Synteny based assembly of the Chloridea subflexa genome

Chloridea subflexa and Chloridea virescens are a pair of closely related Heliothine species with divergent host plant preferences. C. subflexa only feeds on a few species of plants in the genus Physalis, while C. virescens is a broad generalist, feeding on a wide range of host plant species. Investigation of the genetic basis for the unique host plant preferences of this species pair would benefit from high quality genome assemblies. Here we present a novel C. subflexa assembly using Illumina short reads, as well as an updated chromosome-scale genome assembly for C. virescens. To improve the contiguity of the C. subflexa short read assembly, we applied a synteny-based super-scaffolding approach, which leveraged both the new C. virescens chromosome-scale assembly and two other existing Heliothine genomes. While the initial de novo assembly of C. subflexa consisted of 7,654 scaffolds with a genome completeness of 90.8% and a N50 score of 264,374 bp, synteny-based super-scaffolding improved those statistics to 6,354 scaffolds with a N50 value of 1,335,006 bp (C. sub_solid, without breaking the original contigs), and 5,125 scaffolds with a N50 value of 16,413,121 bp (C. sub_unsolid, breaking the original contigs). Our results highlight both the potential and pitfalls of synteny-based super-scaffolding approaches for Illumina short-read assemblies.