Automated improvement of stickleback reference genome assemblies with Lep-Anchor software

We describe an integrative approach to improve contiguity and haploidy of
a reference genome assembly and demonstrate its impact with practical
examples. With two novel features of Lep-Anchor software and a
combination of dense linkage maps, overlap detection and bridging
long reads we generated an improved assembly of the nine-spined
stickleback (Pungitius pungitius) reference genome. We were
able to remove a significant number of haplotypic contigs, detect
more genetic variation and improve the contiguity of the genome,
especially that of X chromosome. However, improved scaffolding
cannot correct for mosaicism of erroneously assembled contigs,
demonstrated by a de novo assembly of a 1.7 Mbp inversion.
Qualitatively similar gains were obtained with the genome of
three-spined stickleback (Gasterosteus aculeatus). The utility of
genome-wide sequencing data in biological research depends heavily on
the quality of the reference genome. Although the reference
genomes have improved, it is evident that the assemblies could still be
refined, especially in non-model study organisms.