西洋梨全基因组bZIP基因家族生物信息学分析

碱性亮氨酸拉链(Basic leucine zipper,bZIP),是广泛存在于真核生物中的保守转录因子,其在植物生长过程中参与重要的调控作用。为了解西洋梨bZIP基因家族相关信息,本研究利用生物信息学的方法,在全基因组水平鉴定并分析了西洋梨bZIP基因家族。结果表明,共鉴定出52个PcbZIP基因,系统进化将其分为9个亚族(A、B、C、E、F、G、H、I和S),PcbZIPs中外显子的个数从1~10个不等,PcbZIP转录因子的氨基酸数目在122~741个,等电点在5.42~10.41,PcbZIP基因都定位在细胞核上。基因定位显示,52个PcbZIP基因不均匀地分布在17条染色体上。本研究对西洋梨bZIP家族基因的鉴定与分析,为进一步开展西洋梨bZIP基因的挖掘与功能验证提供依据。     

香蕉GLP基因家族全基因组鉴定及表达分析

为揭示香蕉类萌发素蛋白(GLP)功能,对香蕉GLP基因家族(MaGLP)进行了全基因组鉴定,分析了基因结构、染色体分布和启动子顺式作用元件和转录因子结合位点(TFBS)分布情况以及编码蛋白的理化性质、保守基序、进化关系,同时基于转录组的结果研究它们在4℃和45℃处理的叶片、枯萎病菌FocTR4处理的根系以及自然成熟和乙烯催熟的不同成熟阶段的果实中的表达情况。结果显示:MaGLP家族共有44个成员,编码区CDS序列长度为567～2 103 bp,分布于除10号染色体外的所有染色体上。大部分GLP基因包含1～2个外显子,多数GLP具有信号肽且主要定位在胞外。进化树分析发现,MaGLP可分为8个亚家族,其中亚家族M为香蕉特有。顺式作用元件和TFBS预测结果显示,MaGLP启动子区存在多种植物激素和逆境胁迫相关响应元件以及7种TFBS。MaGLP成员在香蕉不同组织部位中的表达水平差异较大且受多种胁迫调控。其中MaGLP5-1和MaGLP9-8对各种处理均有响应,MaGLP1-2和MaGLP9-4受高温、低温胁迫抑制,而Ma GLP9-6受高温、低温胁迫诱导,MaGLP5-4受高温和FocTR4...     

辣椒全基因组中LBD转录因子的鉴定与表达分析

利用生物信息学的方法,从辣椒基因组中鉴定出45个LBD基因,这些基因分布于辣椒9条染色体上。该家族成员内含子数整体上不超过3个,结构相对简单。进化关系显示辣椒LBD基因可分为ClassⅠ和ClassⅡ两大类,细分为Ⅰa、Ⅰb、Ⅰc、Ⅰd、Ⅰe、Ⅱa和Ⅱb等7个亚类。不同组织和发育时期的表达模式研究发现,该基因家族具有一定的时空表达特异性。qRT-PCR结果表明,热激胁迫可以明显激活或抑制部分LBD基因的表达,其中ClassⅡ类基因较ClassⅠ类对高温具有更高的敏感性。     

Genome-wide analysis of antioxidant enzyme gene families involved in drought and low-temperature responses in Apple (Malus domestica)

Antioxidant enzymes were well-known for reactive oxygen scavenging and protecting cells from oxidative damage in multiple biotic and abiotic stresses. Aimed to overview of antioxidant enzyme gene families and screen for drought and low-temperature response members, the whole apple antioxidant enzyme genes in apple genome were studied. Out of 73candidates in seven antioxidant enzyme gene families among the entire apple genome, a total of 49 genes were identified, showed more antioxidant enzyme gene members than those in other plant species. A phylogenetic tree based on predicted functional domains and motifs of apple and Arabidopsis antioxidant enzymes revealed 19 putative drought or low-temperature response genes, and 9 out 19 genes belong to five families responded to both drought and low-temperature stresses. Subsequently, cis-elements in those nine antioxidant enzyme gene promoters were examined and abundant elements involved in multiple hormone regulation and abiotic stresses response, including drought and low-temperature were found. The tissue expression specificity for those nine members in eight kinds of tissues was also examined. Screening and identifying both drought and low-temperature response genes provide useful information to understand gene functions and promote application of antioxidant enzyme genes in apple abiotic resistance breeding.     

