A PacBio and Hi-C based proximity-guided assembly of Amaranth pseudo chromosomes

The genus Amaranthus (Caryophyllales: Amaranthaceae) encompasses about 70 species of worldwide distribution. Three species in the genus produce edible seeds. These grain amaranths were food staples among the ancient civilization of Central and South America. These grain species remain important as a food crops in several areas of modern Latin America and have recently received substantial attention as an alternative food crop worldwide. We previously produced a draft genome sequence of A. hypochondriacus using the HiSeq Illumina platform and ALLPATHS assembler. The draft assembly consisted of 3,518 scaffolds with an N50 and L50 of 371kb and 243, respectively. Here we report the development of pseudo chromosomes of A. hypochondriacus using a Phase Genomics Hi-C based proximity-guided assembly. The Hi-C data generated complete chromosome assemblies from the ALLPATHS scaffolds which were then gap filled using PBJELLY2 and ~29x coverage of PacBio long reads. The Hi-C plus PacBio assembly consists of 287 scaffolds with an N50 of 24.7 Mb. Less than 1% of the assembly is N filled gaps and 99.4% of the sequence is grouped, ordered and oriented in 16 haploid chromosomes (L99 = 16). Pseudo chromosomes range in size from 17 - 38 Mb and were tested for correctness using BioNano Optical maps, linkage maps, synteny analysis and Hi-C based reassembly of finished assembly contigs.