葡萄醛酮还原酶(AKR)基因家族的鉴定与表达分析

为明确AKR基因在葡萄非生物胁迫中的作用,利用生物信息学方法对葡萄AKR基因家族(VvAKRs)进行了全基因组鉴定,并验证其在非生物胁迫下的表达规律。结果表明：(1)该基因家族在葡萄基因组中有9个成员,主要分布在5条染色体上;氨基酸残基在275~2 686 aa之间,理论等电点在5.1~9.1之间。(2)系统进化分析表明,该基因家族分为6个亚族,第6亚族VvAKR家族成员最多。(3)密码子偏好性分析结果表明,葡萄AKR基因家族密码子偏好性较弱。(4)共线性分析表明,葡萄9个AKR基因中只有VvAKR8和VvAKR9之间存在共线性关系。(5)qRT PCR分析结果显示,葡萄AKR家族基因在根、茎、叶不同组织中对激素和非生物胁迫的响应程度有差异。非生物胁迫下,VvAKR1、VvAKR3、VvAKR8和VvAKR9基因在葡萄根、茎、叶组织中表达量较高;激素处理下,根组织中VvAKR3、VvAKR6和VvAKR8基因在ABA、MeJA、SA处理下表达量较高;茎组织中VvAKR3基因在NAA、GA₃处理下表达量较高;叶组织中VvAKR1基因在各激素处理下表达量都较高。研究认为,葡萄AKR基因家族在响应葡萄非生物胁迫时发挥着不同的作用,为葡萄抗逆性研究提供了一定的理论依据。     

苹果DREB转录因子家族全基因组鉴定与分析

DREB转录因子属于AP2/ERF转录因子家族,能够与DRE/CRT顺式作用元件特异性结合,调控与逆境应答基因的表达,因而在植物应对低温、干旱、高盐等逆境胁迫中发挥重要作用。该研究利用苹果全基因组数据,通过生物信息学手段鉴定苹果DREB转录因子家族成员,并分析DREB转录因子家族保守域特点与功能及表达情况。结果表明:从苹果全基因组中共鉴定出60个DREB转录因子家族成员,与拟南芥和水稻相比基本一致,通过引入拟南芥DREB基因进行系统发生分析,进一步可以将其细分为6个亚组;结构域和保守元件分析表明,DREB基因家族含有一个AP2保守结构域;染色体定位表明,苹果DREB基因分布于11条染色体上,部分基因存在串联复制现象;基因结构分析显示,该亚家族基因不含内含子。利用同源拟南芥RNA-Seq数据分析结果表明,DREB转录因子家族对低温、ABA调节等非生物胁迫具有调控作用,同时在DREB亚家族中每个亚组响应不同的非生物胁迫;通过分析DREB基因在不同组织中的表达情况,结果显示DREB基因在植物根部中的表达量最强,其次是叶。     

茶树CPP转录因子家族的全基因组鉴定及分析

CPP(cysteine-rich polycomb-like protein)转录因子广泛存在于动植物中,是一类成员数目较少的转录因子家族,在调控植物生长发育和响应非生物胁迫中起重要作用。该研究通过对茶树基因组系统的鉴定,获得10个CsCPP转录因子均具有典型的CXC结构域。系统发育分析将CsCPP家族成员分为4类(A^D),且大部分成员与葡萄在进化关系上更为接近。A类和C类成员的CXC结构域分布在蛋白序列的N端,而B类和D类成员分布在C端。茶树组织表达分析表明,CsCPP转录因子在生长活跃的顶芽和嫩叶中普遍高表达,不同组织的表达水平排序为:顶芽和嫩叶>根和茎>成熟叶和果>老叶和花。启动子分析发现了CsCPP家族成员的启动子区域存在大量的ABA和干旱响应元件;干旱处理下,6个CsCPP成员的表达水平均有不同程度上调,其中4个成员在ABA处理后表达迅速上调,表明CsCPP转录因子可能在ABA介导的干旱胁迫响应中起正调控作用;低温处理下,大部分CsCPP成员的表达均有轻微下调,而CsCPP 2和CsCPP 6的表达水平在6 h达到顶峰,表达量均超过2倍。研究结果为进一步发掘茶树CPP转录因子家族的功能奠定了基础。     

