The origin of bmp16, a novel Bmp2/4 relative, retained in teleost fish genomes.
The origin of bmp16, a novel Bmp2/4 relative, retained in teleost fish genomes.
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DOI：
10.1186/1471-2148-9-277
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发表时间：
2009-12-01
影响因子：
3.4
通讯作者：
Kuraku S
中科院分区：
文献类型：
--
作者：
Feiner N;Begemann G;Renz AJ;Meyer A;Kuraku S
全基因组序列使我们能够对基因库的进化有一个概述。TGFβ超家族包含了许多与脊椎动物发育有关的基因，为研究基因组进化与发育程序进化之间的关系提供了一个理想的系统。作为对脊椎动物基因组测序的生物信息学调查的结果，我们鉴定了TGFβ超家族的一个未表征的成员，命名为bmp 16，其仅限于硬骨鱼物种。我们的分子系统发育研究显示，bmp 16的高亲和力的Bmp 2/4亚家族。重要的是，基于最大似然法的进一步分析明确排除了这种硬骨鱼特异性基因是硬骨鱼特异性基因组复制产物的可能性。这表明在四足动物中缺少bmp 16同源基因是由于二次丢失。原位杂交显示斑马鱼bmp 16在胚胎发育中的鱼鳔、心脏、尾芽、咽期胸鳍和中鳍褶皱的外胚层中表达，以及在5天胚胎中的肠道相关表达。表达模式的比较显示：（1）bmp 16表达的冗余与其同源物在可能的近形表达域，如鳍褶，心脏，尾芽，这可能已经允许其损失的四足动物谱系，和（2）的颅面表达的损失和获得的bmp 16的鱼鳔表达后，Bmp 2，-4和-16之间的基因复制。我们的研究结果强调了记录其他基因家族中基因库和表达模式的继发性变化的重要性。
Whole genome sequences have allowed us to have an overview of the evolution of gene repertoires. The target of the present study, the TGFβ 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 TGFβ 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.
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影响因子：
11.8
作者：
Chung, Won-Suk;Shin, Chong Hyun;Stainier, Didier Y. R.
通讯作者：
Stainier, Didier Y. R.
DOI：
10.1016/j.gep.2009.04.002
发表时间：
2009-06
期刊：
Gene expression patterns : GEP
影响因子：
--
作者：
Danesh SM;Villasenor A;Chong D;Soukup C;Cleaver O
通讯作者：
Cleaver O
DOI：
10.1073/pnas.0602558103
发表时间：
2006-05-16
影响因子：
11.1
作者：
Allendorph, George P.;Vale, Wylie W.;Choe, Senyon
通讯作者：
Choe, Senyon
影响因子：
10.7
作者：
Furlong, Rebecca F.;Younger, Ruth;Holland, Peter W. H.
通讯作者：
Holland, Peter W. H.
影响因子：
1.8
作者：
Chen, D;Zhao, M;Mundy, GR
通讯作者：
Mundy, GR