De novo Genome Assembly of Heterozygous Vitis species Using Next-Generation Sequencing

Date: Sunday, January 10, 2016
Time: 2:30 PM
Room: Royal Palm Salon 5-6
Sagar Patel , South Dakota State University, Brookings, SD
Padmapriya Swaminathan , South Dakota State University, Brookings, SD
Erliang Zeng , University of South Dakota, Vermillion, SD
Anne Fennell , South Dakota State University, Brookings, SD
Vitis vinifera cultivars are widely used for wine, table and raisin production throughout the world. A reference genome for the V. vinifera inbred line (PN40024, ~93% homozygous) is available; however, standard cultivars are highly heterozygous. We evaluated assemblers ALLPATHS-LG and PLATANUS for the assembly of heterozygous genomes using next-generation derived sequences. V. vinifera ‘Sultanina’ reads were downloaded from NCBI (accession no SRP026420) and V. riparia (PI588259) reads were generated from our laboratory. De novo assemblies were developed for the two heterozygous genotypes and the structure and quality of the assemblies were assessed in relation to V. vinifera (PN40024, V2). The Next-Gen sequence library diversity and assembler type influenced the quality of assembly for highly heterozygous species.