茶树GRF基因家族的全基因组鉴定及表达分析

生长调控因子(growth regulating factor,GRF)是植物特有的转录因子家族,在植物生长发育过程中起重要调控作用。该研究利用生物信息学的方法,从茶树基因组中鉴定获得11个CsGRF转录因子家族成员,且均具有完整的特征结构域QLQ和WRC。CsGRF家族成员含有3~6个外显子,基于系统进化关系将CsGRF家族分为6组,且与葡萄及猕猴桃GRF家族的亲缘关系更为接近。不同组织转录组数据分析结果表明,该家族在生长活跃的茶树嫩梢部位高表达。上游启动子区域分析发现大量与植物发育、激素及胁迫响应密切相关的顺式作用元件。荧光定量检测发现,分别有10个和2个CsGRF成员在低温和干旱胁迫处理后呈现显著上调表达,其中CsGRF8和CsGRF11对2种非生物胁迫均有响应;并发现受ABA、MeJA和GA激素处理诱导分别有9个、3个和6个CsGRF基因的表达水平差异显著。研究表明,CsGRF基因家族在茶树生长发育过程及应激反应中起作用,推测CsGRF基因可能通过各种激素信号转导途径参与胁迫响应过程。     

棉花抗逆基因GhAREB4的克隆及功能分析

AREBs转录因子家族基因主要参与干旱、高盐、低温等胁迫应答反应,在植物抵御各种逆境胁迫中起着非常重要的作用。该研究经序列电子拼接克隆了陆地棉GhAREB4基因,该基因全长1 784bp,其开放阅读框为1 227bp,编码408个氨基酸,预测分子量为44.3kD,等电点为8.88。蛋白结构预测发现,该蛋白二级结构中含有bZIP基因家族的保守结构域。系统进化树分析表明,GhAREB4与可可的AREB转录因子同源性最高。绿色荧光蛋白亚细胞定位分析表明,GhAREB4蛋白分布在细胞核内。qRT-PCR分析表明,GhAREB4基因在花中的表达量最高;且GhAREB4基因表达受到干旱、高盐、低温、脱落酸(ABA)等处理的诱导,其可能调控棉花对非生物逆境的耐性响应。研究结果为进一步研究该基因对棉花耐逆调控机制奠定了基础。     

苹果SRS基因家族的鉴定与功能分析北大核心CSCD

SHI-related sequence(SRS)基因家族通过介导激素变化以调控植物成花及生长发育,并且在适应环境胁迫中起重要调控作用。该研究基于苹果(Malus domestica Borkh.)基因组数据,通过生物信息学手段鉴定苹果SRS基因家族成员,并分析SRS基因家族特点与功能及表达情况。结果表明:(1)苹果MdSRS基因家族共包含11个成员,分别命名为MdSRS1-MdSRS11,不均匀地分布在苹果的9条染色体上。(2)MdSRS蛋白包含229~414个不等的氨基酸残基,等电点分布在6.38~9.36之间;亚细胞定位结果表明,MdSRS蛋白大多分布于细胞膜,在细胞核、叶绿体中也有分布。(3)通过引入拟南芥、水稻、番茄及杨树的SRS基因进行系统发育分析表明,将11个MdSRSs分成5个亚族(A-A),在A4中分布最多。(4)顺式作用元件分析表明,11个MdSRSs启动子上游2 000 bp序列分布有激素、环境适应性和逆境诱导等响应元件。(5)荧光定量PCR结果显示,苹果MdSRS基因家族在盐胁迫和干旱胁迫下总体呈下调表达,在ABA胁迫后大多呈上调表达,是具有很大潜力的抗性候选基因,说明SRS家族对ABA调节等非生物胁迫具有调控作用。研究认为,SRS家族的11个成员均参与了调控干旱、盐及ABA胁迫多种逆境的响应,推测在实际苹果生产中对抵御不良环境具有重要作用。     

