Peanut (Arachis hypogaea)
Although appearing as and referred to as a nut, peanut is actually the underground pod of a legume rather than a true nut! Read more about peanuts on PeanutBase website.
Image by Pexels from Pixabay [Pixabay License]
Chromosome-length genome assembly
Download the arahy.Tifrunner.gnm2.J5K5.genome_main.fna.gz file containing the chromosome-length (2n=4x=40) assembly of the peanut genome. All modifications with respect to the previous assembly version are annotated in the arahy.Tifrunner.gnm2.J5K5.genome_main.assembly file. Some basic stats associated with the new reference, arahy.Tifrunner.gnm2.J5K5.genome_main, are listed below. The full data release can be explored here.
Contig length (bp) | Number of contigs | Contig N50 (bp) | Longest contig (bp) |
|---|---|---|---|
2,553,632,056 | 4,139 | 1,493,114 | 9,487,789 |
Scaffold length (bp) | Number of scaffolds | Scaffold N50 (bp) | Longest scaffold (bp) |
|---|---|---|---|
2,557,413,415 | 442 | 135,027,066 | 160,028,458 |
Draft
The chromosome-length genome assembly was generated in collaboration with the International Peanut Genome Initiative. For details, see our paper below.
Bertioli D.J., Jenkins J., Clevenger J., Dudchenko O., Gao D., Seijo D., Leal-Bertioli S.C.M., Ren L., Farmer A.D., Pandey M.K., Samoluk S.S., Abernathy B., Agarwal G., Ballen-Taborda C., Cameron C., Campbell J., Chavarro C., Chitikineni A., Chu Y., Dash S., El Baidouri M., Guo B., Huang W., Do Kim K., Korani W., Lanciano S., Lui C.G., Mirouze M., Moretzsohn M.C., Pham M., Shin J.H., Shirasawa K., Sinharoy S., Sreedasyam A., Weeks N.T., Zhang X., Zheng Z., Sun Z., Froenicke L., Aiden E.L., Michelmore R., Varshney R.K., Holbrook C.C., Cannon E.K.S., Scheffler B.E., Grimwood J., Ozias-Akins P., Cannon S.B., Jackson S.A., Schmutz J, 2019. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nat. Genet. 51, https://doi.org/10.1038/s41588-019-0405-z.
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
Leaves for in situ Hi-C preparation was obtained from Baozhu Guo (USDA) and Rajeev Varshney (ICRISAT).
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). (Please note that the interactive figures are scaled 1:2.) 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 acknowledge the following work.
Bertioli D.J., Jenkins J., Clevenger J., Dudchenko O., Gao D., Seijo D., Leal-Bertioli S.C.M., Ren L., Farmer A.D., Pandey M.K., Samoluk S.S., Abernathy B., Agarwal G., Ballen-Taborda C., Cameron C., Campbell J., Chavarro C., Chitikineni A., Chu Y., Dash S., El Baidouri M., Guo B., Huang W., Do Kim K., Korani W., Lanciano S., Lui C.G., Mirouze M., Moretzsohn M.C., Pham M., Shin J.H., Shirasawa K., Sinharoy S., Sreedasyam A., Weeks N.T., Zhang X., Zheng Z., Sun Z., Froenicke L., Aiden E.L., Michelmore R., Varshney R.K., Holbrook C.C., Cannon E.K.S., Scheffler B.E., Grimwood J., Ozias-Akins P., Cannon S.B., Jackson S.A., Schmutz J, 2019. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nat. Genet. 51, https://doi.org/10.1038/s41588-019-0405-z.
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.