Genome-wide identification, evolutionary expansion, and expression profile of homeodomain-leucine zipper gene family in poplar (Populus trichocarpa).
Genome-wide identification, evolutionary expansion, and expression profile of homeodomain-leucine zipper gene family in poplar (Populus trichocarpa).
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杨树（毛果杨）同源域-亮氨酸拉链基因家族的全基因组鉴定、进化扩展和表达谱
DOI：
10.1371/journal.pone.0031149
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Zhou G
中科院分区：
文献类型：
--
作者：
Hu R;Chi X;Chai G;Kong Y;He G;Wang X;Shi D;Zhang D;Zhou G
背景同源结构域亮氨酸拉链(HD-ZIP)蛋白是植物特有的转录因子，在植物发育中发挥重要作用。虽然前人对HD-zips杨树进行了序列系统发育分析，但到目前为止还没有对模式树种杨树的基因组组织、基因结构和表达纲要进行系统分析。本研究的主要发现是对杨树HD-ZIP基因家族进行了综合分析。在杨树基因组中发现了63个全长HD-ZIP基因。这些杨树HD-ZIP基因在系统发育上聚为4个不同的亚家族(HD-ZIP I-IV)，主要分布在17个连锁群(Lg)上。来自25对近缘杨树的50个基因位于杨树基因组的复制块中，并在进化过程中优先保留。基因组组织分析表明，纯化选择在保持和维持HD-ZIP基因家族中起着关键作用。基因芯片分析表明，21对杨树在不同组织和不同胁迫条件下表达差异，其中5对表现出几乎相同的表达模式，13对部分冗余，3对差异显著。对筛选出的16个杨树HD-ZIP基因在不同组织以及干旱和盐分胁迫下进行了定量实时RT-PCR分析，证实了其组织特异性和胁迫诱导的表达模式。结论基因组组织分析表明，节段性复制对杨树HD-ZIP基因家族的扩增具有重要作用。杨树HD-zips的外显子/内含子组织和保守基序组成在同一亚家族中高度保守，这表明同一亚家族的成员也可能具有保守的功能。基因芯片和定量逆转录聚合酶链式反应分析表明，的63个HD-Zips中有56个是重复基因，这些重复基因可能被实质性的亚功能化所保留。综上所述，这些观察结果可能为未来对杨树HD-ZIP基因的功能分析奠定基础，以揭示其生物学功能。
Background Homeodomain-leucine zipper (HD-ZIP) proteins are plant-specific transcriptional factors known to play crucial roles in plant development. Although sequence phylogeny analysis of Populus HD-ZIPs was carried out in a previous study, no systematic analysis incorporating genome organization, gene structure, and expression compendium has been conducted in model tree species Populus thus far. Principal Findings In this study, a comprehensive analysis of Populus HD-ZIP gene family was performed. Sixty-three full-length HD-ZIP genes were found in Populus genome. These Populus HD-ZIP genes were phylogenetically clustered into four distinct subfamilies (HD-ZIP I–IV) and predominately distributed across 17 linkage groups (LG). Fifty genes from 25 Populus paralogous pairs were located in the duplicated blocks of Populus genome and then preferentially retained during the sequential evolutionary courses. Genomic organization analyses indicated that purifying selection has played a pivotal role in the retention and maintenance of Populus HD-ZIP gene family. Microarray analysis has shown that 21 Populus paralogous pairs have been differentially expressed across different tissues and under various stresses, with five paralogous pairs showing nearly identical expression patterns, 13 paralogous pairs being partially redundant and three paralogous pairs diversifying significantly. Quantitative real-time RT-PCR (qRT-PCR) analysis performed on 16 selected Populus HD-ZIP genes in different tissues and under both drought and salinity stresses confirms their tissue-specific and stress-inducible expression patterns. Conclusions Genomic organizations indicated that segmental duplications contributed significantly to the expansion of Populus HD-ZIP gene family. Exon/intron organization and conserved motif composition of Populus HD-ZIPs are highly conservative in the same subfamily, suggesting the members in the same subfamilies may also have conservative functionalities. Microarray and qRT-PCR analyses showed that 89% (56 out of 63) of Populus HD-ZIPs were duplicate genes that might have been retained by substantial subfunctionalization. Taken together, these observations may lay the foundation for future functional analysis of Populus HD-ZIP genes to unravel their biological roles.
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影响因子：
7.2
作者：
Delarue, M;Prinsen, E;Bellini, C
通讯作者：
Bellini, C
影响因子：
11.6
作者：
AOYAMA, T;DONG, CH;CHUA, NH
通讯作者：
CHUA, NH
DOI：
10.1073/pnas.93.8.3530
发表时间：
1996-04-16
影响因子：
11.1
作者：
Carabelli, M;Morelli, G;Ruberti, I
通讯作者：
Ruberti, I
影响因子：
10.7
作者：
Aso, K;Kato, M;Hasebe, M
通讯作者：
Hasebe, M
影响因子：
7.4
作者：
Baima, S;Possenti, M;Morelli, G
通讯作者：
Morelli, G