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Seahorse Adaptations Explored With New Genome Sequence

NEW YORK (GenomeWeb) – New genomic and transcriptomic data are serving as a source of information for those interested in untangling unusual features found in seahorses.

Researchers from Singapore, Germany, and China sequenced and put together a de novo genome assembly for the tiger tail seahorse, Hippocampus comes. Through comparisons with ray-finned fish sequences, they identified genetic features suspected of contributing to physical features in the tiger tail seahorse — from its stretched out snout and missing mineralized teeth to male pregnancy and vertical body plan. The results appeared online today in Nature.

"Our analyses of the H. comes genome sequence and comparative genomics with other teleosts highlighted several genetic changes that may be involved in the evolution of the unique morphology of seahorses," the study's authors wrote.

The researchers used the Illumina HiSeq 2000 instrument to sequence genomic DNA from a male tiger tail seahorse, generating sequences that were assembled into a de novo assembly stretching some 501.6 million bases and containing an estimated 23,458 protein-coding genes. They also performed RNA sequencing on soft tissue samples such as the gills, brain, muscle, liver, and intestine in male and female H. comes representatives to aide in the genome annotation and to assess gene expression in these seahorse tissues.

For its annotation and analyses, the team compared the genome and transcriptomic sequences to available sequence data for the lined seahorse, H. erectus, and an array of ray-finned fish, including the stickleback, medaka, Nile tilapia, fugu, and platyfish.

Using a phylogenetic tree based on more than 4,000 orthologous genes, the researchers estimated that the seahorse lineage diverged from the lineage leading to the so-called percomorph fish — commonly known as the spiny-finned fish — roughly 103.8 million years ago.

Compared with the other fish, the new seahorse genome contained expansions to gene families suspected of contributing to biological processes needed for hatching and for male seahorses to form brood pouches and nourish developing embryos in them.

On the other hand, H. comes was missing genes implicated in the formation of mineralized tissues such as bones and enamel as well as transcription factor-coding gene that appears to be involved in pelvic fin formation. It also contained fewer-than-usual genes involved in sense of smell, along with contracted collections of conserved non-coding elements that serve as enhancers, repressors, and other regulatory contributors.

There were other differences, too, the authors explained, including ramped up nucleotide and protein evolutionary rates and altered expression profiles for genes that have undergone duplications in the seahorse lineage.

"Our genome-wide analysis highlights several aspects that may have contributed to the highlight specialized body plan and male pregnancy of seahorses," they wrote. "These include a higher protein and nucleotide evolutionary rate, loss of genes, and expansion of gene families, with duplicated genes exhibiting new expression patterns, and loss of a selection of potential cis-regulatory elements."

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