These scripts were used for the genome project of Amaranthus tricolor. A. tricolor, also known as Joseph’s coat and Chinese spinach, is a C4 eudicot in the genus Amaranthus, family Amaranthaceae, order Caryophyllales. It is a vegetable and ornamental amaranth, with high lysine, dietary fiber and squalene content. Chinese cuisine traditionally uses A. tricolor (xiàncài) as a standalone steamed or boiled vegetable dish. For genome assembly, the contig assembly based on HiFi data was very fragment, so Nanopore Ultra-long data was used to link contig to longer scaffolds. The details were in following docs and the reference.
We documented the pipeline used in the paper to scaffold contigs assembled by hifiasm by Oxford Nanopore Ultra-long reads. Please refer to methods for assmebly.
This part included computation of gene expression, differentially expressed genes (DEGs) detection and gene ontology (GO) enrichment analysis. Please refer to methods for transcriptome.
Wang H, Xu D, Wang S, Wang A, Lei L, Jiang F, Yang B, Yuan L, Chen R, Zhang Y, Fan W. Chromosome-scale Amaranthus tricolor genome provides insights into the evolution of the genus Amaranthus and the mechanism of betalain biosynthesis. DNA Res. 2022 Dec 6:dsac050. https://doi.org/10.1093/dnares/dsac050