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Genome Sequences Provide Peek at Adaptation, Sex Chromosome Evolution in Flatfish

NEW YORK (GenomeWeb News) – A genome study focused on the first sequenced flatfish so far is providing insights into sex chromosome evolution and the basis of adaptation to life in deep water near the sea floor. The work appeared online yesterday in Nature Genetics.

An international team led by investigators in China and Germany did whole-genome sequencing on male and female representatives from the Chinese half-smooth tongue sole, Cynoglossus semilaevis. By sorting through sequences from both male and female members of the flatfish species, the researchers detected sets of genes that seem to have undergone changes in the fish as it specialized to life near the sea floor.

They also determined that the sex chromosomes in the smooth tongue sole can likely be traced back to the same ancestral protochromosomes that evolved into the sex-determining "Z" and "W" chromosomes in the bird lineage, albeit through independent and more recent convergent evolution.

"Comparison of the relatively young tongue sole sex chromosomes with those of mammals and birds identified events that occurred during the early phase of sex-chromosome evolution," co-senior authors Manfred Schartl, with the University of Wurzburg, China Ministry of Agriculture researcher Qisheng Tang, and Jun Wang, BGI-Shenzhen's executive director, and their colleagues wrote.

"Pertinent to the current debate about heterogametic sex-chromosome decay," they noted, "we find that massive gene loss occurred in the wake of sex-chromosome 'birth.'"

The half-smooth tongue sole has laterally localized eyes and other asymmetrical features that boost its ability to lurk near the seabed. The flatfish species has something else going for it, too: a chromosome-based sex determination system that involves two "Z" chromosomes in males and a "Z" and "W" chromosome in females.

The W chromosome is also found in birds, the study's authors noted. But the avian version is far older and — similar to the Y chromosome — is suspected to have undergone some degeneration, prompting interest in the younger flatfish version.

"The prevailing theory of the evolution of sex chromosomes predicts that degeneration of the heterogametic sex chromosome is a stepwise process that occurs over an extended period of time," they wrote. "We therefore reasoned that an evolutionarily young W chromosome should be more amenable for sequencing than the highly degenerated … W chromosome of birds and would also provide insights into the early steps of W-chromosome evolution."

For their genomic analysis of C. semilaevis, the researchers used Illumina's HiSeq 2000 instrument to sequence genomic DNA from one female half-smooth tongue sole and one male member of the species, producing a female genome assembly with around 117-fold coverage, on average, and a male genome assembly covered to an average depth of 94-fold.

Because male C. semilaevis carry two Z chromosomes (compared to the Z and W sex chromosome content found in females), the team looked for sequences represented twice as often in the male fish when putting together the male chromosome assembly. Sequences that did not map in males were used in making up the W chromosome assembly.

Together, the complete genome sequence set covered the flatfish genome to more than 200-fold average coverage, which was used to put together a combined genome assembly spanning some 477 million bases — a sequence mapped with variant data, an existing genetic map, and restriction site-associated sequencing.

When they annotated the final genome with the help of more than 12 billion bases of transcriptome sequence, the researchers tracked down 21,516 predicted protein-coding sequences, 285 microRNAs, more than 104 ribosomal RNA genes, and hundreds more transfer RNA or small nuclear RNA genes.

Through a combination of expression profiling and phylogenetic comparisons with other vertebrate creatures, the team looked at C. semilaevis relationships with other fish, identifying genes and chromosomal changes that have contributed to key flatfish features.

On the sex chromosome front, the researchers found evidence that the half-smooth tongue sole's male and female chromosomes likely evolved relatively recently, since the split from bony fish, though chromosomes share ancestry with sex chromosomes in the chicken.

Compared to mammalian and avian sex chromosomes, they noted that the flatfish's male and female chromosomes appear less prone to recombination. Still, the W chromosome showed signs of extensive degeneration and protein-coding sequence loss, despite its recent evolution.

Finally, the analysis offered clues to sex determination processes in the fish, which are partly mediated by temperature. In particular, the group found a key role for dmrt1 in that process, a Z chromosome gene noted for its role in male sex determination in chickens.

"[F]uture studies in tongue sole will be necessary to provide further clues for such a [sex-determining] function of dmrt1," the study's authors concluded, adding that, "[s]tudies on the W chromosomes of other species will be informative with respect to the question of whether W chromosome evolution is just a female version of the much better studied Y chromosome evolution."