Pigeon pea (Cajanus cajan)

India produces the bulk supply of the worlds pigeon peas with approximately 63% of total production grown there! Read more about pigeon peas on Wikipedia.

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Cajanus cajan (Pigeon pea, dahl). Seedpods at Old macadamia nut orchards Waiehu, Maui, Hawaii, by Forrest and Kim Starr, via flickr.com [CC BY 2.0]

Chromosome-length genome assembly

Download the C.cajan_V1.0_HiC.fasta.gz file containing the chromosome-length (2n=22) assembly of the pigeon pea genome. All modifications with respect to the draft (see below) are annotated in the C.cajan_V1.0_HiC.assembly file. Some basic stats associated with the new reference, C.cajan_V1.0_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
558,535,405
76,499
21,835
185,389
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
594,802,861
35,727
53,895,704
62,816,551
Draft

The chromosome-length genome assembly is based on the draft assembly C.cajan_V1.0 (GCF_000340665.1), credited below.

Varshney, R.K., Chen, W., Li, Y., Bharti, A.K., Saxena, R.K., Schlueter, J.A., Donoghue, M.T.A., Azam, S., Fan, G., Whaley, A.M., Farmer, A.D., Sheridan, J., Iwata, A., Tuteja, R., Penmetsa, R.V., Wu, W., Upadhyaya, H.D., Yang, S.-P., Shah, T., Saxena, K.B., Michael, T., McCombie, W.R., Yang, B., Zhang, G., Yang, H., Wang, J., Spillane, C., Cook, D.R., May, G.D., Xu, X., Jackson, S.A., 2012. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat. Biotechnol. 30, 83-89. https://doi.org/10.1038/nbt.2022.

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 leaves cv. asha sample for in situ Hi-C preparation was obtained from Eric Bishop-Von Wettberg (Florida International University), Rajeev Varshey (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). 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.

Varshney, R.K., Chen, W., Li, Y., Bharti, A.K., Saxena, R.K., Schlueter, J.A., Donoghue, M.T.A., Azam, S., Fan, G., Whaley, A.M., Farmer, A.D., Sheridan, J., Iwata, A., Tuteja, R., Penmetsa, R.V., Wu, W., Upadhyaya, H.D., Yang, S.-P., Shah, T., Saxena, K.B., Michael, T., McCombie, W.R., Yang, B., Zhang, G., Yang, H., Wang, J., Spillane, C., Cook, D.R., May, G.D., Xu, X., Jackson, S.A., 2012. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat. Biotechnol. 30, 83-89. https://doi.org/10.1038/nbt.2022.

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.