Narrowleaf lupin cv. Tanjil (Lupinus angustifolius cv. Tanjil)

Narrowleaf lupin is high in protein. In Australia, narrowleaf lupin is used to produce feed for livestock. The cultivar Tanjil was released in 1998 and was a dominant variety for many years owing to its superior disease-resistance characteristics. Read more about Narrowleaf lupin cv. Tanjil on Feedepedia website.

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Photo Description - Narrow-leafed lupin (Lupinus angustifolius) cultivar Coyote in a field near Northam in 2021. Photo Credits and acknowledgements - Lars Kamphuis

Chromosome-length genome assembly

Download the Lupin_pacbio_HiC.fasta.gz file containing the chromosome-length (2n=40) assembly of the Narrowleaf lupin cv. Tanjil genome. All modifications with respect to the draft (see below) are annotated in the Lupin_pacbio_HiC.assembly file. Some basic stats associated with the new reference, Lupin_pacbio_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
652,980,617
2,920
2,641,441
14,146,091
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
653,266,117
2,349
30,711,064
45,676,429
Draft

The chromosome-length genome assembly is based on the draft assembly Lupin_pacbio, credited below.

Garg, G., Kamphuis, L.G., Bayer, P.E., Kaur, P., Dudchenko, O., Taylor, C.M., Frick, K.M., Foley, R.C., Gao, L.-L., Lieberman Aiden, E., Edwards, D., Singh, K.B., 2022. A pan-genome and chromosome-length reference genome of narrow-leafed lupin (Lupinus angustifolius) reveals genomic diversity and insights into key industry and biological traits. Plant J. n/a. https://doi.org/10.1111/tpj.15885.

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 sample for in situ Hi-C preparation was obtained from Lars Kemphius (Curtin University/CSIRO).

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.

Garg, G., Kamphuis, L.G., Bayer, P.E., Kaur, P., Dudchenko, O., Taylor, C.M., Frick, K.M., Foley, R.C., Gao, L.-L., Lieberman Aiden, E., Edwards, D., Singh, K.B., 2022. A pan-genome and chromosome-length reference genome of narrow-leafed lupin (Lupinus angustifolius) reveals genomic diversity and insights into key industry and biological traits. Plant J. n/a. https://doi.org/10.1111/tpj.15885.

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.