NEW YORK (GenomeWeb News) – In a study appearing online this week in Nature Genetics, researchers described findings from an effort to sequence and scrutinize the genome of platyfish, Xiphophorus maculatus — a freshwater fish species that gives birth to live young and exhibits other intriguing traits and behaviors.
An international team led by investigators at Washington University's Genome Institute, the University of Würzburg, and Texas State University sequenced genomic DNA from an inbred female platyfish, producing a genome assembly that housed some 20,366 predicted protein-coding genes, almost 350 non-coding genes, and more than two-dozen pseudogenes.
Through analyses of the genome, genetic mapping, and comparisons with other vertebrates, the team managed to get genetic clues to some of the platyfish's unusual—and, in some cases, mammal-like — traits. The fish is known, for instance, for its ability to give birth to live young, its complex behavioral patterns, and its susceptibility to certain cancers.
"The platyfish genome sequence and analysis have provided new perspectives for several prominent features of this fish model," senior author Wesley Warren, with Washington University's Genome Institute, and colleagues wrote, "including its live-bearing reproductive mode, variation in pigmentation patterns, sex chromosome evolution in action, complex behavior, and both spontaneous and induced carcinogenesis."
The researchers used a combination of Roche 454 Titanium and Illumina GAIIx sequencing to tackle genomic DNA from a female platyfish belonging to the Jp163A strain. They also folded in BAC-end sequence information generated by Sanger sequencing.
Together, the sequence data covered the platyfish genome to an estimated depth of almost 20-fold, on average. Using these sequences, the team initially put together the data with two assembly algorithms before merging the data into a single platyfish genome assembly.
The investigators used a so-called restriction site-associated DNA, or RAD, tagging method to come up with a meiotic map, too, outlining two-dozen platyfish linkage groups.
When they annotated the genome — with the help of transcriptome sequences from various platyfish tissues and stages of development — the researchers unearthed 20,366 predicted protein-coding genes, 348 non-coding genes, 28 pseudogenes, and a wide range of transposable elements.
By putting the platyfish genome and genetic map side-by-side with sequences from other vertebrates, meanwhile, the group got hints about evolution both within and beyond the teleost fish lineage to which platyfish belong.
The researchers' analyses also uncovered genetic clues to some of the platyfish's most notable traits — from the genes contributing to melanoma risk in the fish to those leading to live birth rather than egg-laying.
For instance, a search of the platyfish genome uncovered orthologs of mammalian genes involved in live birth and/or placental function that have apparently been subject to positive selection in the platyfish genome. Even so, selection patterns at reproductive genes were different in platyfish and swordtail (another live-bearing fish) than they were in mammals and marsupials, suggesting that the fish have become capable of live birth through convergent evolution, using somewhat different placental structures.
On the behavioral side, meanwhile, they saw that the platyfish genome contains an over-representation of gene duplicates related to cognition — a pattern that seems to stretch back to a whole-genome duplication event that affected the teleost lineage hundreds of millions of ago.
Some 45 percent of the 190 cognition-related genes duplicated during that event are still duplicated in platyfish, the study authors explained. In contrast, less than one-third of pigmentation gene duplicates and just 15 percent of duplicated liver-related genes have stuck around in the genomes of platyfish and other teleosts.
"This finding supports the hypothesis that paralog retention from the [teleost genome duplication] event may have supported the high level of behavioral complexity in Xiphophorus and other teleosts," Warren and his co-authors concluded.