Abstract
BackgroundThe coelacanth is known as a “living fossil” because of its morphological resemblance to its fossil ancestors. Thus, it serves as a useful model that provides insight into the fish that first walked on land. Retrocopies are a type of novel genetic element that are likely to contribute to genome or phenotype innovations. Thus, investigating retrocopies in the coelacanth genome can determine the role of retrocopies in coelacanth genome innovations and perhaps even water-to-land adaptations.ResultsWe determined the dS values, dN/dS ratios, expression patterns, and enrichment of functional categories for 472 retrocopies in the African coelacanth genome. Of the retrocopies, 85–355 were shown to be potentially functional (i.e., retrogenes). The distribution of retrocopies based on their dS values revealed a burst pattern of young retrocopies in the genome. The retrocopy birth pattern was shown to be more similar to that in tetrapods than ray-finned fish, which indicates a genomic transformation that accompanied vertebrate evolution from water to land. Among these retrocopies, retrogenes were more prevalent in old than young retrocopies, which indicates that most retrocopies may have been eliminated during evolution, even though some retrocopies survived, attained biological function as retrogenes, and became old. Transcriptome data revealed that many retrocopies showed a biased expression pattern in the testis, although the expression was not specifically associated with a particular retrocopy age range. We identified 225 Ensembl genes that overlapped with the coelacanth genome retrocopies. GO enrichment analysis revealed different overrepresented GO (gene ontology) terms between these “retrocopy-overlapped genes” and the retrocopy parent genes, which indicates potential genomic functional organization produced by retrotranspositions. Among the 225 retrocopy-overlapped genes, we also identified 46 that were coelacanth-specific, which could represent a potential molecular basis for coelacanth evolution.ConclusionsOur study identified 472 retrocopies in the coelacanth genome. Sequence analysis of these retrocopies and their parent genes, transcriptome data, and GO annotation information revealed novel insight about the potential role of genomic retrocopies in coelacanth evolution and vertebrate adaptations during the evolutionary transition from water to land.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2178-9) contains supplementary material, which is available to authorized users.
Highlights
The coelacanth is known as a “living fossil” because of its morphological resemblance to its fossil ancestors
We first compared the sequences of each retrocopy and its parent gene, which revealed a total of 235 intact retrocopies with no frameshift mutations or premature stop codons (Fig. 1, Additional file 1: Table S1)
Our study revealed a burst pattern of young retrocopies in the coelacanth genome
Summary
The coelacanth is known as a “living fossil” because of its morphological resemblance to its fossil ancestors. Retrocopies are a type of novel genetic element that are likely to contribute to genome or phenotype innovations. Investigating retrocopies in the coelacanth genome can determine the role of retrocopies in coelacanth genome innovations and perhaps even water-to-land adaptations. Genes that are unnecessary for existence in a new environment are often eliminated during the course of evolution, but genomes acquire novel genetic elements as a source of functional and phenotypic diversity [1]. Retrocopies, one type of novel genetic element, are genome segments that are reverse-transcribed from intronless mRNA and inserted into new positions in the genome (i.e., RNA-based duplication) [1]. Despite the substantial contribution to molecular evolution revealed by studies on retrocopies in humans and fruit flies [10,11,12,13], the patterns of retrocopy formation and effects on genomic dynamics of lower vertebrates remain undetermined
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