Comparative Genome Analysis of Soybean Germplasms By Optical Mapping
Refereed conference paper presented and published in conference proceedings


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AbstractOptical mapping is an imaging technique for capturing enzymatic patterns along DNA molecules of hundredkilobase
scale. It has been applied to different genomic applications including genome assembly, microbial
strain typing, and structural variation detection. Recently, high­throughput technology for optical mapping data
generation raises interest on its applications in comparative genomics. Previous studies using optical mapping
in comparative genomics mainly focuses on detecting structural variations between two genome assemblies,
or between multiple genome assemblies together with a reference. However, result interpretation in the former
becomes difficult when three or more genomes are analyzed. While the latter is able to analyze more
genomes, it is limited by the quality and completeness of the reference. In addition, both approaches cannot
handle well multiple types of variations within the same region, or regions frequently confounded by repetitive
elements, inversions or other large­scale rearrangements. Such regions are usually variation hotspots that
carry important biological meanings.

We introduce an analysis framework using a reference­free approach based on multiple alignment of optical
map contigs. Segments of DNA molecules with signal patterns conserved among samples are grouped as
collinear blocks. Samples with higher similarity as sharing more conserved regions are clustered together,
providing hints for phylogeny. Blocks contributing to most variations between sample clusters are found by
statistical analysis. Further annotation reveals the identities of these blocks as the most representative
features. We anticipate this method can facilitate comparative genome analysis on soybean, which has a high
degree of diversity between different germplasms.

(This work is supported by the UGC Area of Excellence Scheme AoE/M­403/16, the Lo Kwee­Seong
Biomedical Research Fund, and the Lee Hysan Foundation.)
All Author(s) ListClaire Yik Lok Chung, Alden King Yung Leung, Hon ­Ming Lam, Ting Fung Chan
Name of ConferencePlant & Animal Genome XXVI Conference
Start Date of Conference13/01/2018
End Date of Conference17/01/2018
Place of ConferenceSan Diego, CA
Country/Region of ConferenceUnited States of America
Year2018
LanguagesEnglish-United States
Keywordsoptical mapping, soybean, multiple alignment, comparative genomics

Last updated on 2018-05-06 at 11:46