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International Team Takes a Look at Common Carp Genome, Diversity

NEW YORK (GenomeWeb) – In a study appearing online this weekend in Nature Genetics, researchers from China, the US, and Hungary presented findings from their effort to produce a draft genome sequence for the domesticated common carp, Cyprinus carpio, and to assess the genetic diversity present in carp populations from around the world.

The team turned to a combination of sequencing technologies to tackle DNA from a domesticated carp strain called Songpu. After establishing a high-quality assembly that spanned more than 92 percent of the common carp genome, the group went on to re-sequence almost three-dozen more individuals drawn from carp populations in Europe, North America, and China.

From these sequences, the researchers examined everything from the genetic factors behind specific carp features to the evolution of the widely cultivated freshwater fish — peering into relationships between European and Asian carp clades and the genes suspected of influencing some of their distinct physical features.

"In combination with a high-resolution genetic map, the draft genome paves the way for better molecular studies and improved genome-assisted breeding of C. carpio and other closely related species," Xiaowen Sun of the Chinese Academy of Fishery Sciences and Jun Yu of the Chinese Academy of Sciences, the study's co-senior authors, and their colleagues wrote.

Roughly one-tenth of the world's freshwater aquaculture is devoted to producing the common carp, the researchers noted, and even more effort goes into raising related carp species as food or ornamental pets.

But while a range of genetic and genomic resources have been developed for these bony fish in the past, they explained, details of its complete genome — which spans some 50 chromosomes — had yet to be deciphered.

For their new analysis, the team sequenced DNA from a homozygous doubled-haploid line for the domesticated C. carpio strain Songpu using Roche 454, Illumina, and SOLiD instruments.

Together, these reads were used to produce an almost 1.7 billion base genome assembly that covers 92.3 percent of the total common carp genome and contains an estimated 52,610 protein-coding genes, 914 microRNA genes, and more than 500 million sequences stemming from transposable elements.

Using information at almost 3,500 SNPs and some 773 microsatellite makers, the assembly was linked to a carp genetic map to produce 50 sets of linked sequence, each approximately coinciding with a haploid carp chromosome.

The team tested the veracity of its gene annotation using new and existing transcriptome sequences, along with gene prediction and protein homology-based annotation approaches, verifying expression for more than 91 percent of the predicted genes.

The researchers' comparisons with other animals and bony fish offered clues to the fish's past, suggesting the most recent whole-genome duplication event occurred some 8.2 million years ago in the C. carpio lineage.

By re-sequencing 33 common carp accessions from four wild and six domesticated populations, they tracked down nearly 19 million SNPs and almost 1.7 million small insertions and deletions — genetic variants that helped in spelling out the genetic diversity and relationships found in C. carpio.

Two main genetic clusters emerged in the common carp, for instance, with common carp accessions from Asia falling in one clade and European accessions in another. Various carp accessions raised in the US tended to fall into each of these clades, apparently reflecting the introduction of fish from both Europe and Asia over time.

When they compared representatives from the Asian sub-species C. carpio haematopterus and the European sub-species C. carpio carpio — carp varieties known for their dissimilar body shapes, scale features, and skin coloring — the investigators identified just over 200 regions in the genome and some 326 genes that appear to have diverged between the two sub-species.

In an effort to better understand such candidate regions and their role in skin color and scale shape, the team produced deep RNA sequence data on skin samples, revealing hundreds of genes with higher-than-usual expression in skin tissue from each of the sub-species.

"[T]he draft genome assembly presented here provides a valuable resource for genetic, genomic, and biological studies of C. carpio," the authors concluded, "and for improving the aquaculturally important traits of farmed C. carpio and other key [carp] species in aquaculture."