Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

The Genome of Chenopodium quinoa

Construction of chromosome-level assembly is a vital step in achieving the goal of a 'Platinum' genome, but it remains a major challenge to assemble and anchor sequences to chromosomes in autopolyploid or highly heterozygous genomes. High-throughput chromosome conformation capture (Hi-C) technology serves as a robust tool to dramatically advance chromosome scaffolding; however, existing approaches are mostly designed for diploid genomes and often with the aim of reconstructing a haploid representation, thereby having limited power to reconstruct chromosomes for autopolyploid genomes. We developed a novel algorithm (ALLHiC) that is capable of building allele-aware, chromosomal-scale assembly for autopolyploid genomes using Hi-C paired-end reads with innovative 'prune' and 'optimize' steps. Application on simulated data showed that ALLHiC can phase allelic contigs and substantially improve ordering and orientation when compared to other mainstream Hi-C assemblers. We applied ALLHiC on an autotetraploid and an autooctoploid sugar-cane genome and successfully constructed the phased chromosomal-level assemblies, revealing allelic variations present in these two genomes. The ALLHiC pipeline enables de novo chromosome-level assembly of autopolyploid genomes, separating each allele. Haplotype chromosome-level assembly of allopolyploid and heterozygous diploid genomes can be achieved using ALLHiC, overcoming obstacles in assembling complex genomes.

Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data.

Designing Future Crops: Genomics-Assisted Breeding Comes of Age

Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. These advances have led to the development of new tools to facilitate crop improvement. The study of structural variation within species and the characterization of the pan-genome has revealed extensive genome content variation among individuals within a species that is paradigm shifting to crop genomics and improvement. Here, we review advances in crop genomics and how utilization of these tools is shifting in light of pan-genomes that are becoming available for many crop species.

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How the pan-genome is changing crop genomics and improvement

Polyploidy is a major force in plant evolution and speciation. In newly formed allopolyploids, pairing between related chromosomes from different subgenomes (homoeologous chromosomes) during meiosis is common. The initial stages of allopolyploid formation are characterized by a spectrum of saltational genomic and regulatory alterations that are responsible for evolutionary novelty. Here we highlight the possible effects and roles of recombination between homoeologous chromosomes during the early stages of allopolyploid stabilization. Homoeologous exchanges (HEs) have been reported in young allopolyploids from across the angiosperms. Although all lineages undergo karyotype change via chromosome rearrangements over time, the early generations after allopolyploid formation are predicted to show an accelerated rate of genomic change. HEs can also cause changes in allele dosage, genome-wide methylation patterns, and downstream phenotypes, and can hence be responsible for speciation and genome stabilization events. Additionally, we propose that fixation of duplication - deletion events resulting from HEs could lead to the production of genomes which appear to be a mix of autopolyploid and allopolyploid segments, sometimes termed "segmental allopolyploids." We discuss the implications of these findings for our understanding of the relationship between genome instability in novel polyploids and genome evolution.

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Homoeologous Exchanges, Segmental Allopolyploidy, and Polyploid Genome Evolution.

High oil and protein content make tetraploid peanut a leading oil and food legume. Here we report a high-quality peanut genome sequence, comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models. We characterize gene functional groups implicated in seed size evolution, seed oil content, disease resistance and symbiotic nitrogen fixation. The peanut B subgenome has more genes and general expression dominance, temporally associated with long-terminal-repeat expansion in the A subgenome that also raises questions about the A-genome progenitor. The polyploid genome provided insights into the evolution of Arachis hypogaea and other legume chromosomes. Resequencing of 52 accessions suggests that independent domestications formed peanut ecotypes. Whereas 0.42–0.47 million years ago (Ma) polyploidy constrained genetic variation, the peanut genome sequence aids mapping and candidate-gene discovery for traits such as seed size and color, foliar disease resistance and others, also providing a cornerstone for functional genomics and peanut improvement.

