Department of Biology and Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky 40506, USA.
Genome Res. 2011 Aug;21(8):1306-12. doi: 10.1101/gr.116491.110. Epub 2011 Apr 11.
Amphibian genomes differ greatly in DNA content and chromosome size, morphology, and number. Investigations of this diversity are needed to identify mechanisms that have shaped the evolution of vertebrate genomes. We used comparative mapping to investigate the organization of genes in the Mexican axolotl (Ambystoma mexicanum), a species that presents relatively few chromosomes (n = 14) and a gigantic genome (>20 pg/N). We show extensive conservation of synteny between Ambystoma, chicken, and human, and a positive correlation between the length of conserved segments and genome size. Ambystoma segments are estimated to be four to 51 times longer than homologous human and chicken segments. Strikingly, genes demarking the structures of 28 chicken chromosomes are ordered among linkage groups defining the Ambystoma genome, and we show that these same chromosomal segments are also conserved in a distantly related anuran amphibian (Xenopus tropicalis). Using linkage relationships from the amphibian maps, we predict that three chicken chromosomes originated by fusion, nine to 14 originated by fission, and 12-17 evolved directly from ancestral tetrapod chromosomes. We further show that some ancestral segments were fused prior to the divergence of salamanders and anurans, while others fused independently and randomly as chromosome numbers were reduced in lineages leading to Ambystoma and Xenopus. The maintenance of gene order relationships between chromosomal segments that have greatly expanded and contracted in salamander and chicken genomes, respectively, suggests selection to maintain synteny relationships and/or extremely low rates of chromosomal rearrangement. Overall, the results demonstrate the value of data from diverse, amphibian genomes in studies of vertebrate genome evolution.
两栖动物的基因组在 DNA 含量和染色体大小、形态和数量上存在很大差异。需要对这种多样性进行研究，以确定塑造脊椎动物基因组进化的机制。我们使用比较作图研究了墨西哥蝾螈（Ambystoma mexicanum）的基因组织，该物种的染色体数量相对较少（n = 14），基因组非常庞大（>20pg/N）。我们表明，Ambystoma、鸡和人之间的同线性广泛保守，并且保守片段的长度与基因组大小呈正相关。与同源的人类和鸡片段相比，Ambystoma 片段估计长 4 到 51 倍。引人注目的是，标记鸡 28 条染色体结构的基因在定义 Ambystoma 基因组的连锁群中有序排列，并且我们表明这些相同的染色体片段在亲缘关系较远的无尾两栖类（Xenopus tropicalis）中也保守。利用来自两栖动物图谱的连锁关系，我们预测三个鸡染色体是通过融合形成的，九个到十四个是通过分裂形成的，而 12-17 个是直接从祖先四足动物染色体进化而来的。我们进一步表明，一些祖先片段在蝾螈和无尾类分化之前融合，而其他片段则在导致 Ambystoma 和 Xenopus 的谱系中独立且随机融合，因为染色体数量减少了。在蝾螈和鸡基因组中分别大大扩展和收缩的染色体片段之间保持基因顺序关系表明，选择维持同线性关系和/或极低的染色体重排率。总体而言，这些结果表明来自不同的、两栖动物基因组的数据在研究脊椎动物基因组进化方面具有价值。
