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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

Phylogenetic tree based on the transcriptomes of the six wild Nicotiana species and S. lycopersicum. Phylogenetic tree was constructed using the neighbor-joining method with 1000 bootstraps. Bootstrap support is shown at the nodes
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Fig2: Phylogenetic tree based on the transcriptomes of the six wild Nicotiana species and S. lycopersicum. Phylogenetic tree was constructed using the neighbor-joining method with 1000 bootstraps. Bootstrap support is shown at the nodes

Mentions: Large-scale transcriptome data are a potential source of information for multigene phylogenetic analysis (the phylogenomic approach). In this study, 2491 single copy orthologs were identified and two phylogenetic trees were constructed by the neighbor-joining (NJ) method in Phylip [29] (Fig. 2) and maximum likelihood (ML) method in PhyML [30] (Additional file 7). The two phylogenies showed identical topologies. Earlier, Goodspeed placed N. glauca in the section Paniculatae based on evidence from morphology, cytology, biogeography, and crossing experiments [31]. Later, N. glauca was placed in the section Noctiflorae based on analysis of sequences from internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA) [3, 32]. Current phylogenetic analysis of the transcriptomes from six diploid species of Nicotiana with Solanum lycopersicum (tomato) as an outgroup supported the Noctiflorae, Paniculatae, and Tomentoase clades. The phylogenetic trees obtained in the current study placed N. glauca in the section Noctiflorae, supporting the results of previous works by Chase et al. [32]. and Knapp et al. [3].Fig. 2


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)

Phylogenetic tree based on the transcriptomes of the six wild Nicotiana species and S. lycopersicum. Phylogenetic tree was constructed using the neighbor-joining method with 1000 bootstraps. Bootstrap support is shown at the nodes
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Phylogenetic tree based on the transcriptomes of the six wild Nicotiana species and S. lycopersicum. Phylogenetic tree was constructed using the neighbor-joining method with 1000 bootstraps. Bootstrap support is shown at the nodes
Mentions: Large-scale transcriptome data are a potential source of information for multigene phylogenetic analysis (the phylogenomic approach). In this study, 2491 single copy orthologs were identified and two phylogenetic trees were constructed by the neighbor-joining (NJ) method in Phylip [29] (Fig. 2) and maximum likelihood (ML) method in PhyML [30] (Additional file 7). The two phylogenies showed identical topologies. Earlier, Goodspeed placed N. glauca in the section Paniculatae based on evidence from morphology, cytology, biogeography, and crossing experiments [31]. Later, N. glauca was placed in the section Noctiflorae based on analysis of sequences from internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA) [3, 32]. Current phylogenetic analysis of the transcriptomes from six diploid species of Nicotiana with Solanum lycopersicum (tomato) as an outgroup supported the Noctiflorae, Paniculatae, and Tomentoase clades. The phylogenetic trees obtained in the current study placed N. glauca in the section Noctiflorae, supporting the results of previous works by Chase et al. [32]. and Knapp et al. [3].Fig. 2

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