Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis

Abstract

Background: Nicotiana sylvestris and Nicotiana tomentosiformis are members of the Solanaceae family that includes tomato, potato, eggplant and pepper. These two Nicotiana species originate from South America and exhibit different alkaloid and diterpenoid production. N. sylvestris is cultivated largely as an ornamental plant and it has been used as a diploid model system for studies of terpenoid production, plastid engineering, and resistance to biotic and abiotic stress. N. sylvestris and N. tomentosiformis are considered to be modern descendants of the maternal and paternal donors that formed Nicotiana tabacum about 200,000 years ago through interspecific hybridization. Here we report the first genome-wide analysis of these two Nicotiana species.

Results: Draft genomes of N. sylvestris and N. tomentosiformis were assembled to 82.9% and 71.6% of their expected size respectively, with N50 sizes of about 80 kb. The repeat content was 72-75%, with a higher proportion of retrotransposons and copia-like long terminal repeats in N. tomentosiformis. The transcriptome assemblies showed that 44,000-53,000 transcripts were expressed in the roots, leaves or flowers. The key genes involved in terpenoid metabolism, alkaloid metabolism and heavy metal transport showed differential expression in the leaves, roots and flowers of N. sylvestris and N. tomentosiformis.

Conclusions: The reference genomes of N. sylvestris and N. tomentosiformis represent a significant contribution to the SOL100 initiative because, as members of the Nicotiana genus of Solanaceae, they strengthen the value of the already existing resources by providing additional comparative information, thereby helping to improve our understanding of plant metabolism and evolution.

Figure 1

Numbers of transcripts from the merged tissue assemblies with hits to UniProt plant sequences.

Figure 2

Percentage coverage of predicted ORFs from the merged transcript assemblies by homologs from UniProt. Hits were determined by BLAST searches. (a,b) The ORFs were derived from the transcripts from the N. sylvestris (a) and N. tomentosiformis (b) genome assemblies. Dots are indicating the percentage of coverage of the query and the reference for each BLAST hit. Histograms for the coverage of the query and reference show the categorized number of BLAST hits.

Figure 3

Clusters of orthologous genes from N. sylvestris, N. tomentosiformis, tomato and Arabidopsis. The genes for the predicted N. sylvestris and N. tomentosiformis ORFs are from the merged transcript assemblies. Tomato is a representative of Solanaceae and Arabidopsis is a representative eudicot.

Figure 4

Clusters of orthologous genes from the individual tissue and merged sample reads. The gene sequences are derived from RNA-seq reads. (a) The gene clusters for N. sylvestris. (b) The gene clusters for N. tomentosiformis.

Figure 5

Diagrammatic representation of heavy-metal transport and accumulation in Nicotiana leaves. Left circle: cadmium is transported by IRT from the environment in the root, and then by HMA into the phloem. Middle: NA and PCS transport cadmium from the root to the leaves. Right circle: in roots and leaves, cadmium enters cells, where it is transported to the vacuole by HMA, ABC or CAX. ABC also exports cadmium outside of the cell. ABC, ATP-binding cassette transporter; CAX, cation/proton exchanger; HMA, heavy metal ATPase; IRT, iron transporter protein; NA, nicotinamine synthase; PCS, phytochelatin synthase.

Figure 6

Key genes involved in the synthesis of nicotine and nornicotine alkaloids in Nicotiana leaves. The berberine bridge enzyme-like protein converts nicotinic acid and N-methylpyrrolinium cation into nicotine, and nicotine N-deaminase converts it further to nornicotine. AO, L-aspartate oxidase; BBL, berberine bridge enzyme-like protein; MPO, methyleputrescine oxidase; NND, nicotine N-demethylase; PMT, putrecine N-methyltransferase; QPT, quinolinate phosphoribosyltransferase; QS, quinolinate synthase.