Genome organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis

Suzuki, Atsushi; Uno, Yoshinobu; Takahashi, Shuji; Grimwood, Jane; Schmutz, Jeremy; Mawaribuchi, Shuuji; Yoshida, Hitoshi; Takebayashi-Suzuki, Kimiko; Ito, Michihiko; Matsuda, Yoichi; Rokhsar, Daniel; Taira, Masanori

doi:10.1016/j.ydbio.2016.04.014

Genome organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis

Journal Article · Wed Oct 05 00:00:00 EDT 2016 · Developmental Biology

DOI:https://doi.org/10.1016/j.ydbio.2016.04.014· OSTI ID:1633220

Suzuki, Atsushi ^[1]; Uno, Yoshinobu ^[2]; Takahashi, Shuji ^[1]; Grimwood, Jane ^[3]; Schmutz, Jeremy ^[3]; Mawaribuchi, Shuuji ^[4]; Yoshida, Hitoshi ^[1]; Takebayashi-Suzuki, Kimiko ^[1]; Ito, Michihiko ^[4]; Matsuda, Yoichi ^[2]; Rokhsar, Daniel ^[5]; Taira, Masanori ^[6]

Hiroshima University, Higashi-Hiroshima(Japan). Amphibian Research Center
Nagoya University, Furo-cho, Chikusa-ku, Nagoya (Japan)
HudsonAlpha Institute of Biotechnology, Huntsville, AL (United States)
Kitasato University, Minamiku, Sagamihara (Japan)
Univ. of California, Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa (Japan)
Uiversity of Tokyo, Tokyo (Japan)

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. Lastly, these findings provide insights into the function and molecular evolution of TGF-β family genes in response to allotetraploidization.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1633220

Journal Information:: Developmental Biology, Journal Name: Developmental Biology Journal Issue: 2 Vol. 426; ISSN 0012-1606

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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