RT Journal Article SR Electronic T1 Reference Quality Assembly of the 3.5 Gb genome of Capsicum annuum from a Single Linked-Read Library JF bioRxiv FD Cold Spring Harbor Laboratory SP 152777 DO 10.1101/152777 A1 Amanda M. Hulse-Kemp A1 Shamoni Maheshwari A1 Kevin Stoffel A1 Theresa A. Hill A1 David Jaffe A1 Stephen Williams A1 Neil Weisenfeld A1 Srividya Ramakrishnan A1 Vijay Kumar A1 Preyas Shah A1 Michael C. Schatz A1 Deanna M. Church A1 Allen Van Deynze YR 2017 UL http://biorxiv.org/content/early/2017/06/20/152777.abstract AB Background Linked-Read sequencing technology has recently been employed successfully for de novo assembly of multiple human genomes, however the utility of this technology for complex plant genomes is unproven. We evaluated the technology for this purpose by sequencing the 3.5 gigabase (Gb) diploid pepper (Capsicum annuum) genome with a single Linked-Read library. Plant genomes, including pepper, are characterized by long, highly similar repetitive sequences. Accordingly, significant effort is used to ensure the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus. With a phased assembly approach, we targeted a heterozygous F1 derived from a wide cross to assess the ability to derive both haplotypes for a pungency gene characterized by a large insertion/deletion.Results The Supernova software generated a highly ordered, more contiguous sequence assembly than all currently available C. annuum reference genomes. Eighty-four percent of the final assembly was anchored and oriented using four de novo linkage maps. A comparison of the annotation of conserved eukaryotic genes indicated the completeness of assembly. The validity of the phased assembly is further demonstrated with the complete recovery of both 2.5 kb insertion/deletion haplotypes of the PUN1 locus in the F1 sample that represents pungent and non-pungent peppers.Conclusions The most contiguous pepper genome assembly to date has been generated through this work which demonstrates that Linked-Read library technology provides a rapid tool to assemble de novo complex highly repetitive heterozygous plant genomes. This technology can provide an opportunity to cost-effectively develop high-quality reference genome assemblies for other complex plants and compare structural and gene differences through accurate haplotype reconstruction.GbGigabaseBACBacteria artificial chromosomeKbKilobaseMbMegabasePAVPresence absence variantCM334Criollos del Morelos 334QTLQuantitative trait locicMCentiMorgan