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Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite
C E McInerney1, A L Allcock, M P Johnson
1School of Biological Sciences, Queen's University Belfast, Medical Biology Centre, Belfast, Northern Ireland, UK.
Heredity
|April 29, 2010
Summary
Developing microsatellite DNA markers for molluscs is challenging due to high levels of repetitive DNA, particularly transposable elements (TEs). These elements impact genome stability and vary significantly between gastropod species, affecting marker success rates.
Area of Science:
- Genomics
- Molecular Biology
- Marine Biology
Background:
- Developing reliable population DNA molecular markers for molluscs is hindered by unknown factors.
- Microsatellite marker development protocols were applied to three gastropod species: Gibbula cineraria, Littorina littorea, and L. saxatilis.
Purpose of the Study:
- To investigate the reasons behind variable success rates in microsatellite marker development across gastropod species.
- To analyze the genomic characteristics, particularly repetitive DNA content, influencing marker development.
Main Methods:
- Comparative genomic analysis of microsatellite-containing sequences (MCS) from three gastropod species.
- Utilized Repbase scans to identify and classify repetitive DNA, including transposable elements (TEs).
- Examined inter-specific variation in abundance and types of repetitive DNA and TEs.
Main Results:
- Lower microsatellite marker development success in G. cineraria compared to L. littorea and L. saxatilis.
- High incidence of novel, cryptic repetitive DNA in flanking regions of MCS, often identified as TEs.
- Significant inter-specific variation in repetitive DNA and TEs abundance and types (autonomous vs. non-autonomous).
Conclusions:
- Transposable elements and their activity are linked to genome stability and microsatellite marker development success rates in gastropods.
- Non-autonomous TEs, like CvA, may play a significant role in genome rearrangement and act as microsatellite-inducing elements.
- Understanding TE dynamics is crucial for improving molecular marker development in molluscs.
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