Genome-wide identification and analysis of CKX genes in Poncirus trifoliata

Cytokinin oxidase/dehydrogenases (CKXs) in plants are coded by a small multigene family and play important roles in maintaining cytokinin homeostasis. In this study, four CKX genes (i.e. PsCKX1, PsCKX2, PsCKX5, and PsCKX7) were cloned from Poncirus trifoliata. All PsCKXs contained a highly conserved flavin adenine dinucleotide (FAD) binding domain and a cytokinin dehydrogenase 1, FAD/cytokinin binding domain. PsCKX1 and PsCKX2 shared 66.2% and 65.4% identity with AtCKX6 and AtCKX1, respectively, while PsCKX5 and PsCKX7 exhibited less than 45% identity with AtCKXs. The expression analysis under abiotic conditions (NaCl, ABA, 6-BA and drought) revealed that the four PsCKX genes could respond to at least one treatment, and the expression patterns were diverse in root and leaf. Overexpressing four PsCKX genes in tobacco led to diverse phenotypic variations in transgenic plant, including leaf shape, root architecture, and plant height. In addition, the data showed that PsCKX2 and PsCKX5 hold promise to obtain citrus dwarf rootstock with a stronger root system, since the overexpression of them resulted in dwarf plants with more lateral roots. Taken together, the work lays the basis for applications of PsCKX genes in future.     

辣椒GRAS家族全基因组鉴定与表达分析

基于辣椒全基因组数据信息,利用生物信息学方法对CaGRAS基因家族进行了系统鉴定和进化分析,并通过Real-time PCR方法检测了CaGRAS家族组织表达模式和对PEG6000、盐胁迫的应答。结果表明:在辣椒中存在54个CaGRAS基因,除11号染色体外其余染色体均有分布,外显子数1~3,等电点4.97~9.13;系统进化分析显示CaGRAS基因可分为8个进化群;CaGRAS基因具有不同的表达模式,在根、茎、叶片和茎尖中优势表达的基因分别有34、8、3和8个;多数CaGRAS基因能响应PEG6000和盐胁迫,其中CaGRAS11、CaGRAS30、CaGRAS40、CaGRAS44和CaGRAS50受到PEG6000和盐胁迫的强烈诱导。本研究为深入解析CaGRAS家族基因的功能奠定了一定基础。     

辣椒属GRF基因家族全基因组鉴定和表达分析

生长调节因子(Growth-regulating factor,GRF)是一类植物特异的转录因子,其作用涉及植物的生长发育、胁迫和激素信号响应等各个方面。目前还没有关于辣椒GRF的相关报道。利用BLASTP和隐马科夫模型(HMM)在辣椒属(Capsicum)5个参考基因组数据库鉴定了52个GRF家族成员。通过分析发现辣椒GRF转录因子长度为200～745 aa,分子量23～81 kD,理论等电点5.9～9.5。保守结构域和基序分析发现,大多数辣椒GRFN端具有QLQ和WRC保守结构域,C端至少具有FFD、TQL和GGPL结构域之一;少数GRFN端仅具有WRC结构域,C端缺乏保守序列。系统进化分析发现,辣椒GRF转录因子分为5个群,位于同一群的GRF保守结构域位置、基序组成、基因结构相似,辣椒GRF与番茄GRF具有一一对应的进化关系。转录组数据分析表明,CaGRF8在辣椒果实发育早中期表达量高,CaGRF4在果实发育后期表达量较高;低温、干旱、盐和赤霉素处理后辣椒幼苗CaGRF表达量发生明显变化,CaGRF8受到赤霉素诱导表达量升高,而CaGRF4的表达被赤霉素抑制。     

