New Insights on Genome Size Reduction in the High-Polyploid Carnivorous Plant Utricularia gibba from a Long-Read, Third Generation Assembly

Utricularia gibba (the bladderwort, family Lentibulariaceae) is a carnivorous plant with an unusually small nuclear genome, which in our published assembly approximated 82 Mb (Ibarra-Laclette et al., 2013). Despite this small size, syntenic analysis of the U. gibba genome revealed 3 lineage-specific whole genome duplications since common ancestry with tomato and grape. Analysis of gene family turnover showed that over evolutionary time U. gibba both gained and lost genes faster than tomato, grape, Arabidopsis, or Mimulus (Carretero-Paulet et al., 2015). We are further studying these genome evolutionary dynamics through use of PacBio SMRT third generation sequencing. Our PacBio-only de novo assembly (from HGAP.3) has a contig N50 of ~3.4 Mb, with a longest contig of 8.5 Mb. Examination of the contig collection reveals that we have successfully assembled several entire chromosomes, including the 8.5 Mb contig and one as small as 3.8 Mb, nearly 1 Mb shorter than the genome of E. coli K-12. These chromosomes are marked on both ends by Arabidopsis-type telomere repeats, (TTTAGGG)_n. Most notably, the new assembly encompasses a total of ~100 Mb after contaminant filtration, >15 Mb more than our fragmented, published assembly based on 454 and MiSeq reads, which had a scaffold N50 of about 80 Kb. Comparative analysis of the new and old assemblies reveals that most of the difference in genome size relates to repetitive DNA sequences, readily sequenced through by PacBio long reads, that otherwise missed assembly in our short-read approach. While in need of size revision, the U. gibba genome remains the smallest reliably assembled angiosperm genome. We will report new findings on centromeric sequences and other repetitive DNA islands, and how these relate to Utricularia genome evolutionary dynamics. We will also show how the contiguity of the new assembly permits clear resolution of U. gibba's most recent polyploidy event.