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.. CCS Concepts • Computing methodologies ➝ Massively parallel and high-performance simulations. • Applied computing ➝ Life and medical sciences ➝Computational biology ➝ Computational Genomics.

Characterization of Histone Genes from the Bivalve Lucina Pectinata

“…The reads were quality control trimmed and filtered using the Sickle Windowed Adaptive Trimming Tool, discarding reads with <75 bases in length and used a quality score threshold of 15. Then, the trimmed data was assembled with MIRA Version 4.0.2 as described [ 8 ]. The genome assembly was submitted to the NCBI Genbank database, with submission number SUB4511435, the GenBank accession number is pending.…”

“…In order to identify new proteins in this organism, a draft genome was assembled from a genomic library and characterized using semiconductor sequencing chemistry [ 8 ]. To validate the genome assembly and identify histone genes for L. pectinata , a search for Histone-like sequences was performed using the known partial coding sequence of histone H3 from L. pectinata and the nucleotide sequences of the Histone H1, H2A, H2B, H3 and H4 from the clam Solen marginatus ( S. marginatus ) as query sequences using the draft genome as library [ 1 ].…”