Laboratory for Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78464 Konstanz, Germany.
BMC Evol Biol. 2009 Dec 1;9:277. doi: 10.1186/1471-2148-9-277.
Whole genome sequences have allowed us to have an overview of the evolution of gene repertoires. The target of the present study, the TGFbeta superfamily, contains many genes involved in vertebrate development, and provides an ideal system to explore the relationships between evolution of gene repertoires and that of developmental programs.
As a result of a bioinformatic survey of sequenced vertebrate genomes, we identified an uncharacterized member of the TGFbeta superfamily, designated bmp16, which is confined to teleost fish species. Our molecular phylogenetic study revealed a high affinity of bmp16 to the Bmp2/4 subfamily. Importantly, further analyses based on the maximum-likelihood method unambiguously ruled out the possibility that this teleost-specific gene is a product of teleost-specific genome duplication. This suggests that the absence of a bmp16 ortholog in tetrapods is due to a secondary loss. In situ hybridization showed embryonic expression of the zebrafish bmp16 in the developing swim bladder, heart, tail bud, and ectoderm of pectoral and median fin folds in pharyngula stages, as well as gut-associated expression in 5-day embryos.
Comparisons of expression patterns revealed (1) the redundancy of bmp16 expression with its homologs in presumably plesiomorphic expression domains, such as the fin fold, heart, and tail bud, which might have permitted its loss in the tetrapod lineage, and (2) the loss of craniofacial expression and gain of swim bladder expression of bmp16 after the gene duplication between Bmp2, -4 and -16. Our findings highlight the importance of documenting secondary changes of gene repertoires and expression patterns in other gene families.
全基因组序列使我们能够全面了解基因库的进化。本研究的目标是 TGFbeta 超家族，其中包含许多参与脊椎动物发育的基因，为探索基因库的进化与发育程序的进化之间的关系提供了理想的系统。
通过对已测序的脊椎动物基因组进行生物信息学调查，我们鉴定出 TGFbeta 超家族的一个未被描述的成员，命名为 bmp16，它仅限于硬骨鱼物种。我们的分子系统发育研究表明，bmp16 与 Bmp2/4 亚家族具有高度亲和力。重要的是，进一步基于最大似然法的分析明确排除了这种硬骨鱼特有的基因是硬骨鱼特异性基因组加倍的产物的可能性。这表明四足动物中没有 bmp16 直系同源物是由于二次丢失所致。原位杂交显示斑马鱼 bmp16 在胚胎发育中的咽囊阶段在游动囊、心脏、尾芽和胸鳍和中鳍折叠的外胚层中表达，以及在 5 天胚胎中的肠道相关表达。
表达模式的比较揭示了（1）bmp16 与其在假定的祖征表达域（如鳍褶、心脏和尾芽）中的同源物的表达冗余，这可能使其在四足动物谱系中丢失，以及（2）在 Bmp2、-4 和 -16 之间的基因复制后，bmp16 的颅面表达丢失和游动囊表达获得。我们的发现强调了在其他基因家族中记录基因库和表达模式的次要变化的重要性。
