The genome evolution and low-phosphorus adaptation in white lupin

Weifeng Xu,Qianwen Wang,Xing Li,Mehtab Muhammad Aslam,Feiyun Xu,Kang Zhang,Feng Cheng,Xin Zhang,Ying Li,Tianyu Xia,Wei Yuan,Rui Miao,Qian Zhang

doi:10.1038/s41467-020-14891-z

Weifeng Xu, Qianwen Wang + Show 11 more

Open Access

https://doi.org/10.1038/s41467-020-14891-z

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Abstract

White lupin (Lupinus albus) is a legume crop that develops cluster roots and has high phosphorus (P)-use efficiency (PUE) in low-P soils. Here, we assemble the genome of white lupin and find that it has evolved from a whole-genome triplication (WGT) event. We then decipher its diploid ancestral genome and reconstruct the three sub-genomes. Based on the results, we further reveal the sub-genome dominance and the genic expression of the different sub-genomes varying in relation to their transposable element (TE) density. The PUE genes in white lupin have been expanded through WGT as well as tandem and dispersed duplications. Furthermore, we characterize four main pathways for high PUE, which include carbon fixation, cluster root formation, soil-P remobilization, and cellular-P reuse. Among these, auxin modulation may be important for cluster root formation through involvement of potential genes LaABCG36s and LaABCG37s. These findings provide insights into the genome evolution and low-P adaptation of white lupin.

Highlights

White lupin (Lupinus albus) is a legume crop that develops cluster roots and has high phosphorus (P)-use efficiency (PUE) in low-P soils
We confirmed that the white lupin plant used for sequencing had 25 pairs of chromosomes using in situ hybridization (Supplementary Fig. 1)
For genes generated through whole-genome triplication (WGT), we found that Gene Ontology (GO) terms related to the phosphate biology process and root development were enriched in over-retained genes in both L. albus and L. angustifolius (Supplementary Data 3 and 4)

Summary

Introduction

White lupin (Lupinus albus) is a legume crop that develops cluster roots and has high phosphorus (P)-use efficiency (PUE) in low-P soils. Auxin modulation may be important for cluster root formation through involvement of potential genes LaABCG36s and LaABCG37s These findings provide insights into the genome evolution and low-P adaptation of white lupin. Transposable elements (TEs) have been shown to play a role in dominant expression of paralogous genes between sub-genomes in Brassica rapa and maize[12,13]. We use the long-read sequencing of PacBio technology combined with high-throughput chromatin capture (Hi-C) datasets, as well as mRNA-sequencing (mRNA-seq), comparative and evolutionary genomic analysis, pharmacology assays, genetic transformation, physiology, and biochemistry analyses to characterize the reference genome of white lupin and investigate its chromosomal evolution and the molecular basis of its adaptation to low-P availability

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