A chromosome‐scale reference of Chenopodium watsonii helps elucidate relationships within the North American A‐genome Chenopodium species and with quinoa

Abstract

Quinoa (Chenopodium quinoa), an Andean pseudocereal, attained global popularity beginning in the early 2000s due to its protein quality, glycemic index, and high fiber, vitamin, and mineral contents. Pitseed goosefoot (Chenopodium berlandieri), quinoa's North American free‐living sister species, grows on disturbed and sandy substrates across the North America, including saline coastal sands, southwestern deserts, subtropical highlands, the Great Plains, and boreal forests. Together with South American avian goosefoot (Chenopodium hircinum) they comprise the American tetraploid goosefoot complex (ATGC). Superimposed on pitseed goosefoot's North American range are approximately 35 AA diploids, most of which are adapted to a diversity of niche environments. We chose to assemble a reference genome for Sonoran A‐genome Chenopodium watsonii due to fruit morphological and high (>99.3%) preliminary sequence‐match similarities with quinoa, along with its well‐established taxonomic status. The genome was assembled into 1377 scaffolds spanning 547.76 Mb (N50 = 55.14 Mb, L50 = 5), with 94% comprised in nine chromosome‐scale scaffolds and 93.9% Benchmarking Universal Single‐Copy Orthologs genes identified as single copy and 3.4% as duplicated. A high degree of synteny, with minor and mostly telomeric rearrangements, was found when comparing this taxon with the previously reported genome of South American C. pallidicaule and the A‐subgenome chromosomes of C. quinoa. Phylogenetic analysis was performed using 10,588 single‐nucleotide polymorphisms generated by resequencing a panel of 41 New World AA diploid accessions and the Eurasian H‐genome diploid Chenopodium vulvaria, along with three AABB tetraploids previously sequenced. Phylogenetic analysis of these 32 taxa positioned the psammophyte Chenopodium subglabrum on the branch containing A‐genome sequences from the ATGC. We also present evidence for long‐range dispersal of Chenopodium diploids between North and South America.

A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes

“…10 ). A synteny comparison between QQ74-V2 and a newly reported chromosome-scale assembly of the A-genome diploid C. watsonii 24 confirmed the presence of the Cq1B-Cq2B, Cq7B-Cq9B, and Cq2B-Cq4A reciprocal translocations. Finally, patterns of diploid C. pallidicaule and C. suecicum read mapping against the quinoa subgenomes allowed the identification of an additional reciprocal translocation between the homoeologous chromosomes Cq6A and Cq6B (Supplementary Data 5 - 8 , Supplementary Fig.…”

North American pitseed goosefoot (Chenopodium berlandieri) is a genetic resource to improve Andean quinoa (C. quinoa)

“…1 C). Analysis of gene synteny between huauzontle, quinoa (QQ74), the A-genome diploid C. watsonii 60 , and the B-genome diploid C. suecicum 9 indicated a high degree of collinearity among the chromosomes, although several major chromosome rearrangements were evident, including a complex inversion series on chromosome 5A and a reciprocal 4A-6B translocation (Fig. 1 D & E ).…”

“…Homologous genes within the C. berlandieri genome and between the C. berlandieri and quinoa (CoGe id65146) genomes were identified using CoGe SynMap 57 berlandieri. Seeds were germinated and seedlings raised according to previously described protocols 60 and DNA from young leaf tissue was extracted using a standard mini-salts method 62 . DNA was sequenced using Illumina (2 × 150 bp) to reach 10X coverage by Novogene, Inc. (San Diego, CA) 36 .…”

“…berlandieri . Seeds were germinated and seedlings raised according to previously described protocols 60 and DNA from young leaf tissue was extracted using a standard mini-salts method 62 . DNA was sequenced using Illumina (2 × 150 bp) to reach 10X coverage by Novogene, Inc. (San Diego, CA) 36 .…”

“…Blocks of syntenic genes were identified with MCScanX58 and visualized as dotplots using SynVisio59 . Homologous genes between C. watsonii60 and the A subgenomes of C. berlandieri and quinoa, and between the B subgenome of C. formosanum61 and the B subgenomes of C. berlandieri and quinoa, were identified using BLASTp with the num_descriptions 5, -num_alignments 5, and -evalue 1e-10 settings applied. Blocks of syntenic genes were identified with MCScanX and visualized as treeview plots with SynVisio.…”