A multi–step comparison of short–read full plastome sequence assembly methods in grasses

• DOI: 10.12705/634.5
• Publication Date: 2014-08-28T23:49:00Z
• Authors: William P. Wysocki; Lynn G. Clark; Scot A. Kelchner; Sean V. Burke; J. Chris Pires; Patrick P. Edger; Dustin R. Mayfield; Jimmy K. Triplett; J. Travis Columbus; Amanda L. Ingram; Melvin R. Duvall
• Keywords: Sanger sequencing; Sequence assembly; Sequence (biology)

Abstract Technological advances have allowed phylogenomic studies of plants, such as full chloroplast genome (plastome) analysis, to become increasingly popular and economically feasible. Although next–generation short–read sequencing allows for plastomes be sequenced relatively rapidly, it requires additional attention using software assemble these reads into comprehensive sequences. Here we compare the use three de novo assemblers combined with contig assembly methods. Seven plastome sequences were analyzed. Three Sanger–sequenced. The other four assembled from short, single–end read files generated libraries. These represented a total six grass species (Poaceae), one which was in duplicate by two methods allow direct comparisons accuracy. Enumeration missing sequence ambiguities assessments completeness efficiency. All that used Bruijn–based shown produce assemblies comparable Sanger–sequenced but not equally efficient. Contig utilized automatable repeatable processes generally more efficient advantageous when applied larger scale projects many plastomes. However, less required manual did show utility determining lower depth able procedures implemented. here exclusively generate plastomes, could taxonomic groups if previously available. In addition comparing methods, supplemental guide applicable scripts this study.