Identification Of Insect Lineage-specific Transcription Factors And Their Function Analyses

Gene expression patterns vary in different species. Closely related species, even though they share high genome sequence similarities, also follow that pattern. These differences in gene expression and regulation are believed to be the major sources of species phenotypic variation and important factors for evolution. Both changes in cis and trans cause variations of transcriptional regulation. A change in cis regulatory sequence allows a single node in the network to evolve, whereas when a transcription factor(TF) protein evolves, all of its target genes will be affected. Therefore it has been assumed that transcription factors are much more conserved. Recently, researchers have found that more mutations arise in regulatory proteins than expected. Thus, changes in TFs might be an effective way to regulate gene expression, although the exact mechanisms are still unclear. We used comparative genomics approaches to identify the TFs and compared their differences after evolution in insects. We studied the lineage-specific TFs because these may eliminate the error of the data and can be more representative during evolution. We obtained several results, which are explained below.(1) TF numbers of TFs differ among different insects. We identified 26808 TFs in the genomes of 35 insect species and further classified them into 65 TF families. Through the profiles of TFs, I find that even the numbers of TFs in the same TF family are always not the same. Though TFs in lineage always share the same trends, they still differ among closely related species, suggesting that changes in TFs indeed exist and that these huge variations could be important sources of gene regulatory network(GRN) changes or phenotypic variation among species.(2) Variations in lineage-specific TFs change gene regulatory networks. I constructed 45 NJ-trees of TF families, which may have lineage-specific TFs. We found 20 lineage-specific TFs. Of these, 6 lineage-specific TFs(LSTs) are respectively duplicated in Drosophila but not present in other lineages. I constructed the GRNs of these 6 pairs of LSTs in Drosophila melanogaster, respectively. I found that two duplicates of a pair LST diverged in network structure, indicating that the regulatory function of LSTs might change after duplication.(3) The functions between duplicated copies of lineage-specific TFs diverged obviously. From the allele phenotype data of 6 pairs of lineage-specific TFs in Flybase, I found that different duplicated copies of each lineage-specific TF affected different phenotypes. From developmental and tissue RNA-Seq transcriptome data, I found that the transcriptional profiles of lineage-specific TF duplicates are apparently different.I systematically identified the repertoire of transcription factor in different insect species and found that the numbers of transcription factors might have changed in some specific lineage. This is not consistent with thought before that the repertoires of transcription factors are conserved. In addition, I found that duplicated copies of lineage-specific TFs in Drosophila have different functions. The results presented in this study provide some new insights into the evolutionary significance of transcription factor.