Scientists from the University at Buffalo, Nanyang Technological University, and other institutions published results from an effort to elucidate the Utricularia gibba genome using SMRT Sequencing.
U. gibba, also known as the humped bladderwort, is an aquatic carnivorous flowering plant with a remarkably small genome, especially in light of two whole genome duplication events. Genome sequencing and annotation data are reported in the PNAS publication “Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome” from lead author Tianying Lan, senior author Victor Albert, and collaborators. The scientists were interested in using the plant’s genome to learn more about the post-duplication deletion process as well as traits specific to carnivorous plants.
This particular plant’s genome was previously sequenced with short-read technology, producing an 82 Mb assembly “which revealed that its genome gained and deleted gene duplicates significantly faster than those of other genomes,” the scientists note. By applying PacBio long-read technology, the team was able to significantly improve on the original assembly. The de novo genome project resulted in an assembly with a contig N50 of nearly 3.5 Mb. The total size was about 100 Mb, adding more than 18 Mb missed by the short-read assembly. Twenty-four contigs included telomeres, with four of those representing complete chromosomes. “Remarkably, base pair correction using either the PacBio data or Illumina MiSeq reads from our previous assembly led to extremely minor improvements, only 0.071% and 0.01% of total bases, respectively,” Lan et al. write.
The authors present a more complete count of protein-coding genes thanks to the improved assembly. The tally came to 30,689, a nearly 8% increase from estimates based on the short-read assembly. In addition, “unlike the far shorter scaffolds from [the prior] assembly, our largely chromosome-sized contigs permitted us to conservatively distinguish the [whole genome duplication]-derived and tandem duplicate portions of U. gibba’s genome adaptive landscape,” they write. That unique information enabled the team to discover that tandem duplication events were “enriched in metabolic functions potentially important for a carnivorous plant” — including cysteine protease genes expressed only in the plant’s trap — while syntenic duplicates were “enriched for transcription factor functions,” the scientists report. “Such small-scale, tandem duplicates are therefore revealed as essential elements in the bladderwort’s carnivorous adaptation.”
Transposable elements were another area of investigation, with many more TE-derived events found in the PacBio assembly compared to the previous one. “Serving as a good illustration of the repeat discovery power of PacBio sequencing, ∼47% of the total TE assembly space comprised [large retrotransposon derivatives], whereas these elements amounted to only ∼14.6% of TEs in the previous short-read assembly,” the authors write.
For more information, check out this New York Times article covering the project and hear Tanya Renner, paper co-author, speak about carnivorous plants at the PacBio workshop held at the upcoming Plant & Animal Genome Conference on Monday, January 15th at 12:50 PM. Reserve your seat or register for a recording of the presentation.