title: High variability of expression profiles of homeologous genes for Wnt, Hh, Notch, and Hippo signaling pathways in Xenopus laevis.
abstract: Cell signaling pathways, such as Wnt, Hedgehog (Hh), Notch, and Hippo, are essential for embryogenesis, organogenesis, and tissue homeostasis. In this study, we analyzed 415 genes involved in these pathways in the allotetraploid frog, Xenopus laevis. Most genes are retained in two subgenomes called L and S (193 homeologous gene pairs and 29 singletons). This conservation rate of homeologs is much higher than that of all genes in the X. laevis genome (86.9% vs 60.2%). Among singletons, 24 genes are retained in the L subgenome, a rate similar to the average for all genes (82.8% vs 74.6%). In addition, as general components of signal transduction, we also analyzed 32 heparan sulfate proteoglycan (HSPG)-related genes and eight TLE/Groucho transcriptional corepressors-related genes. In these gene sets, all homeologous pairs have been retained. Transcriptome analysis using RNA-seq data from developmental stages and adult tissues demonstrated that most homeologous pairs of signaling components have variable expression patterns, in contrast to the conservative expression profiles of homeologs for transcription factors. Our results indicate that homeologous gene pairs for cell signaling regulation have tended to become subfunctionalized after allotetraploidization. Diversification of signaling pathways by subfunctionalization of homeologs may enhance environmental adaptability. These results provide insights into the evolution of signaling pathways after polyploidization.
authors.affiliation: Graduate School of Arts and Sciences, the University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo 153-8902, Japan. Electronic address: tmichiue@bio.c.u-tokyo.ac.jp.
authors.forename: Tatsuo
authors.initials: T
authors.lastname: Michiue
authors.affiliation: Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Takayoshi
authors.initials: T
authors.lastname: Yamamoto
authors.affiliation: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan.
authors.forename: Yuuri
authors.initials: Y
authors.lastname: Yasuoka
authors.affiliation: Department of Molecular Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima-ku, Tokyo 153-8501, Japan.
authors.forename: Toshiyasu
authors.initials: T
authors.lastname: Goto
authors.affiliation: Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Takafumi
authors.initials: T
authors.lastname: Ikeda
authors.affiliation: Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Kei
authors.initials: K
authors.lastname: Nagura
authors.affiliation: Department of Biology, University of Virginia, Charlottesville, VA 22904, USA.
authors.forename: Takuya
authors.initials: T
authors.lastname: Nakayama
authors.affiliation: Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Masanori
authors.initials: M
authors.lastname: Taira
authors.affiliation: School of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan. Electronic address: tkinoshita@rikkyo.ac.jp.
authors.forename: Tsutomu
authors.initials: T
authors.lastname: Kinoshita
mesh_terms: D000818:Animals; D051157:Frizzled Receptors / Q000096:biosynthesis / Q000235:genetics; D015870:Gene Expression; D020869:Gene Expression Profiling; D016678:Genome; D053823:Hedgehog Proteins / Q000096:biosynthesis / Q000235:genetics*; D058977:Molecular Sequence Annotation; D051880:Receptors, Notch / Q000096:biosynthesis / Q000235:genetics*; D015398:Signal Transduction / Q000235:genetics*; D013347:Subcellular Fractions / Q000378:metabolism; D026801:Synteny; D057891:Tetraploidy; D059467:Transcriptome; D051153:Wnt Proteins / Q000096:biosynthesis / Q000235:genetics*; D060449:Wnt Signaling Pathway / Q000235:genetics; D029867:Xenopus Proteins / Q000096:biosynthesis / Q000235:genetics*; D014982:Xenopus laevis / Q000235:genetics*
chemical_list: D051157:Frizzled Receptors; D053823:Hedgehog Proteins; D051880:Receptors, Notch; D051153:Wnt Proteins; D029867:Xenopus Proteins
keywords: Allotetraploid; Cellular communication; Development; Organogenesis; Signaling pathway; Subfunctionalization; Xenopus