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

Quinoa (Chenopodium quinoa Willd.) is an allotetraploid seed crop with the potential to help address global food security concerns. Genomes have been assembled for three accessions of quinoa; however, all assemblies are fragmented and do not reflect known chromosome biology. Here, we used in vitro and in vivo Hi-C data to produce a chromosome-scale assembly of the Chilean quinoa accession PI 614886 (QQ74). The final assembly spanned 1.326 Gb, of which 90.5% was assembled into 18 chromosome-scale scaffolds. The genome was annotated with 54,499 protein-coding genes, 97% of which were located on the 18 largest scaffolds. We also produced an updated genome assembly for the B-genome diploid C. suecicum and used it, together with the A-genome diploid C. pallidicaule, to identify genomic rearrangements within the quinoa genome, including a large pericentromeric inversion representing 71.7% of chromosome Cq3B. Repetitive sequences comprise 65.20%, 48.61%, and 57.91% of the quinoa, C. pallidicau..., , Detailed list of files in '.tar.gz' folders:
Cquinoa_QQ74_v2_pseudomoleculesANDannotations.tar.gz
-->Cquinoa_QQ74_v2_CDS.fasta (CDS sequences: transcribed sequence, devoid of introns, and devoid of UTRs)
-->Cquinoa_QQ74_v2.fasta (Pseudomolecules and unanchored contigs)
-->Cquinoa_QQ74_v2.gff3 (Gene annotation, including gene, mRNA, CDS, 3' and 5' UTRs)
-->Cquinoa_QQ74_v2_mRNA.fasta (mRNA sequences: transcribed sequence, devoid of introns, but containing UTRs)
-->Cquinoa_QQ74_v2_prot.fasta (Peptide sequences: CDS sequences translated into Amino acid)
-->Cquinoa_QQ74_v2_REPET_classification.txt (TE classification: produced with REPET annotation software)
-->Cquinoa_QQ74_v2_REPET_consensus.fasta (TE consensus sequences: produced with REPET annotation software)
-->Cquinoa_QQ74_v2_REPET.gff3 (TE annotation: performed with REPET software)
 
Csuecicum_v2_pseudomoleculesANDannotations.tar.gz
-->Csuecicum_v2.fasta (Pseudomolecules and uncanchored condigs)
-->Csuecic...,

藜麦（Chenopodium quinoa Willd.）是一种异源四倍体种子作物，可为缓解全球粮食安全危机提供助力。目前已有针对三个藜麦种质的基因组组装结果，但所有组装均存在片段化问题，无法完整反映其已知的染色体生物学特征。本研究利用体外（in vitro）与体内（in vivo）Hi-C测序数据，完成了智利藜麦种质PI 614886（代号QQ74）的染色体级基因组组装。最终组装的基因组序列总长1.326 Gb，其中90.5%的序列被锚定至18条染色体级支架序列（scaffolds）。该基因组共注释得到54499个蛋白质编码基因，其中97%的基因定位在18个最大的支架序列上。本研究还完成了B基因组二倍体瑞典藜（C. suecicum）的更新版基因组组装，并结合A基因组二倍体淡色藜（C. pallidicaule），对藜麦基因组内的基因组重排事件进行了解析，包括一个覆盖Cq3B染色体71.7%的大型着丝粒周缘倒位事件。重复序列占比分别为藜麦65.20%、C. pallidicaule...48.61%与57.91%。

.tar.gz 压缩包内的文件详情如下：
Cquinoa_QQ74_v2_pseudomoleculesANDannotations.tar.gz
→ Cquinoa_QQ74_v2_CDS.fasta（编码序列文件：存储无内含子、无非翻译区（UTR）的转录序列）
→ Cquinoa_QQ74_v2.fasta（拟染色体（pseudomolecules）与未锚定重叠群序列文件）
→ Cquinoa_QQ74_v2.gff3（基因注释文件：涵盖基因、mRNA、CDS、3'及5'非翻译区的注释信息）
→ Cquinoa_QQ74_v2_mRNA.fasta（mRNA序列文件：存储无内含子但包含非翻译区的转录序列）
→ Cquinoa_QQ74_v2_prot.fasta（肽序列文件：由CDS序列翻译得到的氨基酸序列）
→ Cquinoa_QQ74_v2_REPET_classification.txt（转座元件（TE）分类文件：通过REPET注释软件生成）
→ Cquinoa_QQ74_v2_REPET_consensus.fasta（转座元件共识序列文件：通过REPET注释软件生成）
→ Cquinoa_QQ74_v2_REPET.gff3（转座元件注释文件：通过REPET软件完成注释）

Csuecicum_v2_pseudomoleculesANDannotations.tar.gz
→ Csuecicum_v2.fasta（拟染色体与未锚定重叠群序列文件）
→ Csuecic...