Chromosome-Scale Genome Assembly of the Hexaploid Taiwanese Goosefoot “Djulis” (Chenopodium formosanum)
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Oxford University Press
Materia
Long-read sequencing Chromosome-scale Polyploid evolution Retrotransposon LTR Gypsy
Date
2022-07-26Referencia bibliográfica
David E Jarvis... [et al.]. Chromosome-Scale Genome Assembly of the Hexaploid Taiwanese Goosefoot “Djulis” (Chenopodium formosanum), Genome Biology and Evolution, Volume 14, Issue 8, August 2022, evac120, [https://doi.org/10.1093/gbe/evac120]
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BYU Life Sciences BYU DNASC RRID: SCR_017781Abstract
Djulis (Chenopodium formosanum Koidz.) is a crop grown since antiquity in Taiwan. It is a BCD-genome hexaploid (2n=6x =
54) domesticated form of lambsquarters (C. album L.) and a relative of the allotetraploid (AABB) C. quinoa. As with quinoa,
djulis seed contains a complete protein profile and many nutritionally important vitamins and minerals. While still sold locally
in Taiwanese markets, its traditional culinary uses are being lost as diets of younger generations change. Moreover, indigenous
Taiwanese peoples who have long safeguarded djulis are losing their traditional farmlands. We used PacBio sequencing
and Hi-C-based scaffolding to produce a chromosome-scale, reference-quality assembly of djulis. The final genome assembly
spans 1.63 Gb in 798 scaffolds, with 97.8% of the sequence contained in 27 scaffolds representing the nine haploid chromosomes
of each sub-genome of the species. Benchmarking of universal, single-copy orthologs indicated that 98.5% of the
conserved orthologous genes for Viridiplantae are complete within the assembled genome, with 92.9% duplicated, as expected
for a polyploid. A total of 67.8% of the assembly is repetitive, with the most common repeat being Gypsy long terminal
repeat retrotransposons, which had significantly expanded in the B sub-genome. Gene annotation using Iso-Seq data
from multiple tissues identified 75,056 putative gene models. Comparisons to quinoa showed strong patterns of synteny
which allowed for the identification of homoeologous chromosomes, and sub-genome-specific sequences were used to assign
homoeologs to each sub-genome. These results represent the first hexaploid genome assembly and the first assemblies
of the C and D genomes of the Chenopodioideae subfamily.