title: Genome organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis.
abstract: Extracellular factors belonging to the TGF-β family play pivotal roles in the formation and patterning of germ layers during early Xenopus embryogenesis. Here, we show that the vg1 and nodal3 genes of Xenopus laevis are present in gene clusters on chromosomes XLA1L and XLA3L, respectively, and that both gene clusters have been completely lost from the syntenic S chromosome regions. The presence of gene clusters and chromosome-specific gene loss were confirmed by cDNA FISH analyses. Sequence and expression analyses revealed that paralogous genes in the vg1 and nodal3 clusters on the L chromosomes were also altered compared to their Xenopus tropicalis orthologs. X. laevis vg1 and nodal3 paralogs have potentially become pseudogenes or sub-functionalized genes and are expressed at different levels. As X. tropicalis has a single vg1 gene on chromosome XTR1, the ancestral vg1 gene in X. laevis appears to have been expanded on XLA1L. Of note, two reported vg1 genes, vg1(S20) and vg1(P20), reside in the cluster on XLA1L. The nodal3 gene cluster is also present on X. tropicalis chromosome XTR3, but phylogenetic analysis indicates that nodal3 genes in X. laevis and X. tropicalis were independently expanded and/or evolved in concert within each cluster by gene conversion. These findings provide insights into the function and molecular evolution of TGF-β family genes in response to allotetraploidization.
authors.affiliation: Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan. Electronic address: asuzuki@hiroshima-u.ac.jp.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Suzuki
authors.affiliation: Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
authors.forename: Yoshinobu
authors.initials: Y
authors.lastname: Uno
authors.affiliation: Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
authors.forename: Shuji
authors.initials: S
authors.lastname: Takahashi
authors.affiliation: HudsonAlpha Institute of Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA.
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.affiliation: HudsonAlpha Institute of Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.affiliation: School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku, Sagamihara 252-0373, Japan.
authors.forename: Shuuji
authors.initials: S
authors.lastname: Mawaribuchi
authors.affiliation: Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Yoshida
authors.affiliation: Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
authors.forename: Kimiko
authors.initials: K
authors.lastname: Takebayashi-Suzuki
authors.affiliation: School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku, Sagamihara 252-0373, Japan.
authors.forename: Michihiko
authors.initials: M
authors.lastname: Ito
authors.affiliation: Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
authors.forename: Yoichi
authors.initials: Y
authors.lastname: Matsuda
authors.affiliation: University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, CA 94720-3200, USA; US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
authors.forename: Daniel
authors.initials: D
authors.lastname: Rokhsar
authors.affiliation: Department of Biological Sciences, 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
mesh_terms: D000818:Animals; D005075:Biological Evolution; D002874:Chromosome Mapping; D019143:Evolution, Molecular; D017353:Gene Deletion; D020440:Gene Duplication; D016678:Genome; D017404:In Situ Hybridization, Fluorescence; D005810:Multigene Family; D010802:Phylogeny; D011544:Pseudogenes; D013045:Species Specificity; D026801:Synteny; D057891:Tetraploidy; D016212:Transforming Growth Factor beta / Q000235:genetics*; D014981:Xenopus / Q000235:genetics; D029867:Xenopus Proteins / Q000235:genetics*; D014982:Xenopus laevis / Q000235:genetics*
chemical_list: C513103:GDF1 protein, Xenopus; D016212:Transforming Growth Factor beta; D029867:Xenopus Proteins; C094620:nodal3.1 protein, Xenopus
keywords: Genomic structure; TGF-β; Xenopus; gdf1; nodal3; vg1