Alba R, Kelmenson P M, Cordonnier-Pratt M M, Pratt L H
Department of Botany, University of Georgia 30602-7271, USA.
Mol Biol Evol. 2000 Mar;17(3):362-73. doi: 10.1093/oxfordjournals.molbev.a026316.
A reexamination of the genome of the tomato (renamed Solanum lycopersicum L.) indicates that it contains five, or at most perhaps six, phytochrome genes (PHY), each encoding a different apoprotein (PHY). Five previously identified tomato PHY genes have been designated PHYA, PHYB1, PHYB2, PHYE, and PHYF. A molecular phylogenetic analysis is consistent with the hypothesis that the angiosperm PHY family is composed of four subfamilies (A, B, C/F, and E). Southern analyses indicate that the tomato genome does not contain both a PHYC and a PHYF. Molecular phylogenetic analyses presented here, which utilize for the first time full-length PHY sequences from two completely characterized angiosperm gene families, indicate that tomato PHYF is probably an ortholog of Arabidopsis PHYC. They also confirm that the angiosperm PHY family is undergoing relatively rapid differential evolution. Assuming PHYF is an ortholog of PHYC, PHY genes in eudicots are evolving (Ka/site) at 1.52-2.79 times the rate calculated as average for other plant nuclear genes. Again assuming PHYF is an ortholog of PHYC, the rate of evolution of the C and E subfamilies is at least 1.33 times the rate of the A and B subfamilies. PHYA and PHYB in eudicots are evolving at least 1.45 times as fast as their counterparts in the Poaceae. PHY functional domains also exhibit different evolutionary rates. The C-terminal region of angiosperm PHY (codons 800-1105) is evolving at least 2.11 times as fast as the photosensory domain (codons 200-500). The central region of a domain essential for phytochrome signal transduction (codons 652-712) is also evolving rapidly. Nonsynonymous substitutions occur in this region at 2.03-3.75 times the average rate for plant nuclear genes. It is not known if this rapid evolution results from selective pressure or from the absence of evolutionary constraint.
对番茄（现重新命名为茄属番茄L.）基因组的重新研究表明，它含有五个，或者最多可能六个光敏色素基因（PHY），每个基因编码一种不同的脱辅基蛋白（PHY）。五个先前鉴定出的番茄PHY基因已被命名为PHYA、PHYB1、PHYB2、PHYE和PHYF。分子系统发育分析与被子植物PHY家族由四个亚家族（A、B、C/F和E）组成的假说一致。Southern分析表明，番茄基因组中不同时包含PHYC和PHYF。本文进行的分子系统发育分析首次利用了来自两个完全表征的被子植物基因家族的全长PHY序列，结果表明番茄PHYF可能是拟南芥PHYC的直系同源基因。这些分析还证实，被子植物PHY家族正在经历相对快速的分化进化。假设PHYF是PHYC的直系同源基因，双子叶植物中的PHY基因进化速率（Ka/位点）是按其他植物核基因平均计算速率的1.52至2.79倍。再次假设PHYF是PHYC的直系同源基因，C和E亚家族的进化速率至少是A和B亚家族进化速率的1.33倍。双子叶植物中的PHYA和PHYB进化速度至少是禾本科植物中对应基因的1.45倍。PHY功能域也表现出不同的进化速率。被子植物PHY的C末端区域（密码子800 - 1105）进化速度至少是光感受域（密码子200 - 500）的2.11倍。光敏色素信号转导必需结构域的中心区域（密码子652 - 712）也在快速进化。该区域的非同义替换发生率是植物核基因平均速率的2.03至3.75倍。尚不清楚这种快速进化是由选择压力还是缺乏进化限制导致的。
