Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes
Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes
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DOI：
10.1073/pnas.0408539102
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发表时间：
2005-03-01
影响因子：
11.1
通讯作者：
Green, ED
中科院分区：
文献类型：
--
作者：
Margulies, EH;Maduro, VVB;Green, ED
对多种脊椎动物基因组进行测序和比较分析，有助于深入了解生物多样性的遗传基础。到目前为止，这些努力主要集中在真兽目哺乳动物，鸡和鱼。在这篇文章中，我们描述了非真兽目哺乳动物，一组物种占据不寻常的系统发育位置的基因组序列的产生和研究。在三种有袋动物（北美负鼠、南美负鼠和澳大利亚tammar小袋鼠）和一种单孔目动物（鸭嘴兽）基因组中，为相同的直向区生成了一个大的序列数据集（总计>5 Mb）。这些古老的哺乳动物基因组的特点是不寻常的结构特征，相对于G + C和重复内容，以及压缩相对于人类。大约14%和34%的人类序列分别与鸭嘴兽和有袋动物的正向序列形成比对;这些数字明显低于在非灵长类真兽目哺乳动物中观察到的（45-70%）。人类和每种有袋类动物之间的可重复序列并不完全重叠（所有三种动物只有80%相同），鸭嘴兽的可重复序列也不完全包含在有袋类动物的可重复序列中。同义编码位置的系统发育分析表明，鸭嘴兽有一个显着的长分支长度，与人类鸭嘴兽的替代率平均55%以上，与人类有袋类对。最后，对主要哺乳动物谱系的分析揭示了进化上保守的脊椎动物序列的共同存在的不同模式。我们的研究结果证实，从noneutherian哺乳动物的基因组序列可以独特地有助于解开哺乳动物基因组的功能和进化历史。
Sequencing and comparative analyses of genomes from multiple vertebrates are providing insights about the genetic basis for biological diversity. To date, these efforts largely have focused on eutherian mammals, chicken, and fish. In this article, we describe the generation and study of genomic sequences from noneutherian mammals, a group of species occupying unusual phylogenetic positions. A large sequence data set (totaling >5 Mb) was generated for the same orthologous region in three marsupial (North American opossum, South American opossum, and Australian tammar wallaby) and one monotreme (platypus) genomes. These ancient mammalian genomes are characterized by unusual architectural features with respect to G + C and repeat content, as well as compression relative to human. Approximately 14% and 34% of the human sequence forms alignments with the orthologous sequence from platypus and the marsupials, respectively; these numbers are distinctly lower than that observed with nonprimate eutherian mammals (45-70%). The alignable sequences between human and each marsupial species are not completely overlapping (only 80% common to all three species) nor are the platypus-alignable sequences completely contained within the marsupial-alignable sequences. Phylogenetic analysis of synonymous coding positions reveals that platypus has a notably long branch length, with the human-platypus substitution rate being on average 55% greater than that seen with human-marsupial pairs. Finally, analyses of the major mammalian lineages reveal distinct patterns with respect to the common presence of evolutionarily conserved vertebrate sequences. Our results confirm that genomic sequence from noneutherian mammals can contribute uniquely to unraveling the functional and evolutionary histories of the mammalian genome.