辣椒热激蛋白HSP90家族基因鉴定及分析

借助生物信息学工具对辣椒热激蛋白HSP90家族基因进行鉴定,并分析其理化性质、结构特征、系统进化关系以及在各组织器官和高温胁迫下的表达模式。结果表明,辣椒基因组中含有7个HSP90家族基因,分布于5条染色体上,内含子数2～19不等,含有5个保守基序;系统进化关系分析显示辣椒7个HSP90家族基因分为3组;亚细胞定位结果显示辣椒HSP90蛋白定位于细胞质与内质网中;基于已发表的转录组数据进行组织表达分析,HSP90在不同组织中的表达模式不同;高温处理可不同程度地激活HSP90的表达。     

Phylogenetic and expression analysis of the magnesium transporter family in pear,and functional verification of PbrMGT7 in pear pollen

The magnesium ion (Mg²⁺) is the most abundant divalent cation in living cells, and it plays essential roles in various cellular functions. Mg²⁺ homeostasis in plant cells is crucial for plant growth. The MRS2/MGT family of proteins localise to various membranes, and they function during Mg²⁺ transport in plants, but their functions are largely unknown in fruit trees. In this study, we performed a genome-wide analysis to identify the MGT gene family members in the pear Pyrus bretschneideri. Sixteen MGT genes were identified. Analysis of the activity of pear pollen showed that a low-concentration magnesium ion treatment was beneficial for pollen germination and pollen tube growth. None of the 16 MGT genes were expressed in any unique tissue, including pollen, and their expression in magnesium-treated pollen varied greatly, where PbrMGT7 was the most sensitive and it was tested as a representative. PbrMGT7 could functionally complement a bacterial strain deficient in Mg²⁺, thereby indicating a role in magnesium transport. A co-localisation experiment confirmed that PbrMGT7 was localised in the mitochondria, which suggests that PbrMGT7 could mediate Mg-trafficking between the mitochondria and cytosol. Overall, these results suggest that PbrMGT7 is related to Mg²⁺ homeostasis during pear pollen tube growth.??     

梨矮化砧木中矮1号GA20-氧化酶基因克隆与表达分析

中矮1号是中国农业科学院果树研究所选育的梨优良矮化砧木,为研究其矮化机理,利用RT-PCR结合RACE方法克隆了梨矮化砧木中矮1号的1个GA20-氧化酶基因,并对该基因及其氨基酸序列以及该基因在不同生长类型梨品种中不同时期新梢叶片中的表达进行了分析。结果表明,该基因全长1 179 bp,推导编码392个氨基酸,其编码的...     

石榴ARF基因家族鉴定及表达分析

【目的】筛选并分析石榴生长素响应因子(auxin response factor,ARF)基因家族,为解析石榴ARF基因功能及信号转导调控机制的研究提供参考。【方法】利用生物信息学工具,系统地分析石榴ARF基因家族成员的基因结构、蛋白理化性质、蛋白结构、保守基序、系统进化和RNA-Seq数据。【结果】石榴全基因组中鉴定出19个可能的ARF家族基因,根据系统发育树可以划分为4类。PgARF基因家族成员的扩张与全基因组复制事件有关,存在串联重复现象。RNA-Seq数据分析表明,PgARF有一定的组织表达特异性,存在假基因化和新功能化的可能。【结论】整合以上基因结构、系统发育与进化、RNA-Seq表达等分析结果,发现石榴ARF蛋白具有典型的B3、Auxin_resp结构域,多数还具有Aux/IAA结构域。石榴ARF基因家族基因结构和保守基序的进化与进化时间相关,同时家族成员扩张主要与全基因组复制事件相关。     

