Abstract
Paired box (PAX) genes are transcription factors that play important roles in embryonic development. Although the PAX gene family occurs in animals only, it is widely distributed. Among the vertebrates, its 9 genes appear to be the product of complete duplication of an original set of 4 genes, followed by an additional partial duplication. Although some studies of PAX genes have been conducted, no comprehensive survey of these genes across the entire taxonomic unit has yet been attempted. In this study, we conducted a detailed comparison of PAX sequences from 188 chordates, which revealed restricted variation. The absence of PAX4 and PAX8 among some species of reptiles and birds was notable; however, all 9 genes were present in all 74 mammalian genomes investigated. A search for signatures of selection indicated that all genes are subject to purifying selection, with a possible constraint relaxation in PAX4, PAX7, and PAX8. This result indicates asymmetric evolution of PAX family genes, which can be associated with the emergence of adaptive novelties in the chordate evolutionary trajectory.
Highlights
Paired box (PAX) genes are transcription factors that play key roles in several aspects of embryonic development and organogenesis [1,2,3]
In vitro studies identified PAX1/9 and PAX1/9b in this species [33], as well as the PAX7, PAX2 [34], PAX6 [33,34,35,36,37], PAX3/PAX7 genes [36]. This in vitro information, which was confirmed by our genome data, suggests that Petromyzon marinus contains genes corresponding to the 4 ancestral PAX genes in addition to a second copy of the PAX1/9 and PAX3/7 type
This suggests that a duplication of the PAX1/9 and PAX3/7 genes occurred in the lamprey or jawless lineage, the possibility of an ancient genome duplication event with subsequent lineage-specific modifications cannot be discarded [12]
Summary
Paired box (PAX) genes are transcription factors that play key roles in several aspects of embryonic development and organogenesis [1,2,3]. The PAX family is specific to the animal lineage, the evolutionary history of these genes remains uncertain. Phylogenetic analyses indicated that a single PAX gene of each subfamily was present in the ancestral chordate and gave rise to the amphioxus PAX. Ohno [9], suggested that the early vertebrate lineage underwent one (1 R) or more ($2 R) whole genome duplications (WGDs). These processes were considered to provide additional possibilities for diversified evolution and/or speciation. The second round of whole genome duplication most likely occurred after the divergence of invertebrate chordate lineages from the ancestral vertebrate, there is controversy about the exact branch at which the phenomenon occurred [11,16,17,18]
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