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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

Comparison of ORF length between hit and no hit proteins in NR database. For N. glauca, N. noctiflora, N. cordifolia, N. knightiana, N. setchellii, N. tomentosiformis, longer ORFs were more likely to have BLASTp homologs in protein database
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Fig1: Comparison of ORF length between hit and no hit proteins in NR database. For N. glauca, N. noctiflora, N. cordifolia, N. knightiana, N. setchellii, N. tomentosiformis, longer ORFs were more likely to have BLASTp homologs in protein database

Mentions: Besides, a higher (>90 %) match rate in the NR database was shown by ORFs with >200 aa in length, whereas ORFs shorter than 200 aa exhibited a lower match rate (Fig. 1). An almost similar match rate pattern was observed in the annotation for Swiss-Prot database (Additional file 4).Fig. 1


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)

Comparison of ORF length between hit and no hit proteins in NR database. For N. glauca, N. noctiflora, N. cordifolia, N. knightiana, N. setchellii, N. tomentosiformis, longer ORFs were more likely to have BLASTp homologs in protein database
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig1: Comparison of ORF length between hit and no hit proteins in NR database. For N. glauca, N. noctiflora, N. cordifolia, N. knightiana, N. setchellii, N. tomentosiformis, longer ORFs were more likely to have BLASTp homologs in protein database
Mentions: Besides, a higher (>90 %) match rate in the NR database was shown by ORFs with >200 aa in length, whereas ORFs shorter than 200 aa exhibited a lower match rate (Fig. 1). An almost similar match rate pattern was observed in the annotation for Swiss-Prot database (Additional file 4).Fig. 1

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