Abstract Detail

Comparative Genomics/Transcriptomics

Ou, Shujun [1], Chen, Jinfeng [2], Jiang, Ning [3].

Assessing genome assembly quality using the LTR Assembly Index (LAI).

Assembling a plant genome is challenging due to the abundance of repetitive sequences. While many quality metrics have been developed, there is a lack of measures for assessing the assembly continuity of intergenic and repetitive sequence space. LTR retrotransposons (LTR-RTs) is the major intersperse repeat in plants and one of the poorest assembled contents due to its long length (up to 20 Kb) and high identity (nearly 100%) nature. In practice, we found more LTR-RTs were assembled in genomes with higher quality. Based on this idea, we propose a new genome metric called LTR Assembly Index (LAI) that evaluates the continuity of a de novo assembly based on LTR-RTs. After correcting for the dynamic of LTR-RTs using the identity of LTR sequences, LAI becomes robust between genomes with varying backgrounds of LTR-RTs. Moreover, LAI could be used for assembler selection and identifying low-quality genomic regions. We also reveal the limitation of short-read-based genome sequencing in decoding repetitive sequences and the significant gain of sequence continuity by using long-read sequencing methods.

Related Links:
Link to the software download (GitHub)

1 - Michigan State University, 1066 Bogue St, Room A326, East Lansing, MI, 48823, United States
2 - University of California, Riverside, Department of Plant Pathology and Microbiology, Riverside, CA, 92507, USA
3 - Michigan State University, 1066 Bogue St, Room A330, East Lansing, MI, 48823, United States

Keywords:
genome
assembly continunity
LTR retrotransposon
LTR Assembly Index.

Presentation Type: Oral Paper
Session: 25, Comparative Genomics and Transcriptomics II
Location: 102/Mayo Civic Center
Date: Tuesday, July 24th, 2018
Time: 1:00 PM
Number: 25001
Abstract ID:649
Candidate for Awards:Margaret Menzel Award