Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library

Abstract

Genomics: Linking up the pepper genome A new method of genome sequencing, ‘Linked Reads,’ has proven efficient and cost-effective in tests on a complex plant genome. Reference genomes have become the tool of choice for answering biological questions about crop species. However, existing methods of genome sequencing have drawbacks, particularly for large and complex plant genomes: older techniques tend to generate low-quality sequences, and newer ones are prohibitively expensive. A US team led by Amanda Hulse-Kemp and Allen Van Deynze of the University of California, Davis, USA, tested a novel ‘Linked-Read’ approach taken from human genomics on the pepper, Capsicum annuum. The method links together short fragments from the same larger section of DNA during sequencing. The resulting genome was more complete than any previous Capsicum sequence, and heralds the opportunity to obtain new, affordable genomic resources for plant breeding.