Northern Snakehead Fish Genome Sequenced

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Northern Snakehead Fish Genome Sequenced

China have sequenced and started analyzing a draft genome assembly for the Northern snakehead fish, Channa argus — work they described in the journal GigaScience yesterday.

The East Asian freshwater fish, which is a widely used food source in Asia and parts of Africa, is considered invasive in North America, the team explained, prompting interest in new methods for detecting and controlling the aggressive species at sites where it was introduced. Meanwhile, its ability to travel over short stretches of land makes the Northern snakehead biologically intriguing, particularly for those studying fish breathing methods, evolution, and more.

Using short- and long-insert libraries prepared with genomic DNA from a female C. argus at the Chinese Academy of Fishery Sciences, the investigators did Illumina HiSeq 2000 shotgun sequencing, followed by de novo assembly — producing a 615.3 million base draft assembly that contained an estimated 19,877 protein-coding genes based on an annotation that tapped into available RNA sequence data for more than a dozen Northern snakehead tissues and comparisons with other fish genome sequences.

"The draft genome assembly will be [a] valuable resource for genetic breeding, environmental DNA detection of invasive species, and biological studies on this economically important teleost fish," senior author Peng Xu, a researcher affiliated with the Key Laboratory of Aquatic Genomics, the Chinese Academy of Fishery Sciences, and Xiamen University, and his co-authors wrote. "Based on these genomic data, researchers will be able to develop genetic markers for further quantitative trait locus and genome-wide association studies on growth traits. These markers will also be very useful for DNA barcoding in screening invasive C. argus for ecological protection."

In addition to annotating the new Northern snakehead genome, the team used Core Eukaryotic Genes Mapping Approach (CEGMA) software and single copy vertebrate gene set information from BUSCO to assess the quality and completeness of the assembly.

And with sequences from more than 1,900 single-copy genes and predicted proteomic patterns in C. argus and other fish, the researchers performed phylogenetic analyses that placed the Northern snakehead within the fish family tree, identifying two-dozen gene families that appear to be Northern snakehead-specific.

Their analyses indicated that nearly 19 percent of sequences in the new genome stemmed from repeat sequences, with long interspersed nuclear elements making up the greatest proportion of those repeats.

From their results so far, and anticipated applications of the draft genome, the study's authors said the Northern snakehead genome "will provide a valuable genetic resource for further biomedical investigations" of the fish.