A chromosome-scale assembly ofBrassica carinata(BBCC) accession HC20 containing resistance to multiple pathogens and an early generation assessment of introgressions intoB. juncea(AABB)

SummaryBrassica carinata(BBCC) commonly referred to as Ethiopian mustard is a natural allotetraploid containing the genomes ofBrassica nigra(BB) andBrassica oleracea(CC). It is an oilseed crop endemic to the Northeastern regions of Africa. Although it is grown in a limited manner,B. carinatais of value as it is resistant/highly tolerant to most of the pathogens affecting cultivated Brassica species of the U’s triangle that are grown worldwide as oilseed and vegetable crops. We report a chromosome-scale genome assembly ofB. carinataaccession HC20 using long-read Oxford Nanopore and Illumina sequencing and BioNano optical maps. The assembly has a scaffold N50 of ~39.8 Mb and covers ~1.11 Gb of the genome. We compared the available long-read genome assemblies of the six species of the U’s triangle and found a highly conserved gene number and collinearity suggesting thatB. juncea(AABB),B. napus(AACC), andB. carinataare strict allopolyploids. We cataloged the nucleotide-binding and leucine-rich repeat immune receptor (NLR) repertoire ofB. carinataresulting in the identification of 465 NLRs. We investigated the extent and nature of early generation genomic interactions between the subgenomes ofB. carinataandB. junceain interspecific crosses between the two species. We found that C chromosome additions are well tolerated, with homoeologous exchanges occurring between the A and C genomes. Based on the genomic interactions, we propose strategies to utilize the interspecific crosses for transferring disease resistance fromB. carinatatoB. junceaand other Brassica species.