/pdf/the-genome-of-cultivated-peanut-provides-insight-into-legume-2tmoflph52.pdf

The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication

1Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, Oil Crops Research Institute, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China. 2School of Life Sciences, North China University of Science and Technology, Tangshan, China. 3School of Genomics and Bio-Big-Data, Chengdu University of Traditional Chinese Medicine, Chengdu, China. 4Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA. 5Nextomics Biosciences Institute, Wuhan, China. 6College of Agriculure and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China. 7Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India. 8Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia. 9These authors contributed equally: Weijian Zhuang, Xiyin Wang. ✉e-mail: weijianz1@163.com; wangxiyin@vip.sina.com; r.k.varshney@cgiar.org The origin of peanut (Arachis hypogaea) has been the focal point of peanut studies1–3. In our previous research, by calculating Ks values for collinear gene pairs and the expansion time of transposable elements, we inferred that peanut polyploidization occurred ~450,000 years ago and that the sequenced Arachis duranensis was not a direct descendent of the ancestor of the A-subgenome donor1. However, Bertioli et al. suggest that polyploidization happened <10,000 years ago, aided by human activities, and that the sequenced A. duranensis was a close relative of the A-subgenome donor2. In replying to Bertioli et al.4, we performed multiple analyses using diverse evolutionary models and obtained new lines of evidence that support our former inference1 and suggest likely ongoing DNA flow between different lines of peanuts, diploid or tetraploid. We first performed Ks analysis to date the origin of tetraploid peanut and the divergence of the Ad (A. duranensis) and Bd (Arachis ipaensis) diploid genomes5, At and Bt (the A and B subgenomes of A. hypogaea), Ad and At, and Bd and Bt (Supplementary Data 1). This approach can distinguish recent evolutionary events such as the formation of Brassica napus ~7,500–12,500 years ago (ref. 6). If tetraploid peanut originated as recently as a few thousand years ago, Ks analysis should have the power to discern this. Surely, if two homeologous or orthologous genes are very similar, Ks may lack resolution: for example, PAML outputs 0 when the Ks value is <0.0001 (ref. 7). Thanks to comments from Bertioli et al.4, we reinvestigated whether the removal of genes with Ks = 0 is reasonable. The Ks histograms for Ad–Bd and At–Bt (Shitouqi) comparisons (Fig. 1a,b) have bimodal distributions with peaks at Ks of ~0.03 and 0 (95% confidence interval, 0.0301–0.0310 and 0.0303–0.0312, respectively; Supplementary Table 1). A bimodal distribution is not consistent with the hypothesis that gene pairs at 0 are merely highly conserved, but instead suggests a different phenomenon. It is clear that Ks = 0 cannot be used to infer the split time of the A and B genomes and subgenomes, ignoring the major peak at ~0.030–0.031. The average genome sequence similarity between the diploid A and B genomes is 90.45%, and the tetraploid A and B subgenomes have 90.28% identity1,2,5 (Fig. 2 and Supplementary Data 2a,b). Accordingly, we could only use the second peak for correct inference, which indicated that the two diploids diverged 3.7 million years ago, which is similar to a previous estimate1 based on a mutation rate of 8.12 × 10−9 Ks per year. The same bimodal distribution of Ks for the At–Bt comparison is evident from the Tifrunner genome, with a much higher peak at Ks = 0 (Fig. 1e), again with a divergence time of ~3.7 million years ago for the A and B genomes. We further used EMMIX8 to perform time estimation and characterized the Ks mean and covariance for each pair of subgenomes, with very similar results (Supplementary Table 1). Bimodal distributions also occurred for the Ad–At and Bd–Bt Ks values, only with sharper peaks at Ks = 0 (Fig. 1c,d). If ignoring the peaks at Ks = 0, we infer the split times to be approximately 366,869–457,612 years ago (Ks of ~0.003 for the Bd–Bt comparison and ~0.0037 for the Ad–At comparison), as inferred in our previous publication1 and in line with analysis of the Tifrunner genome (Fig. 1f,g). These times were also confirmed with peak identities of ~98.72% (average 95.84%) and 99.48% (average 97.70%) obtained by BLAST analysis, corresponding to 128 and 52 differences per 10,000 nucleotides, dating divergence to 800,000 and 325,000 years ago for the Ad–At and Bd–Bt pairs, respectively1 (Fig. 2c,d and Supplementary Data 2; see also Fig. 2c in ref. 1). The modal peaks calculated by MUMmer were lower but still conformed (Fig. 2e,g). Are the Arachis genes with Ks = 0 highly conserved in evolution? If peaks at Ks = 0 represent conserved genes, then their low mutation rates are part of a distribution that reflects the overall divergence of paralogous and homoeologous genes. To investigate this, five alignments of randomly selected genes were linked and Ks values were inferred with the Nei–Gojobori approach implemented in PAML7. The peaks in the Ad–At and Bd–Bt Ks distributions continued to indicate that divergence occurred several million years ago, albeit with differing origins in cultivars Shitouqi and Tifrunner for the Ad–At and Bd–Bt pairs, respectively (Extended Data Fig. 1), implying that genes in peaks at Ks = 0 are not highly conserved in Arachis. Furthermore, we compared inferred Medicago orthologous genes9 to peanut homologs with Ks = 0 or Ks > 0 (Extended Data Fig. 2), by calculating Ks. The genes in these two groups had similar distribution patterns, indicating that genes with Ks = 0 in tetraploid peanut are not highly conserved in legume evolution. Reply to: Evaluating two different models of peanut’s origin

Meng Yang

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The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication

Reply to: Evaluating two different models of peanut's origin.