De novo Genome Assembly Tool Comparison for Highly Heterozygous Species Vitis vinifera cv. Sultanina

Document Type

Article

Publication Date

2015

Abstract

Vitis vinifera cultivars are widely used for wine, table and raisin production throughout the world. A reference genome for an inbred line is available; however, standard cultivars are highly heterozygous. The heterozygosity makes it difficult to select an optimal assembler for de novo genome assembly. Here we have compared de novo genome assembly of the V. vinifera cv. Sultanina, a pivotal table grape genotype by ALLPATHS-LG and PLATANUS tools. Sequence reads were downloaded from NCBI using study accession SRP026420 and assembled using PLATANUS and ALLPATHS-LG assemblers. PLATANUS can manage high-throughput data from highly heterozygous samples while ALLPATHS-LG is used for different types of genomes like homozygous prokaryotes and eukaryotes. Comparison of assembly quality results by QUAST tool plots (cumulative, GC content and NGx) indicated the results of PLATANUS tool were more closely related with reference genome of V. vinifera than the results of ALLPATHS-LG. The PLATANUS assembly had a greater number of large contigs and scaffolds. The PLATANUS NG50 was two times that of the ALLPATHS-LG NG50. PLATANUS is a suitable tool for de novo genome assembly for V. vinifera cv. Sultanina and other highly heterozygous species.

Publication Title

2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI of Published Version

10.1109/BIBM.2015.7359957

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