Comparative sequence analysis of the Phytochrome C gene and its upstream region in allohexaploid wheat reveals new data on the evolution of its three constituent genomes
Comparative sequence analysis of the Phytochrome C gene and its upstream region in allohexaploid wheat reveals new data on the evolution of its three constituent genomes
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DOI：
10.1007/s11103-005-6801-z
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发表时间：
2005-07-01
影响因子：
5.1
通讯作者：
Doust, AN
中科院分区：
文献类型：
--
作者：
Devos, KM;Beales, J;Doust, AN
面包小麦是一种等位六倍体，基因组组成为AABBDD。光敏色素C是一个参与光形态发生的基因，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各为单拷贝，并映射到第5组染色体长臂上的同源位置。对小麦PhyC基因的三个同源拷贝和上游约5kb的序列比较分析表明，PhyC基因高度保守，但上游区域经常被插入逆转录元件和其他重复序列打断。所研究区域的一个重复序列似乎是在二倍体小麦基因组分化之前插入的，但被降解到只能在氨基酸水平上观察到A和D拷贝之间的相似性。在不同的小麦品种中，PhyC基因中存在不同的折叠元件和微型逆重复转座元件（MITE） 5'。后者可能是小麦基因组中活性螨家族的第一个例子。一些保守的非编码序列也被鉴定出可能代表功能调控元件。3个小麦生理同源物的序列分化水平（K-s）表明，二倍体小麦祖先的分化发生在大约6.9万年前，比先前估计的2.5-4.5万年前要早得多。K-a/K-s比值< 0.15，表明这三个同源基因都处于纯化选择中，可能代表功能性PhyC基因。RT-PCR证实了A、B和D拷贝的表达。利用基因组不同部分的序列估计小麦基因组进化年龄的差异可能反映了一些小麦基因组的马赛克起源。
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 (K-s) 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. K-a/K-s 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.