Intragenic isochores (intrachores) in the platelet phosphofructokinase gene of Passeriform birds

•There are short intragenic isochores in PPFK gene of birds from Passeriformes order.•3GC of two exons overlapped with intrachores is higher than 80%.•Clusters of transcription factor binding sites were predicted in those intrachores.•Conserved microRNA precursors and TSSs were predicted in those areas.•Two intrachores were formed in the period from 91.4 to 47.1 Mya.

Total GC-content in the platelet phosphofructokinase gene of Zebra Finch (Taeniopygia guttata) is low (37.53 ± 0.51%), while there are short areas (about 300 nucleotides in length) with increased GC-content overlapping its exon 4 and exon 17. GC-content in third codon positions (3GC) of those two exons is equal to 88.42 and 80.00%, respectively, while overall 3GC of the coding region is equal to 49.9%. Similar distribution of GC-content has been found in platelet phosphofructokinase genes of other birds from Passeriformes order. According to the results of phylogenetic analysis, formation of those areas with high G + C started from 91.4 to 47.1 million years ago, since there are no such peaks of GC-content in homologous genes of other birds and reptiles. There are clusters of transcription factor binding sites in those areas with higher GC-content, as well as microRNA precursors conserved in Zebra Finch and Flycatcher genes. According to our hypothesis those intragenic isochores (intrachores) may be consequences of autonomous microRNA precursor transcription at certain period(s) of embryogenesis and gametogenesis, when the platelet phosphofructokinase gene itself is not expressed. Transcription-associated mutational pressure existing during those periods may cause the increase in rates of AT to GC mutations in those genes which are transcribed.