

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BackgroundNicotiana belongs to the Solanaceae family that includes important crops such as tomato, potato, eggplant, and pepper. Nicotiana species are of worldwide economic importance and are important model plants for scientific research. Here we present the comparative analysis of the transcriptomes of six wild diploid Nicotiana species. Wild relatives provide an excellent study system for the analysis of the genetic basis for various traits, especially disease resistance.ResultsWhole transcriptome sequencing (RNA-seq) was performed for leaves of six diploid Nicotiana species, i.e. Nicotiana glauca, Nicotiana noctiflora, Nicotiana cordifolia, Nicotiana knightiana, Nicotiana setchellii and Nicotiana tomentosiformis. For each species, 9.0–22.3 Gb high-quality clean data were generated, and 67,073–182,046 transcripts were assembled with lengths greater than 100 bp. Over 90 % of the ORFs in each species had significant similarity with proteins in the NCBI non-redundant protein sequence (NR) database. A total of 2491 homologs were identified and used to construct a phylogenetic tree from the respective transcriptomes in Nicotiana. Bioinformatic analysis identified resistance gene analogs, major transcription factor families, and alkaloid transporter genes linked to plant defense.ConclusionsThis is the first report on the leaf transcriptomes of six wild Nicotiana species by Illumina paired-end sequencing and de novo assembly without a reference genome. These sequence resources hopefully will provide an opportunity for identifying genes involved in plant defense and several important quality traits in wild Nicotiana and will accelerate functional genomic studies and genetic improvement efforts of Nicotiana or other important Solanaceae crops in the future.Electronic supplementary materialThe online version of this article (doi:10.1186/s40709-016-0048-5) contains supplementary material, which is available to authorized users.

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Molecular diversity in the genus Nicotiana as revealed by randomly amplified polymorphic DNA

Cited by 8 publications

References 9 publications

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks inSolanumandNicotianaspecific databases

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks inSolanumandNicotianaspecific databases

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

Sequencing and characterization of leaf transcriptomes of six diploid Nicotiana species

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