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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

Histogram presentation of GO classification. The GO annotation results from the ORFs of six Nicotiana species are summarized in three main categories: biological process, cellular component and molecular function. The right y-axis indicates the number of genes in a category. The left y-axis indicates the percentage of a specific category of genes in that main category
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Fig4: Histogram presentation of GO classification. The GO annotation results from the ORFs of six Nicotiana species are summarized in three main categories: biological process, cellular component and molecular function. The right y-axis indicates the number of genes in a category. The left y-axis indicates the percentage of a specific category of genes in that main category

Mentions: Gene ontology (GO) [35] provides ontologies of defined terms representing gene product properties and describes gene products in terms of their associated biological processes, cellular components, and molecular functions. In this study, 36,508, 35,846, 43,279, 20,370, 30,079 and 27,592 annotated ORFs corresponding to N. glauca, N. noctiflora, N. cordifolia, N. knightiana, N. setchellii, and N. tomentosiformis, respectively, were assigned to one or more sub-categories of GO terms. The GO terms of the subcategories are presented in Fig. 4. For the six wild Nicotiana species, among these groups, genes involved in “metabolic process” and “cellular process” were the most highly represented in the biological process category. Genes involved in other important biological processes such as biological regulation, response to stimulus, and anatomical structure formation process were also identified. Furthermore, a relatively large number of sequences were found to be involved in the metabolism of pigmentation. Within the cellular components category, “cell” and “cell parts” were the most highly represented groups. The molecular function category comprised proteins involved in “binding” and “catalytic activity”. These six wild Nicotiana transcriptomes shared broad similarities in the three main categories and many subcategories except viral reproduction.Fig. 4


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)

Histogram presentation of GO classification. The GO annotation results from the ORFs of six Nicotiana species are summarized in three main categories: biological process, cellular component and molecular function. The right y-axis indicates the number of genes in a category. The left y-axis indicates the percentage of a specific category of genes in that main category
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig4: Histogram presentation of GO classification. The GO annotation results from the ORFs of six Nicotiana species are summarized in three main categories: biological process, cellular component and molecular function. The right y-axis indicates the number of genes in a category. The left y-axis indicates the percentage of a specific category of genes in that main category
Mentions: Gene ontology (GO) [35] provides ontologies of defined terms representing gene product properties and describes gene products in terms of their associated biological processes, cellular components, and molecular functions. In this study, 36,508, 35,846, 43,279, 20,370, 30,079 and 27,592 annotated ORFs corresponding to N. glauca, N. noctiflora, N. cordifolia, N. knightiana, N. setchellii, and N. tomentosiformis, respectively, were assigned to one or more sub-categories of GO terms. The GO terms of the subcategories are presented in Fig. 4. For the six wild Nicotiana species, among these groups, genes involved in “metabolic process” and “cellular process” were the most highly represented in the biological process category. Genes involved in other important biological processes such as biological regulation, response to stimulus, and anatomical structure formation process were also identified. Furthermore, a relatively large number of sequences were found to be involved in the metabolism of pigmentation. Within the cellular components category, “cell” and “cell parts” were the most highly represented groups. The molecular function category comprised proteins involved in “binding” and “catalytic activity”. These six wild Nicotiana transcriptomes shared broad similarities in the three main categories and many subcategories except viral reproduction.Fig. 4

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