Wild tobacco genomes reveal the evolution of nicotine biosynthesis

Xu, Shuqing; Brockmoeller, Thomas; Navarro‐Quezada, Aura; Kuhl, Heiner; Gase, Klaus; Ling, Zhihao; Zhou, Wenwu; Kreitzer, Christoph; Stanke, Mario; Tang, Haibao; Lyons, Eric; Pandey, Priyanka; Pandey, Sarvesh; Timmermann, Bernd; Gaquerel, Emmanuel; Baldwin, Ian T.

doi:10.1101/107565

Cited by 43 publications

(60 citation statements)

References 48 publications

(57 reference statements)

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“…We amplified and sequenced the cDNA of IFR and CHAL among the seven Nicotiana species. Phylogenetic analyzes of the cDNA sequences of IFR and CHAL among these closely related species were consistent to the analysis based on the genomic sequences: NaIFR3 originated in the ancestor of N. attenuata and N. obtusifolia (~12.5MYA) 21 and NaCHAL3 occurs specifically in the clade of Petunioides (~9.1 MYA) 22 .…”

Section: Resultssupporting

confidence: 72%

Evolution of a novel and adaptive floral scent in wild tobacco

Guo

Lackus

Köllner

et al. 2019

Preprint

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1 Many plants emit diverse floral scents that mediate plant-environment interactions and 2 attain reproductive success. However, how plants evolve novel adaptive floral volatiles 3 remains unclear. Here, we show that in the wild tobacco, Nicotiana attenuata, a dominant 4species-specific floral volatile (benzyl acetone, BA) that attracts pollinators and deters 5 florivore is synthesized by phenylalanine ammonia-lyase 4 (NaPAL4), isoflavone reductase 3 6 (NaIFR3), and chalcone synthase 3 (NaCHAL3). Transient expression of NaFIR3 alone in N. 7 attenuata leaves is sufficient and necessary for ectopic foliar BA emissions, and the BA 8 emission level is increased by co-expressing NaIFR3 with NaPAL4 and NaCHAL3. 9 Independent changes in transcription in all three genes contributed to intraspecific variations 10 of floral BA emission. However, among species, the gain-of-expression in NaIFR3 resulted in 11 the biosynthesis of BA that was only found in N. attenuata. This study suggests that novel 12 metabolic pathways associated with adaptation can arise via re-configurations of gene 13 expression. 14

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Section: Resultssupporting

confidence: 72%

Evolution of a novel and adaptive floral scent in wild tobacco

Guo

Lackus

Köllner

et al. 2019

Preprint

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“…Previous studies have revealed a similar pattern of relatively recent Gypsy proliferation in other Solanaceae species, including a substantial excess of Gypsy elements (12 fold more frequent than Copia elements) within the hot pepper genome compared to domestic tomato (Kim et al 2014). Similarly, genome size variation scales with variation in the number of Gypsy repeats among four Nicotiana species (Xu et al 2017). In contrast, within Solanum the larger genome size of wild species S. pennellii compared to domesticated tomato is associated with a recent proliferation of Copia-like elements (Bolger et al 2014).…”

Section: Transposable Elements Contribute To Genome Size Evolution Acmentioning

confidence: 56%

Genome sequence ofJaltomataaddresses rapid reproductive trait evolution and enhances comparative genomics in the hyper-diverse Solanaceae

Kostyun

Moyle

2018

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Within the economically important plant family Solanaceae, Jaltomata is a rapidly evolving genus that has extensive diversity in flower size and shape, as well as fruit and nectar color, among its ~80 species. Here we report the whole-genome sequencing, assembly, and annotation, of one representative species (Jaltomata sinuosa) from this genus. Combining PacBio long-reads (25X) and Illumina short-reads (148X) achieved an assembly of approximately 1.45 Gb, spanning ~96% of the estimated genome. 96% of curated single-copy orthologs in plants were detected in the assembly, supporting a high level of completeness of the genome. Similar to other Solanaceous species, repetitive elements made up a large fraction (~80%) of the genome, with the most recently active element, Gypsy, expanding across the genome in the last 1-2 million years.Computational gene prediction, in conjunction with a merged transcriptome dataset from 11 tissues, identified 34725 protein-coding genes. Comparative phylogenetic analyses with six other sequenced Solanaceae species determined that Jaltomata is most likely sister to Solanum, although a large fraction of gene trees supported a conflicting bipartition consistent with substantial introgression between Jaltomata and Capsicum after these species split. We also identified gene family dynamics specific to Jaltomata, including expansion of gene families potentially involved in novel reproductive trait development, and loss of gene families that accompanied the loss of self-incompatibility.This high-quality genome will facilitate studies of phenotypic diversification in this rapidly radiating group, and provide a new point of comparison for broader analyses of genomic evolution across the Solanaceae.

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“…To generate the input dataset, we selected the predicted protein sequences from recently sequenced Nicotiana species (Sierro et al, 2013(Sierro et al, , 2014Xu et al, 2017) generated using the NCBI Eukaryotic Genome Annotation Pipeline ( Figure 1) and used CD-HIT at a 95% identity cut-off to reduce the redundancy and remove partial sequences (Figure 1, Step 1). The resulting dataset, Nicotiana_db95, contains 85,453 protein-encoding sequences from various Nicotiana species.…”

Section: Re-annotation Of Gene-models In the N Benthamiana Genome Asmentioning

confidence: 99%

Homology-guided re-annotation improves the gene models of the alloploid Nicotiana benthamiana

Kourelis

Kaschani

et al. 2018

Preprint

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Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft assemblies appear incorrect. Here we present an improved re-annotation of the Niben1.0.1 draft genome assembly guided by gene models from other Nicotiana species. This approach overcomes problems caused by mis-annotated exon-intron boundaries and mis-assigned short read transcripts to homeologs in polyploid genomes. With an estimated 98.1% completeness; only 53,411 protein-encoding genes; and improved protein lengths and functional annotations, this new predicted proteome is better than the preceding proteome annotations. This dataset is more sensitive and accurate in proteomics applications, clarifying the detection by activity-based proteomics of proteins that were previously mis-annotated to be inactive. Phylogenetic analysis of the subtilase family of hydrolases reveal a pseudogenisation of likely homeologs, associated with a contraction of the functional genome in this alloploid plant species. We use this gene annotation to assign extracellular proteins in comparison to a total leaf proteome, to display the enrichment of hydrolases in the apoplast.

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Wild tobacco genomes reveal the evolution of nicotine biosynthesis

Cited by 43 publications

References 48 publications

Evolution of a novel and adaptive floral scent in wild tobacco

Evolution of a novel and adaptive floral scent in wild tobacco

Genome sequence ofJaltomataaddresses rapid reproductive trait evolution and enhances comparative genomics in the hyper-diverse Solanaceae

Homology-guided re-annotation improves the gene models of the alloploid Nicotiana benthamiana

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