title: Genesis of the vertebrate FoxP subfamily member genes occurred during two ancestral whole genome duplication events.
abstract: The vertebrate FoxP subfamily genes play important roles in the construction of essential functional modules involved in physiological and developmental processes. To explore the adaptive evolution of functional modules associated with the FoxP subfamily member genes, it is necessary to study the gene duplication process. We detected four member genes of the FoxP subfamily in sea lampreys (a representative species of jawless vertebrates) through genome screenings and phylogenetic analyses. Reliable paralogons (i.e. paralogous chromosome segments) have rarely been detected in scaffolds of FoxP subfamily member genes in sea lampreys due to the considerable existence of HTH_Tnp_Tc3_2 transposases. However, these transposases did not alter gene numbers of the FoxP subfamily in sea lampreys. The coincidence between the "1-4" gene duplication pattern of FoxP subfamily genes from invertebrates to vertebrates and two rounds of ancestral whole genome duplication (1R- and 2R-WGD) events reveal that the FoxP subfamily of vertebrates was quadruplicated in the 1R- and 2R-WGD events. Furthermore, we deduced that a synchronous gene duplication process occurred for the FoxP subfamily and for three linked gene families/subfamilies (i.e. MIT family, mGluR group III and PLXNA subfamily) in the 1R- and 2R-WGD events using phylogenetic analyses and mirror-dendrogram methods (i.e. algorithms to test protein-protein interactions). Specifically, the ancestor of FoxP1 and FoxP3 and the ancestor of FoxP2 and FoxP4 were generated in 1R-WGD event. In the subsequent 2R-WGD event, these two ancestral genes were changed into FoxP1, FoxP2, FoxP3 and FoxP4. The elucidation of these gene duplication processes shed light on the phylogenetic relationships between functional modules of the FoxP subfamily member genes.
authors.affiliation: College of Life Science, Xinyang Normal University, 464000, Xinyang, China; Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, 464000, Xinyang, China; Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China; College of Life Science, Sichuan University, 610064, Chengdu, China. Electronic address: shavisong@xynu.edu.cn.
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Song
authors.affiliation: Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China. Electronic address: tangyz@cib.ac.cn.
authors.forename: Yezhong
authors.initials: Y
authors.lastname: Tang
authors.affiliation: College of Life Science, Sichuan University, 610064, Chengdu, China.
authors.forename: Yajun
authors.initials: Y
authors.lastname: Wang
mesh_terms: D000818:Animals; D005075:Biological Evolution; D017124:Conserved Sequence; D005399:Fishes / Q000145:classification / Q000235:genetics*; D051858:Forkhead Transcription Factors / Q000235:genetics* / Q000378:metabolism; D020440:Gene Duplication; D016678:Genome; D006801:Humans; D007798:Lampreys / Q000145:classification / Q000235:genetics*; D008116:Lizards / Q000145:classification / Q000235:genetics*; D051379:Mice; D009419:Nerve Tissue Proteins / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D025941:Protein Interaction Mapping; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D011956:Receptors, Cell Surface / Q000235:genetics / Q000378:metabolism; D018094:Receptors, Metabotropic Glutamate / Q000235:genetics / Q000378:metabolism; D011988:Receptors, Thyroid Hormone / Q000235:genetics / Q000378:metabolism; D012097:Repressor Proteins / Q000235:genetics* / Q000378:metabolism; D013045:Species Specificity; D014981:Xenopus / Q000145:classification / Q000235:genetics*
chemical_list: C486626:FOXP1 protein, human; D051858:Forkhead Transcription Factors; D009419:Nerve Tissue Proteins; C492116:PLXNA1 protein, human; D020033:Protein Isoforms; D011956:Receptors, Cell Surface; D018094:Receptors, Metabotropic Glutamate; D011988:Receptors, Thyroid Hormone; D012097:Repressor Proteins; C102718:metabotropic glutamate receptor 3
keywords: Evolution; Gene duplication; Phylogenetic analysis; Protein-protein interaction; Whole genome duplication