Emrich Scott J, Li Li, Wen Tsui-Jung, Yandeau-Nelson Marna D, Fu Yan, Guo Ling, Chou Hui-Hsien, Aluru Srinivas, Ashlock Daniel A, Schnable Patrick S
Interdepartmental Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, Iowa 50011, USA.
Genetics. 2007 Jan;175(1):429-39. doi: 10.1534/genetics.106.064006. Epub 2006 Nov 16.
As an ancient segmental tetraploid, the maize (Zea mays L.) genome contains large numbers of paralogs that are expected to have diverged by a minimum of 10% over time. Nearly identical paralogs (NIPs) are defined as paralogous genes that exhibit > or = 98% identity. Sequence analyses of the "gene space" of the maize inbred line B73 genome, coupled with wet lab validation, have revealed that, conservatively, at least approximately 1% of maize genes have a NIP, a rate substantially higher than that in Arabidopsis. In most instances, both members of maize NIP pairs are expressed and are therefore at least potentially functional. Of evolutionary significance, members of many NIP families also exhibit differential expression. The finding that some families of maize NIPs are closely linked genetically while others are genetically unlinked is consistent with multiple modes of origin. NIPs provide a mechanism for the maize genome to circumvent the inherent limitation that diploid genomes can carry at most two "alleles" per "locus." As such, NIPs may have played important roles during the evolution and domestication of maize and may contribute to the success of long-term selection experiments in this important crop species.
作为一种古老的分段四倍体，玉米（Zea mays L.）基因组包含大量旁系同源基因，预计随着时间的推移，这些基因至少会有10%的差异。几乎相同的旁系同源基因（NIPs）被定义为同一性大于或等于98%的旁系同源基因。对玉米自交系B73基因组“基因空间”的序列分析，结合湿实验室验证，发现保守估计至少约1%的玉米基因有一个NIP，这一比例大大高于拟南芥中的比例。在大多数情况下，玉米NIP对的两个成员都有表达，因此至少具有潜在功能。具有进化意义的是，许多NIP家族的成员也表现出差异表达。一些玉米NIP家族在遗传上紧密连锁而另一些则不连锁，这一发现与多种起源模式一致。NIPs为玉米基因组提供了一种机制，以规避二倍体基因组每个“基因座”最多只能携带两个“等位基因”这一固有限制。因此，NIPs可能在玉米的进化和驯化过程中发挥了重要作用，并且可能有助于在这种重要作物物种中进行长期选择实验的成功。