沙棘HrTCP转录因子家族鉴定及其干旱胁迫下的表达分析

TCP家族是植物特有的响应高盐、干旱等非生物胁迫的重要转录因子.该研究基于沙棘转录组数据,利用生物信息学与qRT-PCR对HrTCP转录因子家族进行鉴定,预测其家族成员的结构和功能,为解析TCP转录因子调控沙棘抵御干旱胁迫的作用机制奠定基础.结果表明:(1)获得了 11个HrTCP转录因子成员,并命名为HrTCP2/4...     

Effects of postharvest storage and dormancy status on ABA content, metabolism, and expression of genes involved in ABA biosynthesis and metabolism in potato tuber tissues

At harvest, and for an indeterminate period thereafter, potato tubers will not sprout and are physiologically dormant. Abscisic acid (ABA) has been shown to play a critical role in tuber dormancy control but the mechanisms controlling ABA content during dormancy as well as the sites of ABA synthesis and catabolism are unknown. As a first step in defining the sites of synthesis and cognate processes regulating ABA turnover during storage and dormancy progression, gene sequences encoding the ABA biosynthetic enzymes zeaxanthin epoxidase (ZEP) and 9-cis-epoxycarotenoid dioxygenase (NCED) and three catabolism-related genes were used to quantify changes in their relative mRNA abundances in three specific tuber tissues (meristems, their surrounding periderm and underlying cortex) by qRT-PCR. During storage, StZEP expression was relatively constant in meristems, exhibited a biphasic pattern in periderm with transient increases during early and mid-to-late-storage, and peaked during mid-storage in cortex. Expression of two members of the potato NCED gene family was found to correlate with changes in ABA content in meristems (StNCED2) and cortex (StNCED1). Conversely, expression patterns of three putative ABA-8′-hydroxylase (CYP707A) genes during storage varied in a tissue-specific manner with expression of two of these genes rising in meristems and periderm and declining in cortex during storage. These results suggest that ABA synthesis and metabolism occur in all tuber tissues examined and that tuber ABA content during dormancy is the result of a balance of synthesis and metabolism that increasingly favors catabolism as dormancy ends and may be controlled at the level of StNCED and StCYP707A gene activities Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Genome-Wide Identification and Expression Analysis of the CrRLK1L Gene Family in Apple (Malus domestica)

It has been reported that members of the Catharanthus roseus receptor-like kinase1-like kinase (CrRLK1L) gene family detect cell wall integrity, cell-to-cell communication, and biotic and abiotic stress. We performed a comprehensive study including the genome-wide identification, characterization, and gene expression analysis of CrRLK1Ls in apple (Malus domestica). Sixty-seven M. domestica CrRLK1Ls (MdCrRLK1Ls) were identified based on their domain structure. Molecular weight and pI ranged from 52.36–141 kDa and 5.05–8.9, respectively. They were distributed across 16 of the 18 chromosomes and classified into five phylogenetic branches. Exon-intron structural analysis indicated a wide range of exon numbers. Collinearity analysis showed that both segmental-and tandem-duplication contributed to the expansion of this family. Cis-elements in the MdCrRLK1L promoter region responded mainly to light, circadian rhythm, phytohormones, and biotic or abiotic stress. Many members exhibited tissue-specific expression patterns and differentially expressed under biotic stresses, which may contribute to the different functional roles of MdCrRLK1Ls under physiological stress and/or pathological conditions. This study provides new insights into the CrRLK1Ls in Malus spp.

