De novo assembly of lucina pectinata genome using ion torrent reads

Abstract

Lucina pectinata is a bivalve that lives in sulfide-rich environments and houses intracellular sulfide oxidizing endosymbiont. This organism is an ideal model to understand adaptive mechanisms and chemoautotrophic endosymbiosis in organisms living in sulfide-rich environments. However, only three hemoglobins have been completely characterized at protein and gene level leaving a gap in understanding the biology of this organism. In this work, we produced draft genomic assemblies with data produced by the Ion Proton Next Generation Sequencing System using both the MIRA4 and SPAdes assemblers. We compare and contrast these draft assemblies using metrics such as N50, total assembled length, number of predicted genes and other measures. We conclude that de novo assembly of eukaryotic organisms with NGS data from the Ion technology family remains complicated and may benefit from the use of multiple genome assemblers.