Improvement of the Genome Assembly of Lettuce (Lactuca sativa) Using Dovetail/in vitro Proximity Ligation.

The Compositae are the most successful family of flowering plants on the planet in terms of number of species and diversity of habitats colonized.  Although it does not contain any of the top six food crops, the Compositae family includes many important edible, medicinal, noxious, and invasive species.  Lettuce (Lactuca sativa) is one of the most valuable vegetable crops with an annual value of over $2.4 billion.  L. sativa is diploid with 2n=2x=18 chromosomes and a genome size of 2.7 Gb.  We had previously sequenced and assembled the lettuce genome using Illumina sequencing of a variety of libraries and SOAPdenovo.  This resulted in contig and scaffold N₅₀s of 11.7 Kb and 476.0 Kb respectively covering 2.3 Gb.  There were 21,686 scaffolds greater than 1 Kb. Genotyping using whole genome shotgun sequencing validated the assembly and assigned 97% of the assembly into genetic bins ordered along nine chromosomal pseudomoloecules.  We used the HiRise program developed by Dovetail Genomics to improve the contiguity of the assembly and increase the scaffold N₅₀ using reads from multiple Chicago libraries, which were generated with their in vitro proximity ligation technique.  The improved assembly was validated genetically; nearly all the super-scaffolds were genetically correct.  Misjoins in the previous assembly were identified and rectified.  The currrent assembly has half the number of scaffolds, incorporated previously unmapped scaffolds, and a scaffold N₅₀ of 1.81 Mb.  The new assembly has greatly helped our analyses of paleopolyploidy, resistance gene clusters, and genomic regions being targeted for map-based cloning.