Fig. 4

Chromosome evolution in amaranth. a Syntenic relationship between putative homoeologous chromosomes, with colored lines connecting orthologous gene pairs in the amaranth subgenomes. b Syntenic relationship between orthologous genes of amaranth chromosomes (designated with the prefix Chr) and beet chromosomes (designated with the prefix Bv). Because the chromosomes comprising each subgenome in amaranth are not known, the arrangement of amaranth chromosomes into two sets of 8 is arbitrary and does not necessarily reflect the make-up of the two subgenomes. c Syntenic dotplot of coding sequences in Chr1 and Bv9, indicating that Chr1 is a likely head-to-tail fusion of homoeologous chromosomes. The light and dark blue colors distinguish the two halves of Chr1 and correspond to the colors in b. d Model for the evolution of chromosome number in related species of the Amaranthaceae. Amaranth, quinoa, and beet are arranged according to their accepted organismal phylogeny, with orange, gray, and blue boxes representing haploid chromosomes in each species. The orange and blue boxes represent orthologous chromosomes between the species as indicated in b and from [28]. Numbers above or below select chromosomes in amaranth and quinoa represent chromosomes orthologous to the corresponding beet chromosomes. Black stars indicate lineage-specific whole genome duplications