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Scientists Reveal Recent Autosome-to-Y Duplication Event in Drosophila

Tuesday, October 20, 2015

Drosophila_melanogaster1Following on the heels of characterizing 18 Mst77Y genes that were tandemly duplicated within a 96 kb region (Krsticevic FJ, et al., 2015), scientists from institutes in Brazil, Austria, and the United States recently published a study in which they also used the Drosophila melanogaster data release from PacBio to characterize a region of the Y chromosome that had never before been accessible.

In a paper published in PNAS, entitled “Birth of a new gene on the Y chromosome of Drosophila melanogaster,” lead author Antonio Bernardo Carvalho, senior author Andrew Clark, and collaborators detail their find of a gene duplicated from an autosome. “We emphasize the utility of PacBio technology in dealing with difficult genomic regions,” the authors write. “PacBio produced a seemingly error-free assembly of the FDY region, something that has eluded us for years of hard work.”

The 55 kb region, which consists of several pseudogenes as well as the newly discovered functional FDY gene, has been challenging to sequence and assemble since it exists only on the Y chromosome and is full of highly repetitive sequence. Some 75% of its length, the scientists report, is made up of transposable elements.

Their discovery was worth the wait. Unlike mammalian Y chromosomes, which are thought to evolve primarily by gene loss, the Drosophila Y chromosome appears to be the result of millions of years of gene gains. The team demonstrates that the new gene they detected, named FDY for flagrante delicto Y, was formed about 2 million years ago in a single duplication event of the gene vig2 and its flanking sequence from chromosome 3R. That flanking sequence originally included four other genes, “but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis,” the scientists report. Today, FDY shares 98% sequence identity with its vig2 parent.

The paper details the team’s effort to sequence the FDY region, using RT-PCR, clonal sequencing, and publicly available genome assemblies. Most existing assemblies did not fully cover the region. “Fortunately … the PacBio [MHAP] assemblies covered not only FDY, but also substantial flanking regions,” the scientists write. With that resource, they had their first view of the full sequence of the region. By comparing it to Sanger and Illumina sequence data, they concluded that the PacBio assembly is complete and accurate.

Carvalho et al. went on to figure out when FDY likely appeared in the genome. Their sequence divergence analysis suggests that the duplication occurred once, about 2 million years ago. The gene was found in samples of D. melanogaster from around the world, but does not appear in the fly’s closest relatives.

“Hence a female-biased gene (vig2) gave rise to a testis-biased gene (FDY),” the authors write. “This seems to be a case of gene duplication followed by neofunctionalization, the first reported, to our knowledge, for the Drosophila Y.”

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