Efforts Towards Building a Reference Genome from Draft Assemblies of Amaranthus hypochondriacus

Advances in sequencing technologies and genome assembly tools have enabled individual investigators to interrogate the phenotypes or traits of species of interest at genome level. Generating draft genomes of novel eukaryotic species is becoming rather routine. Draft genomes of a large number of plants has allowed us to comprehend diversity of species at the proteome level. However, for translation to aid breeding efforts, a reference genome at chromosome level resolution is necessary, which remains a challenge without high resolution physical maps. This limitation is often augmented by obtaining long reads from PacBio and/or bionano genomics. Here, we present our efforts to improve the draft genome of A. hypochondriacus (Karnataka variety) using both 30X coverage of PacBio reads and the genome of Plainsman variety of A. hypochondriacus from public repository. Utilizing just the error-corrected PacBio reads using the high quality reads from Illumina, we increased the horizontal coverage of the genome to 100% from 58% and reduction in the number of scaffolds to 49,532 from 136,549. A better resolution of repeats (33%) was also obtained over Illumina-only assembly that yielded 13.76 % repeats. Scaffolding the PacBio assembly further based on the genome of Plainsman variety of A. hypochondriacus, we could reduce the number of scaffolds further down to 15,586 increasing N50 to 107,365 from 16,147. We also present the comparison between the two A. hypochondriacus genomes at the level of nucleotides, proteome and repeat regions.