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Comparative genomics of chondrichthyan Hoxa clusters
John F Mulley1, Ying-Fu Zhong, Peter Wh Holland
1Department of Zoology, University of Oxford, South Parks Road, Oxford, OX13PS UK. john.mulley@zoo.ox.ac.uk
BMC Evolutionary Biology
|September 4, 2009
Summary
Cartilaginous fish genomes, like the Little Skate and Horn Shark, show high conservation of Hoxa clusters. This suggests ancient non-coding elements are retained, aiding DNA studies but complicating bioinformatics.
Area of Science:
- Genomics
- Evolutionary Biology
- Comparative Genomics
Background:
- Chondrichthyes (cartilaginous fish) are evolutionarily significant as the sister group to all other jawed vertebrates.
- Few comparative genomic studies exist for chondrichthyans, and none within the group.
- The Hoxa cluster is crucial for understanding vertebrate development and evolution.
Purpose of the Study:
- To sequence and analyze the complete Hoxa cluster of the Little Skate (Leucoraja erinacea).
- To compare the Little Skate Hoxa cluster with that of the Horn Shark (Heterodontus francisci) and Elephant Shark (Callorhinchus milii).
- To investigate the conservation of coding and non-coding elements within cartilaginous fish genomes.
Main Methods:
- Complete sequencing and assembly of a BAC clone containing the Little Skate Hoxa cluster.
- Comparative analysis of coding sequences and conserved non-coding elements between species.
- Identification of novel potential non-coding RNAs within the Skate Hoxa cluster.
Main Results:
- High conservation of the Hoxa cluster between Little Skate and Horn Shark, with 20 ultraconserved elements identified.
- Significantly higher conservation (20 elements) compared to human-marsupial comparisons (3 elements).
- Discovery of novel potential non-coding RNAs in the Little Skate Hoxa cluster, some conserved across species.
Conclusions:
- The Hoxa cluster of the Little Skate is highly similar to that of the Horn Shark, despite 180 million years of divergence.
- Cartilaginous fish genomes exhibit greater conservation than tetrapods or teleosts, likely retaining ancestral non-coding elements.
- This high conservation aids homologous DNA isolation but presents challenges for identifying chondrichthyan-specific non-coding DNA.
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