Abstract Detail

Comparative Genomics/Transcriptomics

Landis, Jacob [1], Hernandez, Adriana [2], Pinilla Vargas, Maria [3], Zhang, Jing [4], Karimi, Nisa [5], Chan, Pattricia [6], Eifler, Evan [7], Givnish, Thomas [8], Strickler, Susan [9], Specht, Chelsea [2].

Five gigs and then some: assembling a large reference genome in the Liliales (Calochortus venustus; Liliaceae).

The ability to de novo assemble a reference genome in non-model systems is starting to be commonplace using a combination of long- and short-read sequencing technology. Across the angiosperm tree of life several clades still lack a quality reference genome assembly with one such clade being the Liliales. Here we set forth to assemble a reference genome for Calochortus venustus. With an estimated genome size of 5.5 Gbp, the sequencing data and computational resources needed to assemble a high-quality reference are not trivial. Using a combination of Illumina short-reads and Oxford Nanopore long-reads, multiple iterations of the assembly were done with different parameters. The two most complete assemblies in terms of total assembled bases and presence of benchmarking universal single copy orthologs (BUSCO) were the MaSuRCA (using both short- and long-reads) and Flye (raw long-reads) assemblies which were subsequently polished with POLCA. Annotation of the assembled genomes with the MAKER pipeline utilized both Illumina RNA-Seq data, as well as complete (and nearly complete) transcripts sequenced with Oxford Nanopore. Current work aims to generate a chromosome-level assembly using proximity ligation (Hi-C). We show the utility the draft assemblies offer for population genetic and phylogenetic analyses in Calochortus.

1 - Cornell University, School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14850, USA
2 - Cornell University, Section of Plant Biology & the L.H. Bailey Hortorium, 502 Mann Library, Ithaca, NY, 14853, United States
3 - Cornell University, Ithaca, NY, 14853, United States
4 - Boyce Thompson Institute
5 - University Of Wisconsin - Madison, Department Of Botany, 430 Lincoln Drive, Madison, WI, 53706, United States
6 - University Of Wisconsin Madison, Botany, Birge Hall, Madison, WI, 53703, United States
7 - UW Madison, Botany, 430 Lincoln Dr., Madison, WI, 53706, United States
8 - University Of Wisconsin-Madison, Department Of Botany, Birge Hall, 430 Lincoln Drive, Madison, WI, 53706, United States
9 - Boyce Thompson Institute For Plant Research , 533 Tower Road, Ithaca, NY, 14853, United States

Keywords:
Calochortus
Genome Assembly
Liliaceae
Flye.

Presentation Type: Poster
Session: P1, Comparative Genomics/Transcriptomics Posters
Location: Virtual/Virtual
Date: Monday, July 19th, 2021
Time: 5:00 PM(EDT)
Number: P1GT008
Abstract ID:737
Candidate for Awards:None