| Given the rapid accumulation of genomic data, we have known that there exists gene number difference among organisms,just in the same genome, the different genes or gene families are various in number. How the genes origin and evolution, studies on this question will not only help solve this question itself, but also shed light on related evolutionary questions such as speciation. Furthermore, it will also help to promote the related applications, such as new drugs design or manual directional selection. Become many genes in various genomes are too old, the hallmarks of gene creation were obscured by subsequent mutations in the long period of evolution, it is difficult to study the initial molecular events in gene origination and the population dynamic processes following the events. Compared with old genes, young genes retain many structural and sequence features that are important for understanding initial events in new gene origin. However, as the basic unit of genes, the origin and evolution of exons remain largely unknown. Following the thought of young genes, it is necessary to find young exons if we want to understand origin and evolution of new exons. In this article, we used the human genome and ESTs of pig as out groups, we report the first example of two young exons identified in the zinc finger protein 39 genes (zfp39) of rodents. Since they are unique sequences in the rodent genomes and no homologous sequences were found in human and pig, we speculate that the young exons originated after the divergence of primates and rodents (80 million years ago) and before the divergence of mouse and rat (16 million years ago) through exonization of intronic sequences. To shed light on the evolution of new exons in zfp39, we calculated the Ka and Ks and performed Z test on new exons, nonsynonymous substitution rate (K, 0.180) is significantly higher synonymous substitution rate (Ks, 0.068) at 0.05 level suggested that this exon was subject to positive selection, which indicates functional divergence between mouse and rat. We further analyzed the population data in mouse. First, we performed Tajima's D, Fu and Li test on new exon including part of flanking intonic sequences. These tests don't significantly deviate from neutral expectations, which indicate that mutations in introns are selectively neutral. we compared the nucleotide diversities (π) between new exon and introns. The πvalue on the introns (0.00735) is significantly higher than on the new exon (0.00179, P<0.001). As control, πvalue (0.00373) on the partial sequences of the fifth old exon is lower than on the introns at 0.001 levels and higher on the new exon at 0.05 levels. These evidences demonstrate that both exons are under negative selection. Comparing the fifth exon, a stronger functional constraint is detected on the new exon, implying important function on the second exon. The above results suggested that the new exons have undergone the functional constrains and functional divergence between mouse and rat. The following question concern what function of the new exons are, what effect the new exons have on the zfp39 and what functional difference is between mouse and rat. We further analyzed the peptides encoded by the new exon. The results reveal that the structure of peptides are similar to nuclear localization signals (NLS), the divergence of the new exons between mouse and rat form two different NLS. Zfp39 as a number of KRAB-zfp deeply influence functions of genes that code for transcription repression factors that have important function in gene regulation network. From genomic regulation network level, the new exon should deeply enhance the complexity of gene regulation. In this article, we depicted evolution of new exon in rodents, just like hypothesis that we had provide, when the exon had emerged, it should been rapidly fixed under the positive selection and under the neglective selection in the following evolution. |
