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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

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. / Garg, Gagan; Kamphuis, Lars G.; Bayer, Philipp E.; Kaur, Parwinder; Dudchenko, Olga; Taylor, Candy M.; Frick, Karen M.; Foley, Rhonda C.; Gao, Ling Ling; Aiden, Erez Lieberman; Edwards, David; Singh, Karam B.

In: Plant Journal, Vol. 111, No. 5, 2022, p. 1252-1266.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Garg, G, Kamphuis, LG, Bayer, PE, Kaur, P, Dudchenko, O, Taylor, CM, Frick, KM, Foley, RC, Gao, LL, Aiden, EL, Edwards, D & Singh, KB 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 Journal, vol. 111, no. 5, pp. 1252-1266. https://doi.org/10.1111/tpj.15885

APA

Garg, G., Kamphuis, L. G., Bayer, P. E., Kaur, P., Dudchenko, O., Taylor, C. M., Frick, K. M., Foley, R. C., Gao, L. L., Aiden, E. L., 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 Journal, 111(5), 1252-1266. https://doi.org/10.1111/tpj.15885

Vancouver

Garg G, Kamphuis LG, Bayer PE, Kaur P, Dudchenko O, Taylor CM et al. 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 Journal. 2022;111(5):1252-1266. https://doi.org/10.1111/tpj.15885

Author

Garg, Gagan ; Kamphuis, Lars G. ; Bayer, Philipp E. ; Kaur, Parwinder ; Dudchenko, Olga ; Taylor, Candy M. ; Frick, Karen M. ; Foley, Rhonda C. ; Gao, Ling Ling ; Aiden, Erez Lieberman ; Edwards, David ; Singh, Karam B. / 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. In: Plant Journal. 2022 ; Vol. 111, No. 5. pp. 1252-1266.

Bibtex

@article{446f6c962dbc42bfb9448f7a12fa0e23,
title = "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",
abstract = "Narrow-leafed lupin (NLL; Lupinus angustifolius) is a key rotational crop for sustainable farming systems, whose grain is high in protein content. It is a gluten-free, non-genetically modified, alternative protein source to soybean (Glycine max) and as such has gained interest as a human food ingredient. Here, we present a chromosome-length reference genome for the species and a pan-genome assembly comprising 55 NLL lines, including Australian and European cultivars, breeding lines and wild accessions. We present the core and variable genes for the species and report on the absence of essential mycorrhizal associated genes. The genome and pan-genomes of NLL and its close relative white lupin (Lupinus albus) are compared. Furthermore, we provide additional evidence supporting LaRAP2-7 as the key alkaloid regulatory gene for NLL and demonstrate the NLL genome is underrepresented in classical NLR disease resistance genes compared to other sequenced legume species. The NLL genomic resources generated here coupled with previously generated RNA sequencing datasets provide new opportunities to fast-track lupin crop improvement.",
keywords = "Genistoids, legume, pan-genome assembly, quinolizidine alkaloids, resistance genes, seed storage proteins",
author = "Gagan Garg and Kamphuis, {Lars G.} and Bayer, {Philipp E.} and Parwinder Kaur and Olga Dudchenko and Taylor, {Candy M.} and Frick, {Karen M.} and Foley, {Rhonda C.} and Gao, {Ling Ling} and Aiden, {Erez Lieberman} and David Edwards and Singh, {Karam B.}",
note = "Publisher Copyright: {\textcopyright} 2022 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.",
year = "2022",
doi = "10.1111/tpj.15885",
language = "English",
volume = "111",
pages = "1252--1266",
journal = "Plant Journal",
issn = "0960-7412",
publisher = "Wiley-Blackwell",
number = "5",

}

RIS

TY - JOUR

T1 - 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

AU - Garg, Gagan

AU - Kamphuis, Lars G.

AU - Bayer, Philipp E.

AU - Kaur, Parwinder

AU - Dudchenko, Olga

AU - Taylor, Candy M.

AU - Frick, Karen M.

AU - Foley, Rhonda C.

AU - Gao, Ling Ling

AU - Aiden, Erez Lieberman

AU - Edwards, David

AU - Singh, Karam B.

N1 - Publisher Copyright: © 2022 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

PY - 2022

Y1 - 2022

N2 - Narrow-leafed lupin (NLL; Lupinus angustifolius) is a key rotational crop for sustainable farming systems, whose grain is high in protein content. It is a gluten-free, non-genetically modified, alternative protein source to soybean (Glycine max) and as such has gained interest as a human food ingredient. Here, we present a chromosome-length reference genome for the species and a pan-genome assembly comprising 55 NLL lines, including Australian and European cultivars, breeding lines and wild accessions. We present the core and variable genes for the species and report on the absence of essential mycorrhizal associated genes. The genome and pan-genomes of NLL and its close relative white lupin (Lupinus albus) are compared. Furthermore, we provide additional evidence supporting LaRAP2-7 as the key alkaloid regulatory gene for NLL and demonstrate the NLL genome is underrepresented in classical NLR disease resistance genes compared to other sequenced legume species. The NLL genomic resources generated here coupled with previously generated RNA sequencing datasets provide new opportunities to fast-track lupin crop improvement.

AB - Narrow-leafed lupin (NLL; Lupinus angustifolius) is a key rotational crop for sustainable farming systems, whose grain is high in protein content. It is a gluten-free, non-genetically modified, alternative protein source to soybean (Glycine max) and as such has gained interest as a human food ingredient. Here, we present a chromosome-length reference genome for the species and a pan-genome assembly comprising 55 NLL lines, including Australian and European cultivars, breeding lines and wild accessions. We present the core and variable genes for the species and report on the absence of essential mycorrhizal associated genes. The genome and pan-genomes of NLL and its close relative white lupin (Lupinus albus) are compared. Furthermore, we provide additional evidence supporting LaRAP2-7 as the key alkaloid regulatory gene for NLL and demonstrate the NLL genome is underrepresented in classical NLR disease resistance genes compared to other sequenced legume species. The NLL genomic resources generated here coupled with previously generated RNA sequencing datasets provide new opportunities to fast-track lupin crop improvement.

KW - Genistoids

KW - legume

KW - pan-genome assembly

KW - quinolizidine alkaloids

KW - resistance genes

KW - seed storage proteins

U2 - 10.1111/tpj.15885

DO - 10.1111/tpj.15885

M3 - Journal article

C2 - 35779281

AN - SCOPUS:85135845441

VL - 111

SP - 1252

EP - 1266

JO - Plant Journal

JF - Plant Journal

SN - 0960-7412

IS - 5

ER -

ID: 318543058