     

水稻NAM基因家族的全基因组鉴定及表达分析

植物特异性转录因子NAM家族从属于NAC转录因子超家族,在植株生长发育、生理代谢以及应对各种胁迫反应中均发挥重要作用。该研究采用生物信息学方法鉴定水稻基因组中的NAM基因,分析其时空表达模式、亚细胞定位以及蛋白相互作用,并采用实时定量qRT PCR方法分析不同外源激素(如SA、ABA和MeJA)以及非生物胁迫(包括干旱、盐和冷)处理下各NAM基因的表达特征,为进一步探索NAM基因在非生物胁迫中的功能和应激机制以及激素调控途径奠定基础。结果显示：(1)从水稻基因组中共鉴定出48个NAM基因,进化分析将其分为5个亚家族;NAM基因在水稻基因组中存在9对片段复制事件。(2)组织表达分析显示,NAM基因在水稻不同组织及发育时期表现特异性表达,特别是叶鞘、茎和节的生长过程中高表达,且大多数是核定位,并存在多种蛋白互作。(3)实时定量qRT PCR表达分析显示,10个NAM基因在不同组织中均特异表达;大部分NAM基因在盐和干旱胁迫下表达上调,而在冷胁迫下表达降低;SA、ABA和MeJA处理均可显著改变各NAM基因的表达水平。研究表明,NAM基因在水稻生长发育、激素应答和非生物胁迫响应中具有重要作用。     

Genome-wide identification,systematic analysis and characterization of <Emphasis Type="Italic">SRO</Emphasis> family genes in maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.)

SIMILAR TO RCD ONE (SRO) is a small plant-specific gene family, which play essential roles in plant growth and development as well as in abiotic stresses. However, the function of SROs in maize is still unknown. In our study, six putative SRO genes were isolated from the maize genome. A systematic analysis was performed to characterize the ZmSRO gene family. The ZmSRO gene family was divided into two groups according to the motif and intron/exon analysis. Phylogenetic analysis of them with other plants showed that the clades of SROs along with the divergence of monocot and dicot and ZmSROs were more closely with OsSROs. Many abiotic stress response and hormone-induced cis-regulatory elements were identified from the promoter region of ZmSROs. Furthermore, RNA-seq analysis indicated that SRO genes were widely expressed in different tissues and development stages in maize, and the expression divergence was also obviously observed. Analyses of expression in response to PEG6000 and NaCl treatment, in addition to exogenous application of ABA and GA hormones showed that the majority of the members display stress-induced expression patterns. Taken together, our results provide valuable reference for further functional analysis of the SRO gene family in maize, especially in abiotic stress responses.     

大豆GeBP转录因子基因家族的生物信息学分析

GeBP转录因子调控植物表皮毛的生长发育,并且参与控制植物叶片的发育。该文利用生物信息学方法,在大豆全基因组范围内搜索GeBP基因家族,并从氨基酸理化性质、基因结构、染色体的物理分布、系统进化、序列比对、功能结构域、组织表达情况等基本特征方面对GmGeBP基因家族进行分析。结果表明:(1)共获得9个GmGeBP转录因子基因家族成员,其中仅2个基因含有内含子,且都只有1个内含子,表明该家族成员基因构造比较简单但稳定。(2)GmGeBP编码的蛋白分子量为39.65~49.24 kD,理论等电点为4.65~9.08;这些成员基本上都是酸性氨基酸,属于亲水性、不稳定蛋白。(3)这9个基因不均匀的分布于7条染色体上,10和20号染色体上分别分布2个GeBP基因,3、5、13、15、19号染色体上各分布1个基因。(4)系统进化分析表明,大豆与拟南芥对应的GeBP成员亲缘关系较近,分别聚类到4个分支,而与水稻的距离较远。(5)结构域分析表明,9个GmGeBP成员都包含DUF573结构域,推测该部分在GeBP转录因子中很可能是与靶标基因顺式作用元件互作的结构域。(6)通过分析大豆GmGeBP转录因子基因家族的组织表达,发现不同基因在大豆不同组织的表达量不同,具有一定的特异性。该文对大豆GeBP转录因子基因家族的分析和鉴定为进一步研究大豆表皮毛发育的分子作用提供了理论基础。