TY - CHAP
T1 - Whole-Genome Sequencing, Assembling, and Annotation of Brassica oleracea Genomes
AU - Guo, Ning
AU - Bonnema, Guusje
AU - Wang, Shenyun
AU - Liu, Fan
PY - 2021/3/5
Y1 - 2021/3/5
N2 - A high-quality reference genome is critical for understanding genome structure, genetic variation, and evolution of a species. Of the three available Brassica oleracea genomes, cabbage ‘Cap02-12’ and kale-like rapid-cycling ‘TO1000’ were sequenced and assembled by short reads, hindering assembly through complex repeat regions, while broccoli ‘HDEM’ was assembled using Nanopore long reads combined with optical mapping. In this chapter we present the de novo genome assembly of cauliflower inbred line ‘Korso’ using a strategy combining PacBio long reads, optical mapping, and chromosome-contact maps (Hi-C). The assembly and annotation results of cauliflower ‘Korso’ are compared with the different genome assemblies published before. B. oleracea genome assemblies of cauliflower and broccoli, generated by new long-range technologies (PacBio and Nanopore) were longer, completer, and more continuous, with fewer errors, with improved annotation protein-coding genes, transposon distributions, and centromere positions and sequences. Compared to all other three assemblies, more repeat elements were predicted in ‘Korso’, and the arrangement of the genomic blocks representing the three subgenomes was improved. The availability of new morphotype specific high-quality reference genomes offers an unprecedented opportunity for extensive comparison of intraspecific genome diversity in B. oleracea.
AB - A high-quality reference genome is critical for understanding genome structure, genetic variation, and evolution of a species. Of the three available Brassica oleracea genomes, cabbage ‘Cap02-12’ and kale-like rapid-cycling ‘TO1000’ were sequenced and assembled by short reads, hindering assembly through complex repeat regions, while broccoli ‘HDEM’ was assembled using Nanopore long reads combined with optical mapping. In this chapter we present the de novo genome assembly of cauliflower inbred line ‘Korso’ using a strategy combining PacBio long reads, optical mapping, and chromosome-contact maps (Hi-C). The assembly and annotation results of cauliflower ‘Korso’ are compared with the different genome assemblies published before. B. oleracea genome assemblies of cauliflower and broccoli, generated by new long-range technologies (PacBio and Nanopore) were longer, completer, and more continuous, with fewer errors, with improved annotation protein-coding genes, transposon distributions, and centromere positions and sequences. Compared to all other three assemblies, more repeat elements were predicted in ‘Korso’, and the arrangement of the genomic blocks representing the three subgenomes was improved. The availability of new morphotype specific high-quality reference genomes offers an unprecedented opportunity for extensive comparison of intraspecific genome diversity in B. oleracea.
U2 - 10.1007/978-3-030-31005-9_4
DO - 10.1007/978-3-030-31005-9_4
M3 - Chapter
SN - 9783030310035
T3 - Compendium of Plant Genomes (CPG)
SP - 35
EP - 49
BT - The Brassica oleracea Genome
A2 - Liu, S.
A2 - Snowdon, R.
A2 - Kole, C.
PB - Springer
ER -