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

SUMMARY 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.

The NLRomes of Zea mays NAM founder lines and Zea luxurians display presence–absence variation, integrated domain diversity, and mobility

“…Although we found significantly more NLRs in the Z. luxurians accession, the majority clustered closely with NAM line NLRs and the increased count was partially driven by high heterozygosity (Table S3). The recently released pangenome of lupin revealed an even lower number of NLRs (67) and dramatically lower levels of diversity, with nearly all NLR genes fixed in both breeding lines and wild accessions (Garg et al, 2022). How maize and other species with relatively low NLR counts cope with disease pressure despite dramatically lower NLR counts and diversity requires additional investigation.…”

“…The NLR complements of dozens of plant species have been identified thus far, and recent work by Van de Weyer et al revealed a nearly complete picture of the Arabidopsis NLRome, representing a significant step forward in the understanding of intraspecific NLR diversity (Van de Weyer et al, 2019 ). Since this initial work in Arabidopsis , the pangenomes of numerous plant species have been sequenced, leading to a much more complete picture of the total NLR complement of many species, including rice, barley, wheat, rapeseed, soybean, pigeon pea, lupin, and a number of other important crops and wild relatives (Dolatabadian et al, 2020 ; Garg et al, 2022 ; Jayakodi et al, 2020 ; Li et al, 2021 ; Liu, Du, et al, 2020 ; Shang et al, 2022 ; Walkowiak et al, 2020 ; Zhao et al, 2020 ). Such work has revealed extremely variable numbers of NLRs and levels of NLR diversity, with species NLR counts ranging from a few dozen to thousands per line.…”

Proteomic analysis revealed that the oomyceticide phosphite exhibits multi-modal action in an oomycete pathosystem

“…Our study aims to deconvolute the biochemistry of this system and gain a clearer insight into the pathways altered by phosphite. L. angustifolius (lupin) is used as a model as it is susceptible to P. cinnamomi infection, it has a published genome sequence required for proteomics work, and it grows rapidly compared to native and horticultural P. cinnamomi hosts 39,50 .…”

“…The proteomes between phosphite-treated MU94-48 and CPSM366 were compared to simultaneously gain insight into the effects of phosphite on sensitive P. cinnamomi and understand the differences between phosphite sensitivity and tolerance. The mass spectra obtained from the in planta assay were matched to the L. angustifolius genome consisting of 39,339 protein-coding sequences 39 . For protein identification, 1 or more 95% confidence peptides were used.…”

The unexplored diversity of wild lupins provides rich genomic resources and insights into lupin evolution

“…Whole-genome sequences have been published for two lupin crops, namely L. angustifolius (Hane et al 2017) and L. albus (Hufnagel et al 2020) (Hufnagel et al 2020) providing some insight into lupin genome structure, diversity and evolution, but information from wild relatives is needed to take full advantage of lupin genetic resources. The genetic diversity of lupins has been highlighted by chromosome number and genome size (Naganowska et al 2003, Susek et al 2016 as well as epigenomic (Susek et al 2017) and phylogenetic analysis (Aïnouche and Bayer 2004), and more recently the development of pan-genomes for L. albus (Hufnagel et al 2021) and L. angustifolius (Garg et al 2022).…”