Hybrid de novo genome assembly using Oxford Nanopore Technology, 10X Genomics Linked-Reads sequencing, and Bionano optical map of a non-model species: the case of the melon-cotton aphid Aphis gossypii
Abstract
Insect species challenge high quality genome production because of their small size, the combination of high polymorphism and heterozygosity, the presence of repeat regions, and the pooling of polymorphic individuals to form libraries. No highly resolved genome is available for aphids which are major pests of cultivated plants. Aphis gossypii genome is expected with 339 Mbp in 4 pairs of chromosomes. To minimize heterozygosity, we focused on a lineage, C9, with a low estimated heterozygosity, and we pooled individuals deriving from clonal reproduction. We produced a high quality genome from 10X Genomics Linked-Reads (10X Genomics), long reads (Oxford Nanopore Technology: ONT), and Optical Map (Bionano), in order to compare advantages of combining different methods. We also produced a genome of a more heterozygous clone, NM1, but without an optical map support.
Domains
Environmental Sciences
Origin : Files produced by the author(s)