Abstract Detail

Comparative Genomics/Transcriptomics

Landis, Jacob [1], De La Cerda, Gisel [2], Hernandez, Adriana [3], Zhang, Jing [4], Powell, Adrian [4], Givnish, Thomas [5], Specht, Chelsea [6], Strickler, Susan [7].

Utilizing the long and the short: comparison of different genome assembly programs for a 5.5 GB Liliales genome.

Even though the average genome size of the angiosperms is approximately 5 GB, most assembly approaches are designed and tested on genomes that are smaller in size. The computational resources needed to assemble larger genomes do not scale linearly and working with large genomes can result in challenges not observed with smaller genomes. Here we present results comparing long-read and hybrid genome assemblies of Calochortus venustus (Liliaceae), including many of the most common approaches. We also explore the impact of using raw Nanopore long-reads versus error corrected long-reads in different assembly methods. We find that the majority of genome assemblers used in the literature struggle with handling a modest amount of sequencing data (35x long-reads and 40x short-reads) and to an extent the quality of the resulting assembly correlates with computational resources needed, with faster assemblies generally producing more fragmented, smaller assemblies. As expected, closely related species with smaller amounts of long-read data produced more fragmented assemblies compared to species with more data. Surprisingly, we see a decrease in quality of the assembled genome when using error corrected Nanopore reads compared to the raw Nanopore reads that are more error prone. Overall, this manuscript provides a comparison of common genome assemblers when trying to assemble larger plant genomes, highlighting the comparisons between completeness of the assembly versus the computational resources needed for each assembly.

1 - Cornell University
2 - 419 E King Rd , Ithaca, CA, 14850, United States
3 - Cornell University, School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Ithaca, NY, 14853, United States
4 - Boyce Thompson Institute
5 - University Of Wisconsin-Madison, Department Of Botany, 315 Birge Hall, 430 Lincoln Drive, Madison, WI, 53706, United States
6 - Cornell University, Plant Biology, Plant Science, 236 Tower Road, Ithaca, NY, 14851, United States
7 - Boyce Thompson Institute For Plant Research , 533 Tower Road, Ithaca, NY, 14853, United States

Keywords:
Calochortus
monocot
genome assembly
Nanopore.

Presentation Type: Oral Paper
Number: CGT3002
Abstract ID:180
Candidate for Awards:None