Reevaluating Emx gene phylogeny: homopolymeric amino acid tracts as a potential factor obscuring orthology signals in cyclostome genes

BMC Evolutionary Biology

Research Article

Fumiaki Sugahara¹  Miyuki Noro²  Shigehiro Kuraku³ 

[1] Division of Biology, Hyogo College of Medicine, 1-1 Mukogawa-cho, 663-8501, Nishinomiya, Japan;Evolutionary Morphology Laboratory, RIKEN, 2-2-3 Minatojima-minami, 650-0047, Kobe, Japan;Genome Resource and Analysis Unit, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minami, 650-0047, Kobe, Japan;Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, 650-0047, Kobe, Japan;

关键词: Emx;    Gene duplication;    Cyclostome;    Lamprey;    Hagfish;    Conserved synteny;    Homopolymeric amino acid (HPAA) tracts;   

DOI  :  10.1186/s12862-015-0351-z

 received in 2014-11-03, accepted in 2015-04-15,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundVertebrate Emx genes, retained as multiple copies, are expressed in a nested pattern in the early embryonic forebrain and required for its regionalization. This pattern seems to have originated in a vertebrate common ancestor; however, a previous analysis, reporting two lamprey Emx genes, claimed independent Emx gene duplications in both cyclostome (extant jawless fish) and gnathostome (jawed vertebrate) lineages after their divergence. This scenario is neither parsimonious nor consistent with the hypothesis that genome expansion occurred before the cyclostome-gnathostome split, which is supported by recent genome-wide analyses.ResultsWe isolated and sequenced cDNA of two hagfish Emx genes and performed intensive molecular phylogenetic analyses, including the hagfish and/or lamprey Emx genes. The lamprey genes tended to attract each other in inferred phylogenetic trees, an effect that tended to be relaxed on inclusion of the hagfish genes. The results of these analyses suggest that cyclostome EmxB is orthologous to gnathostome Emx2, which was also supported by conserved synteny. Homopolymeric amino acid (HPAA) tracts represent a remarkable feature of the lamprey Emx sequences, and a comparative genome-wide scan revealed that lamprey proteins exhibit a unique pattern of HPAA tract accumulation.ConclusionsOur analysis, including hagfish Emx genes, suggests that gene duplications gave rise to Emx1, -2 and -3 before the cyclostome-gnathostome split. We propose that independent HPAA tract accumulations in multiple ancient duplicates, as identified in lamprey Emx gene products, may have led to erroneous identification of gene duplication in the lamprey lineage. Overall, our reanalysis favors the scenario that the nested Emx expression pattern in mouse and lamprey shares a common origin.

【 授权许可】

Unknown   
© Noro et al. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.