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Sequencing and characterization of leaf transcriptomes of six diploid Nicotiana species.

Long N, Ren X, Xiang Z, Wan W, Dong Y - J Biol Res (Thessalon) (2016)

Bottom Line: 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.Bioinformatic analysis identified resistance gene analogs, major transcription factor families, and alkaloid transporter genes linked to plant defense.This 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.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Life Science and Technology, Kunming University of Science and Technology, South Jingming Road No.727, Kunming, 650500 Yunnan China.

ABSTRACT

Background: Nicotiana 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.

Results: Whole 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.

Conclusions: This 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.

No MeSH data available.


Related in: MedlinePlus

Pathway assignment based on KEGG from the six wild Nicotiana species. a Classification based on metabolism categories; b classification based on secondary metabolism categories
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Fig3: Pathway assignment based on KEGG from the six wild Nicotiana species. a Classification based on metabolism categories; b classification based on secondary metabolism categories

Mentions: ORFs of six wild Nicotiana species were compared with KEGG (Kyoto Encyclopedia of Genes and Genomes) database using BLASTp with an e-value less than 10−5, and the corresponding pathways were established. For the six species, 55.24–60.12 % of ORFs were successfully annotated to KEGG pathways (Table 2). Genes within the same pathway usually cooperate with each other to exercise their biological function, and hence pathway-based analysis contributes to the exploration of biological functions and interactions of genes [33]. The sequence annotation in KEGG largely contained metabolic pathways of major biomolecules such as carbohydrates, amino acids, lipids, nucleotides, etc. (Fig. 3a). The metabolic pathways with most representation by proteins were those of carbohydrate metabolism and amino acid metabolism. In the secondary metabolism, for N. glauca, N. noctiflora, N. cordifolia, N. knightiana, N. setchellii, N. tomentosiformis, 687, 817, 1064, 518, 779 and 677 proteins were classified into 14 subcategories, respectively (Fig. 3b). Among them, the cluster for “Phenylpropanoid biosynthesis” represents the largest group followed by “Stilbenoid, diarylheptanoid and gingerol biosynthesis”. The phenypropanoid pathway is often considered to be involved in plant resistance [34]. Flavonoids and glucosinolates are secondary metabolites that play important roles in protecting plants against pathogens. We also found unigenes involved in the biosynthesis of flavonoid and glucosinolate. The results will facilitate the discovery of novel genes involved in the specific metabolic pathways and secondary metabolic pathways and will provide a valuable resource for investigating the defense-related pathways in Nicotiana and other Solanaceae species.Fig. 3


Sequencing and characterization of leaf transcriptomes of six diploid Nicotiana species.

Long N, Ren X, Xiang Z, Wan W, Dong Y - J Biol Res (Thessalon) (2016)

Pathway assignment based on KEGG from the six wild Nicotiana species. a Classification based on metabolism categories; b classification based on secondary metabolism categories
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4835900&req=5

Fig3: Pathway assignment based on KEGG from the six wild Nicotiana species. a Classification based on metabolism categories; b classification based on secondary metabolism categories
Mentions: ORFs of six wild Nicotiana species were compared with KEGG (Kyoto Encyclopedia of Genes and Genomes) database using BLASTp with an e-value less than 10−5, and the corresponding pathways were established. For the six species, 55.24–60.12 % of ORFs were successfully annotated to KEGG pathways (Table 2). Genes within the same pathway usually cooperate with each other to exercise their biological function, and hence pathway-based analysis contributes to the exploration of biological functions and interactions of genes [33]. The sequence annotation in KEGG largely contained metabolic pathways of major biomolecules such as carbohydrates, amino acids, lipids, nucleotides, etc. (Fig. 3a). The metabolic pathways with most representation by proteins were those of carbohydrate metabolism and amino acid metabolism. In the secondary metabolism, for N. glauca, N. noctiflora, N. cordifolia, N. knightiana, N. setchellii, N. tomentosiformis, 687, 817, 1064, 518, 779 and 677 proteins were classified into 14 subcategories, respectively (Fig. 3b). Among them, the cluster for “Phenylpropanoid biosynthesis” represents the largest group followed by “Stilbenoid, diarylheptanoid and gingerol biosynthesis”. The phenypropanoid pathway is often considered to be involved in plant resistance [34]. Flavonoids and glucosinolates are secondary metabolites that play important roles in protecting plants against pathogens. We also found unigenes involved in the biosynthesis of flavonoid and glucosinolate. The results will facilitate the discovery of novel genes involved in the specific metabolic pathways and secondary metabolic pathways and will provide a valuable resource for investigating the defense-related pathways in Nicotiana and other Solanaceae species.Fig. 3

Bottom Line: 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.Bioinformatic analysis identified resistance gene analogs, major transcription factor families, and alkaloid transporter genes linked to plant defense.This 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.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Life Science and Technology, Kunming University of Science and Technology, South Jingming Road No.727, Kunming, 650500 Yunnan China.

ABSTRACT

Background: Nicotiana 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.

Results: Whole 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.

Conclusions: This 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.

No MeSH data available.


Related in: MedlinePlus