A chromosome‐levelAmaranthus cruentusgenome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop

Abstract

Summary Traditional crops have historically provided accessible and affordable nutrition to millions of rural dwellers but have been neglected, with most modern agricultural systems over‐reliant on a small number of internationally traded crops. Traditional crops are typically well‐adapted to local agro‐ecological conditions and many are nutrient‐dense. They can play a vital role in local food systems through enhanced nutrition (particularly where diets are dominated by starch crops), food security and livelihoods for smallholder farmers, and a climate‐resilient and biodiverse agriculture. Using short‐read, long‐read and phased sequencing technologies, we generated a high‐quality chromosome‐level genome assembly for Amaranthus cruentus, an under‐researched crop with micronutrient‐ and protein‐rich leaves and gluten‐free seed, but lacking improved varieties, with respect to productivity and quality traits. The 370.9 Mb genome demonstrates a shared whole genome duplication with a related species, Amaranthus hypochondriacus. Comparative genome analysis indicates chromosomal loss and fusion events following genome duplication that are common to both species, as well as fission of chromosome 2 in A. cruentus alone, giving rise to a haploid chromosome number of 17 (versus 16 in A. hypochondriacus). Genomic features potentially underlying the nutritional value of this crop include two A. cruentus‐specific genes with a likely role in phytic acid synthesis (an anti‐nutrient), expansion of ion transporter gene families, and identification of biosynthetic gene clusters conserved within the amaranth lineage. The A. cruentus genome assembly will underpin much‐needed research and global breeding efforts to develop improved varieties for economically viable cultivation and realization of the benefits to global nutrition security and agrobiodiversity.

De novo Transcriptome Assembly and Comprehensive Annotation of Two Tree Tomato Cultivars (Solanum betaceum Cav.) with Different Fruit Color

“…Although tree tomato is one of the most promising fruit crops in the Mediterranean and temperate regions [4], its genomic landscape has not yet been explored yet. Other unexploited crops similar to the tree tomato, such as the cape gooseberry (Physalis peruviana L.) and amaranth (Amaranthus cruentus L.), have greatly benefited from genomic studies, which have fostered the dissection of multiple agronomic traits and breeding programs [35][36][37]. In this study, we conducted the de novo transcriptome assembly of two tree tomato cultivars to provide useful genomic data for the improvement of this unexploited but emerging crop.…”

Plant Metabolic Gene Clusters: Evolution, Organization, and Their Applications in Synthetic Biology

“…An in silico analysis using Plantismash revealed the presence of 10 orthologous gene clusters in the genomes of Amaranthus cruentus and Amaranthus hypochondriacus related to secondary metabolism. However, their in planta functional role is not conclusive (Ma et al, 2021). Comparative genome analysis of four genera of Amaranthaceae (Amaranthus, Beta, Chenopidum, and Spinacia) provided conclusive evidence about the co-occurrence of betalain pigment-producing genes on a specific chromosome, but in spinach (Spinacia oleracea) and quiona (Chenopodium quinoa) additional copies of the genes were found to exist.…”

“…Comparative genome analysis of four genera of Amaranthaceae (Amaranthus, Beta, Chenopidum, and Spinacia) provided conclusive evidence about the co-occurrence of betalain pigment-producing genes on a specific chromosome, but in spinach (Spinacia oleracea) and quiona (Chenopodium quinoa) additional copies of the genes were found to exist. This could be due to tandem gene duplication mechanisms (Ma et al, 2021).…”

syntenet: an R/Bioconductor package for the inference and analysis of synteny networks

“…Thus, exploring the evolution of duplicated genes and genomes can help explain how new traits arise and diversify across taxa. Identifying collinear or syntenic regions (here used as synonyms, i.e., different genomic segments showing conserved gene content and order) within genomes has become standard practice to detect signatures of whole-genome duplications (WGD) and the genomic rearrangements that typically follow WGD events (Liu et al, 2022;Ma et al, 2021;Vanneste et al, 2013;Wan et al, 2021). Synteny analyses can also be performed to compare different genomes to provide insights on population structure, species divergence, and the evolution of gene families and traits (Jayakodi et al, 2020;Li et al, 2022;Tang et al, 2022;Zhang et al, 2021;Zhou et al, 2017).…”