Devos Katrien M, Beales James, Ogihara Yasunari, Doust Andrew N
John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK.
Plant Mol Biol. 2005 Jul;58(5):625-41. doi: 10.1007/s11103-005-6801-z.
Bread wheat is an allohexaploid with genome composition AABBDD. Phytochrome C is a gene involved in photomorphogenesis that has been used extensively for phylogenetic analyses. In wheat, the PhyC genes are single copy in each of the three homoeologous genomes and map to orthologous positions on the long arms of the group 5 chromosomes. Comparative sequence analysis of the three homoeologous copies of the wheat PhyC gene and of some 5 kb of upstream region has demonstrated a high level of conservation of PhyC, but frequent interruption of the upstream regions by the insertion of retroelements and other repeats. One of the repeats in the region under investigation appeared to have inserted before the divergence of the diploid wheat genomes, but was degraded to the extent that similarity between the A and D copies could only be observed at the amino acid level. Evidence was found for the differential presence of a foldback element and a miniature inverted-repeat transposable element (MITE) 5' to PhyC in different wheat cultivars. The latter may represent the first example of an active MITE family in the wheat genome. Several conserved non-coding sequences were also identified that may represent functional regulatory elements. The level of sequence divergence (Ks) between the three wheat PhyC homoeologs suggests that the divergence of the diploid wheat ancestors occurred some 6.9 Mya, which is considerably earlier than the previously estimated 2.5-4.5 Mya. Ka/Ks ratios were <0.15 indicating that all three homoeologs are under purifying selection and presumably represent functional PhyC genes. RT-PCR confirmed expression of the A, B and D copies. The discrepancy in evolutionary age of the wheat genomes estimated using sequences from different parts of the genome may reflect a mosaic origin of some of the Triticeae genomes.
普通小麦是一种基因组组成为AABBDD的异源六倍体。光敏色素C是一个参与光形态建成的基因，已被广泛用于系统发育分析。在小麦中，PhyC基因在三个同源基因组中均为单拷贝，且定位于第5组染色体长臂上的直系同源位置。对小麦PhyC基因的三个同源拷贝以及约5 kb上游区域进行的比较序列分析表明，PhyC具有高度保守性，但上游区域经常因反转录元件和其他重复序列的插入而中断。在研究区域中的一个重复序列似乎在二倍体小麦基因组分化之前就已插入，但已降解到仅在氨基酸水平上才能观察到A拷贝和D拷贝之间的相似性。在不同小麦品种中发现了PhyC 5'端存在回文元件和微型反向重复转座元件（MITE）的差异证据。后者可能代表小麦基因组中活跃MITE家族的首个实例。还鉴定出了几个保守的非编码序列，它们可能代表功能性调控元件。三个小麦PhyC同源基因之间的序列分歧水平（Ks）表明，二倍体小麦祖先的分化发生在约690万年前，这比之前估计的250 - 450万年前要早得多。Ka/Ks比值<0.15，表明所有三个同源基因都受到纯化选择，大概代表功能性PhyC基因。RT-PCR证实了A、B和D拷贝的表达。使用来自基因组不同部分的序列估计的小麦基因组进化年龄差异可能反映了一些小麦族基因组的嵌合起源。
