Natural bone fragmentation in the blind cave-dwelling fish, Astyanax mexicanus: candidate gene identification through integrative comparative genomics.
Natural bone fragmentation in the blind cave-dwelling fish, Astyanax mexicanus: candidate gene identification through integrative comparative genomics.
复制标题
DOI：
10.1111/ede.12131
复制
发表时间：
2016-01
影响因子：
2.9
通讯作者：
Carlson BM
中科院分区：
文献类型：
--
作者：
Gross JB;Stahl BA;Powers AK;Carlson BM
在黑暗和营养贫乏的地下环境中生存的动物进化出许多极端的表型。其中包括颅面复合体的巨大变化，其中许多是由遗传控制的。这些表型可以证明不对称的遗传信号，其中QTL在面部的一侧检测到，而在另一侧检测不到。由于基因组资源有限，QTL的致病基因难以鉴定。我们通过寻找介导第三亚眶骨（SO3）直接低于眼窝的断裂的候选基因来完成这项任务。我们利用新出现的Astyanax资源整合了位置基因组信息，并将这些间隔与达尼奥雷里奥基因组的同源（syntenic）区域联系起来。我们确定了一个离散的，大约6 Mb的保守区域，其中可能存在导致SO3碎片化的基因。我们通过对整个生活史中洞穴和地表形态的mRNA-seq分析，研究了这段时间内表现出显著差异表达的基因。然后，我们根据GO术语注释评估了在颅面进化和发育中已知作用的基因。最后，我们筛选了该区域的编码序列变化，确定了两个关键基因：转化生长因子β3 （tgfb3）和骨形态发生蛋白4 （bmp4）。在这些候选基因中，tgfb3最有希望，因为它在多个发育阶段表现出显著的差异表达，与断裂关键位点接近（<1 Mb），并与多种其他动物系统（包括人类）的非综合征性颅缝裂和畸形有关。这两种异常都类似于我们在SO3碎片中观察到的融合失败表型。这种综合方法将能够发现导致复杂颅面特征的致病遗传病变，类似于人类颅面疾病。这项工作强调了穴居鱼类作为颅面疾病的强大进化模型的价值，并证明了综合系统水平研究在揭示自然界颅面畸变的遗传基础方面的力量。
Animals that colonize dark and nutrient-poor subterranean environments evolve numerous extreme phenotypes. These include dramatic changes to the craniofacial complex, many of which are under genetic control. These phenotypes can demonstrate asymmetric genetic signals wherein a QTL is detected on one side of the face but not the other. The causative gene(s) underlying QTL are difficult to identify with limited genomic resources. We approached this task by searching for candidate genes mediating fragmentation of the third suborbital bone (SO3) directly inferior to the orbit of the eye. We integrated positional genomic information using emerging Astyanax resources, and linked these intervals to homologous (syntenic) regions of the Danio rerio genome. We identified a discrete, approximately 6 Mb, conserved region wherein the gene causing SO3 fragmentation likely resides. We interrogated this interval for genes demonstrating significant differential expression using mRNA-seq analysis of cave and surface morphs across life history. We then assessed genes with known roles in craniofacial evolution and development based on GO term annotation. Finally, we screened coding sequence alterations in this region, identifying two key genes: transforming growth factor β3 (tgfb3) and bone morphogenetic protein 4 (bmp4). Of these candidates, tgfb3 is most promising as it demonstrates significant differential expression across multiple stages of development, maps close (<1 Mb) to the fragmentation critical locus, and is implicated in a variety of other animal systems (including humans) in non-syndromic clefting and malformations of the cranial sutures. Both abnormalities are analogous to the failure-to-fuse phenotype that we observe in SO3 fragmentation. This integrative approach will enable discovery of the causative genetic lesions leading to complex craniofacial features analogous to human craniofacial disorders. This work underscores the value of cave-dwelling fish as a powerful evolutionary model of craniofacial disease, and demonstrates the power of integrative system-level studies for informing the genetic basis of craniofacial aberrations in nature.