To test the extent of intron gain in placental-specific gene families the presence of intron gain has been analyzed in KRAB and SCAN ZNF genes, especially in those orthologous genes that originated in the ancestor of placentals ()150 orthologous genes were analyzed). The analysis has shown that the amount of intron gain in these genes is not as high as in the case of TE-derived domesticated genes and retrogenes, but a number of cases with intron gain can, even so, be recognized. The analysis of placental-specific domesticated genes, retrogenes and placental-specific transcription factors (~200 were analyzed) has shown that numerous intron gains occurred in the ancestor of placentals and that intron gain is still ongoing in mammals. This study provides the first evidence for numerous intron gains in the ancestor of placental mammals.
COBISS.SI-ID: 25309479
Vertebrates, especially mammals, possess numerous single copy domesticated genes (DGs) that have originated from the intronless multicopy transposable elements. However, the origin and evolution of the retroelement-derived DGs (RDDGs) that originated from Metaviridae has been only partially elucidated, due to absence of genome data or to limited analysis of a single family of DGs. We traced the genesis and regulatory wiring of the Metaviridae-derived DGs through phylogenomic analysis, using whole-genome information from more than 90 chordate genomes. Phylogenomic analysis of these DGs in chordate genomes provided direct evidence that major diversification has occurred in the ancestor of placental mammals. Analysis of syntenic loci has shown that diverse RDDGs and their chromosomal positions were fully established in the ancestor of placental mammals. By analysis of active Metaviridae lineages in amniotes, we have demonstrated that RDDGs originated from retroelement remains. The chromosomal gene movements of RDDGs were highly dynamic only in the ancestor of placental mammals. During the domestication process, de novo acquisition of regulatory regions is shown to be a prerequisite for the survival of the DGs. The origin and evolution of de novo acquired promoters and untranslated regions in diverse mammalian RDDGs have been explained by comparative analysis of orthologous gene loci. The origin of placental mammal-specific innovations and adaptations, such as placenta and newly evolved brain functions, was most probably connected to the regulatory wiring of DGs and their rapid fixation in the ancestor of placental mammals.
COBISS.SI-ID: 26492711
Our approach and methodology can be used for any highly divergent protein superfamily in making sense out of genome sequence data and in understanding their evolution.
COBISS.SI-ID: 23152679
The large amount of recently accumulated genome-wide data on TEs in diverse lineages of sauropsids has provided a remarkable opportunity to review current knowledge about TEs of sauropsids in their genomic context.
COBISS.SI-ID: 23528999