Beyond the Arabidopsis genome: Opportunities for comparative genomics
Beyond the Arabidopsis genome: Opportunities for comparative genomics
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DOI：
10.1104/pp.004051
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发表时间：
2002-08-01
期刊：
影响因子：
7.4
通讯作者：
Preuss, D
中科院分区：
文献类型：
--
作者：
Hall, AE;Fiebig, A;Preuss, D
像大多数高等真核生物一样，开花植物被认为含有数量惊人的相似基因。然而，被子植物基因组的大小在很大范围内变化--从50Mb到超过12万Mb。比较图谱显示，大量的改变有助于植物之间的基因组多样性。随着时间的推移，染色体被破坏、重组、部分或全部复制，甚至被消除，最终导致生殖隔离和物种形成。然而，造成这种变化的机制，以及修复这些变化的进化力量，还没有被很好地理解。对植物基因组的比较分析有望阐明驱动这些变化的选择压力；这种研究将阐明整个基因组水平上的变化，以及特定序列水平上的变化，包括基因、重复元件和其他非编码区。虽然低分辨率的遗传图谱可以识别染色体的总体变化，但要清楚地了解这些变化背后的机制，就需要进行多物种序列比较。这样的分析揭示了基因组的组成、组织和功能成分，并提供了对近缘物种之间组成的地区差异的洞察。此外，序列比较阐明了进化史；例如，核苷酸插入/缺失(INDELs)的逐步积累只有在分析多个物种时才变得清晰。比较序列分析还有助于基因预测和序列注释，并有助于识别和定义调控元件，包括启动子、增强子和转录因子结合位点(Kent和Zahler，2000；Koch等人，2001b)。
Like most higher eukaryotes, flowering plants are believed to contain surprisingly similar numbers of genes. Nevertheless, angiosperm genome sizes vary over a wide range—from 50 Mb to over 120,000 Mb. Comparative mapping has shown that numerous alterations contribute to genomic diversity among plants. Over time, chromosomes are broken, reassembled, partially or wholly duplicated, and even eliminated, ultimately resulting in reproductive isolation and speciation. However, the mechanisms that create such variation, and the evolutionary forces that fix these changes, are not well understood. Comparative analyses of plant genomes promise to clarify the selective pressures driving these changes; such investigations will elucidate alterations at the level of whole genomes, as well as those at the level of specific sequences, including genes, repetitive elements, and other non-coding regions. Although low-resolution genetic maps can identify gross chromosomal alterations, a clear understanding of the mechanisms behind these changes requires multispecies sequence comparisons. Such analyses reveal the composition, organization, and functional components of genomes and provide insight into regional differences in composition between related species. In addition, sequence comparisons elucidate evolutionary history; for example, the stepwise accumulation of nucleotide insertions/deletions (indels) only becomes clear with the analysis of multiple species. Comparative sequence analysis also aids in gene prediction and sequence annotation, and facilitates the identification and definition of regulatory elements, including promoters, enhancers, and transcription factor-binding sites (Kent and Zahler, 2000; Koch et al., 2001b).