Large white petunia (Petunia axillaris)
Petunias were named for... tobacco! In 1803, the French botanist Antoine Laurent de Jussieu named the genus Petunia because the plant was a close relative of tobacco, at that time called "petun" in France. Read more about large white petunias on Laidback Gardner website.
Petunia axillaris, photo by Dick Culbert, from flickr.com [Attribution 2.0 Generic (CC BY 2.0)]
Chromosome-length genome assembly
Download the Petunia_axillaris_v1.6.2_genome_HiC.fasta.gz file containing the chromosome-length (2n=14) assembly of the large white petunia genome. All modifications with respect to the draft (see below) are annotated in the Petunia_axillaris_v1.6.2_genome_HiC.assembly file. Some basic stats associated with the new reference, Petunia_axillaris_v1.6.2_genome_HiC, are listed below. The full data release can be explored here.
Contig length (bp) | Number of contigs | Contig N50 (bp) | Longest contig (bp) |
|---|---|---|---|
1,217,958,452 | 217,140 | 24,514 | 238,434 |
Scaffold length (bp) | Number of scaffolds | Scaffold N50 (bp) | Longest scaffold (bp) |
|---|---|---|---|
1,261,744,291 | 89,762 | 138,298,383 | 189,397,759 |
Draft
The chromosome-length genome assembly is based on the draft assembly Petunia_axillaris_v1.6.2_genome, credited below.
Bombarely, Aureliano, Michel Moser, Avichai Amrad, Manzhu Bao, Laure Bapaume, Cornelius S. Barry, Mattijs Bliek, et al. 2016. "Insight into the Evolution of the Solanaceae from the Parental Genomes of Petunia Hybrida." Nature Plants 2 (6): 16074. https://doi.org/10.1038/nplants.2016.74.
Method
3D Assembly was performed using 3D-DNA pipeline (Dudchenko et al., Science, 2017). The genome was reviewed using Juicebox Assembly Tools (Dudchenko et al., bioRxiv, 2018). See Methods for more information.
Hi-C sample
The leaf samples for in situ Hi-C preparation was provided to us by Michel Moser and Cris Kuhlemeier at Universitat Bern and Bonnie Bartel at Rice University.
Hi-C Contact maps
Hi-C data was aligned to the draft reference using Juicer (Durand, Shamim et al., Cell Systems, 2016), and contact maps visualizing the alignments with respect to the draft and the new reference were built using 3D-DNA (Dudchenko et al., Science, 2017). The contact maps can be explored below via Juicebox.js interactive tool (Robinson et al., Cell Systems, 2018). To explore the assembly in greater detail, please download the .hic and .assembly files from the data release folder and use Juicebox Assembly Tools (Dudchenko et al., bioRxiv, 2018).
References
If you use this genome assembly in your research, please check that the conditions of use associated with the draft permit it, and acknowledge the following work.
Bombarely, Aureliano, Michel Moser, Avichai Amrad, Manzhu Bao, Laure Bapaume, Cornelius S. Barry, Mattijs Bliek, et al. 2016. "Insight into the Evolution of the Solanaceae from the Parental Genomes of Petunia Hybrida." Nature Plants 2 (6): 16074. https://doi.org/10.1038/nplants.2016.74.
Dudchenko, O., Batra, S.S., Omer, A.D., Nyquist, S.K., Hoeger, M., Durand, N.C., Shamim, M.S., Machol, I., Lander, E.S., Aiden, A.P., Aiden, E.L., 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95. https://doi.org/10.1126/science.aal3327.
Dudchenko, O., Shamim, M.S., Batra, S., Durand, N.C., Musial, N.T., Mostofa, R., Pham, M., Hilaire, B.G.S., Yao, W., Stamenova, E., Hoeger, M., Nyquist, S.K., Korchina, V., Pletch, K., Flanagan, J.P., Tomaszewicz, A., McAloose, D., Estrada, C.P., Novak, B.J., Omer, A.D., Aiden, E.L., 2018. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. bioRxiv 254797. https://doi.org/10.1101/254797.
Disclaimer
This is a work in progress. If you notice any discrepancies in the map or have data that confirms or contradicts the suggested reference, please email us at thednazoo@gmail.com or leave a comment on the Forum.