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Small RNA Sequencing Study Offers Peek into Vertebrate Evolution

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – A new small RNA sequencing study is providing insights into how some jawless vertebrate animals called the agnathans are related to one another and to jawed vertebrates, known as gnathostomes.

A team of researchers from the US, UK, and France used high-throughput sequencing to look at the small RNA repertoire in hagfish and lamprey specimens, comparing these patterns to those found in jawed vertebrates. The research, scheduled to appear online this week in the Proceedings of the National Academy of Sciences, suggests that the present day jawless vertebrates, known as cyclostomes because of their round mouths, may belong to a single evolutionary lineage rather than arising from parallel lineages.

Those involved in the study say the results also underscore the importance of microRNAs in vertebrate biology.

"The prolific origin of miRNA families in the vertebrate stem-lineage and organs supports the idea that miRNAs played a pivotal role, as part of a broader gene regulatory landscape, in the assembly of the vertebrate body plan," co-corresponding author Kevin Peterson, a molecular paleobiology researcher at Dartmouth College, and his co-authors wrote.

Although several molecular and morphological studies of hagfish and lamprey have been done, the researchers explained, debate remains over whether these cyclostomes both belong to the same jawless vertebrate evolutionary lineage or whether they represent separate lineages, with hagfish belonging to a group more closely related to gnathostomes.

To address such questions, Peterson and his co-workers used Roche 454 and Illumina platforms to sequence small RNA libraries from brook lamprey larvae, several sea lamprey tissues, and an Atlantic hagfish, along with small RNA libraries from a jawed vertebrate, the catshark.

When they compared the miRNA profiles in lamprey, hagfish, and gnathostomes, the researchers found that hagfish lack only two of the nearly four-dozen miRNA libraries found in both lamprey and gnathostomes. The two jawless animals also shared four more miRNA families not found in jawed vertebrates.

Combined with miRNA sequence, morphological, and other data, the small RNA patterns are consistent with monophyly between hagfish and lamprey, the team explained, noting that "the acquisition of miRNA families, miRNA genes, and the nucleotide substitution patterns of conserved miRNA genes all support cyclostome monophyly."

Nevertheless, the researchers noted that the overall miRNA expression patterns seem to be largely conserved across vertebrate species. For instance, they found that 202 of the 269 known or predicted microRNA genes in the sea lamprey, Petromyzon marinus, are conserved in other animals.

And the team's miRNA expression experiments in several sea lamprey tissues indicate that each has its own miRNA repertoire — findings that they say supports the idea that "miRNAs were instrumental in the evolutionary origin of vertebrate-specific organs."

"[P]rofiling the miRNA expression within nine organs of P. marinus shows conservation with known expression profiles in homologous organs across vertebrates," they explained. "Our data suggest that the role of miRNAs within specific organs is coincident with their appearance within the genome, and thus, miRNAs may have played a role in the acquisition of organismal complexity in vertebrates."

Based on their findings, the team also argues that shared features found in lampreys and gnathostomes actually represent ancestral vertebrate features that were lost from the hagfish lineage.

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