De-novo chromosome level assembly of plant genomes from long read sequence data

Abstract

Recent advances in the sequencing and assembly of plant genomes have allowed the generation of genomes with increasing contiguity and sequence accuracy. The chromosome level assembly of the contigs generated from long read sequencing has involved the use of proximity analysis (Hi-C) or traditional genetic maps to guide the placement of sequence contigs within chromosomes. The development of highly accurate long reads by repeated sequencing of circularized DNA (PacBio HiFi) has greatly increased the size of contigs. We now report the use of HiFiasm to assemble the genome of Macadamia jansenii. a genome that has been used as model to test sequencing and assembly. This achieved almost complete chromosome level assembly from the sequence data alone without the need for higher level chromosome map information. Eight of the 14 chromosomes were represented by a single large contig and the other 6 assembled into 2-4 main contigs. The small number of chromosome breaks appear to be due to highly repetitive regions of ribosomal genes that cannot be assembled by these approaches. De novo assembly of near complete chromosome level plant genomes now seems possible using these sequencing and assembly tools. Further targeted strategies might allow these remaining gaps to be closed.

Macadamia germplasm and genomic database (MacadamiaGGD): A comprehensive platform for germplasm innovation and functional genomics in Macadamia

“…In addition, the genomes of M. integrifolia (249 contigs, N50 = 5.3 Mb, 738 Mb), M. tetraphylla (153 contigs, N50 = 10.0 Mb, 707 Mb), M. ternifolia (211 contigs, N50 = 6.4 Mb, 716 Mb), and M. jansenii (284 contigs, N50 = 4.5 Mb, 738 Mb) were assembled by use of the PacBio HiFi TGS platform (Sharma et al, 2021a). The genome of M. jansenii has been improved by Hi-C assembly (219 scaffolds, N50 = 52 Mb, 758 Mb) (Sharma et al, 2021c) and was further updated by the latest hifiasm assembly (779 contigs, N50 = 46 Mb, 826 Mb) (Sharma et al, 2021b). Recently, the genome of the cultivar HAES 344 was sequenced and assembled into 14 pseudochromosomes by the use of Illumina NovaSeq and PacBio Sequel II sequencing (5387 contigs, N50 = 281 kb, 794 Mb) (Lin et al, 2022).…”