Skip to main content
Premium Trial:

Request an Annual Quote

Sequence Analyses Suggest Shark, Skate Group Missing Some Key Developmental Genes

NEW YORK (GenomeWeb News) – A set of genes thought to be essential to embryonic development in animals is absent from the genomes of some cartilaginous fish, a new study suggests.

In a brief report in Science today, researchers from the Mount Desert Island Biological Laboratory and the University of Cambridge reported that, unlike other jawed vertebrates characterized so far, the dogfish shark, Scyliorhinus canicula, and the little skate, Leucoraja erinacea, do not express representatives from all four Hox gene clusters during development.

Moreover, while genes from three of the four clusters were present in the genome of the little skate, genes from one cluster, called HoxC, were missing. On the other hand, consistent with past work, the team found that the genome of the elephant shark, Callorhinchus milii, contains genes from each of the four Hox clusters.

Based on their analyses, investigators believe a subset of the Hox genes has been selectively lost from the genomes of cartilaginous fish in a sub-group known as the elasmobranchs, but not in other cartilaginous fish such as the holocephali group, which contains the elephant shark. If so, they say, it's possible that some Hox genes are more dispensable than long believed.

"If elasmobranchs do not need HoxC genes to develop properly, we must consider the possibility that there is more flexibility in the role of the various Hox clusters than we previously thought," MDIBL researcher Benjamin King, the study's first author, said in a statement.

Past studies in animals ranging from fruit flies to mammals have underscored the importance of the transcription factor-coding Hox genes in patterning and body plan organization during embryonic development. The genomes of jawed vertebrates, for example, typically house at least one gene from each of four Hox gene clusters: HoxA, HoxB, HoxC, and HoxD. But King and his colleagues now believe that is not always the case.

For their comparisons, the team used sequencing-based gene expression data for two elasmobranchs, the dogfish shark and the little skate, and one holocephalan, the elephant shark. They also assessed whole-genome sequence data for little skate, which was sequenced to an average of around 26 times coverage by King and other members of a group known as the North East Cyberinfrastructure Consortium from Maine, New Hampshire, Vermont, Rhode Island, and Delaware.

While gene expression data indicated that the elephant shark expresses 45 Hox genes during development — including genes from all four Hox clusters — neither the dogfish shark nor the little skate expressed HoxC genes, the researchers found. Instead, these elasmobranchs expressed 34 Hox genes during development, all from the HoxA, HoxB, and HoxD clusters.

Moreover, analyses of the little skate genome hint that the lack of HoxC expression during development is a consequence of genomic deletion in the elasmobranchs rather than transcriptional silencing. In contrast to the elephant shark genome, which contains 11 HoxC genes, as well as microRNA sequences within the HoxC region, the researchers did not find any of the HoxC genes or neighboring miRNAs in the little skate genome.

"Our data suggest that the lack of HoxC gene expression during L. erinacea and S. canicula development is attributable to a genomic deletion of the entire HoxC cluster in these taxa," they wrote. "The most likely scenario is that the entire HoxC cluster was lost in a single genomic reduction event after the divergence of holocephalans and elasmobranchs but before the divergence of batoids [skates and rays] and sharks."

The Scan

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.