Jul 18, 2016

The haplotype-resolved genome sequence of hexaploid Ipomoea batatas reveals its evolutionary history

BioRxiv : the Preprint Server for Biology
Jun YangMartin Vingron

Abstract

Although the sweet potato, Ipomoea batatas , is the seventh most important crop in the world and the fourth most significant in China, its genome has not yet been sequenced. The reason, at least in part, is that the genome has proven very difficult to assemble, being hexaploid and highly polymorphic; it has a presumptive composition of two B1 and four B2 component genomes (B1B1B2B2B2B2). By using a novel haplotyping method based on de novo genome assembly, however, we have produced a half haplotype-resolved genome from ~267Gb of paired-end sequence reads amounting to roughly 60-fold coverage. By phylogenetic tree analysis of homologous chromosomes, it was possible to estimate the time of two whole genome duplication events as occurring about 525,000 and 341,000 years ago. Our analysis also identified many clusters of genes for specialized compounds biosynthesis in this genome. This half haplotype-resolved hexaploid genome represents the first successful attempt to investigate the complexity of chromosome sequence composition directly in a polyploid genome, using direct sequencing of the polyploid organism itself rather than of any of its simplified proxy relatives. Adaptation and application of our approach should provide highe...Continue Reading

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Mentioned in this Paper

Gene Polymorphism
Ipomoea batatas
Genome
Avian Crop
Genome Assembly Sequence
Nucleic Acid Sequencing
Phylogenetic Analysis
LUC7L3 gene
Potato
Genomics

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