西瓜全基因组ClTCP转录因子的鉴定与表达分析

<正>目的与意义:TCP蛋白是植物特有的一类转录因子,对植物的生长发育及形态建成起着重要的调控作用,比如:种子萌发、植株分枝、叶和花的发育等过程。西瓜是世界性的重要经济作物,栽培面积广阔,经济效益显著。但是关于西瓜TCP基因家族的研究至今还没有报道。本研究利用生物信息学分析,功能预测与验证等方法,揭示西瓜TCP     

Cloning and identification of novel miRNAs in the flower organs of Korla fragrant pear at anthesis

The objective of the study was to learn more about some newly identified miRNAs related to calyx persistence in Korla fragrant pear (Pyrus sinkiangensis Yu). Small RNAs were subjected to high-throughput sequencing after extraction from the ovaries and sepals of flowers with either a deciduous or a persistent calyx. Differentially expressed miRNAs were screened, and 73 new miRNAs were obtained. Twenty of these new miRNAs were selected to further validate all of the new miRNAs. Their mature miRNAs were cloned and identified, the secondary structures of the precursor miRNAs (pre-miRNAs) were analysed, and then qRT-PCR analysis was conducted. The results showed that the mature sequences of nine new miRNAs (novel_miRNA) in different samples were consistent with the results of high-throughput sequencing. Overall, this study improved current methods for the molecular cloning and identification of fruit tree miRNA. Nine new miRNA types were identified. This study laid a good foundation for elucidating the biological functions of these new miRNAs.     

Isolation and expression analysis of differentially expressed genes in stem tissue of the Greek lemon cv. Adamopoulou

Lemon (Citrus limon (L.) Burm. f.) is susceptible to mal secco, a serious vascular disease caused by the fungus Phoma tracheiphila (Petri) Kant. and Gik., as well as low temperatures. The greek lemon cultivar Adamopoulou, thought to be derived from the Portuguese cultivar Lisbon, exhibits enhanced resistance to mal secco and cold as opposed to cv. Lisbon. Suppression subtractive hybridization (SSH) was employed for the isolation of differentially expressed genes in lemon stem tissue. A subtractive cDNA library was constructed and a total of 296 clones were sequenced. The obtained sequences were edited, resulting in 56 non-redundant ESTs. Sequence analysis revealed homology to previously identified genes involved in defense mechanisms against biotic and abiotic stresses, as well as sequences with no significant similarity in the GenBank. Selected ESTs were analyzed by real-time PCR for confirmation purposes. This analysis revealed significant expression differences between the two cultivars for genes expressing allantoinase, ultraviolet-B-repressible protein, 4-coumarate:CoA ligase and other proteins that are known to be upregulated under biotic and abiotic stress conditions.     

葡萄NHX基因家族的鉴定和表达分析

【目的】探究葡萄NHX基因家族生物信息学特性及在非生物胁迫下的表达情况,以期筛选出与非生物胁迫相关的家族成员,从而为葡萄抗逆性研究提供理论依据。【方法】以拟南芥、水稻及胡扬NHX基因序列为基础,对葡萄NHX基因进行同源克隆、染色体定位、氨基酸组成成分、理化性质、motif、蛋白质二级结构以及基因芯片表达等分析,同时利用qRT-PCR技术分析葡萄NHX基因家族表达情况。【结果】葡萄NHXs可分为2个亚族,主要分布在第1、5、7、14、15、19号染色体上,其外显子数为12～23个;VvNHX06的氨基酸数最少,有291个,VvNHX07的氨基酸数最多,有1141个。Motif分析发现,N端含有典型的锌指结构,蛋白质二级结构以α-螺旋和无规则卷曲为主。亚细胞定位预测发现,葡萄NHX基因主要分布在细胞膜、内质网、线粒体、液泡和细胞质中。基因芯片表达显示,使用NaCl、ABA和PEG处理后,葡萄叶片中VvNHX02和VvNHX06基因表达量均呈上升趋势。qRT-PCR分析结果表明,在200 mmol·L~(-1)NaCl、100 mmol·L~(-1)ABA处理后的葡萄叶片中,VvNHX06表达量显著增加,分别是对照的30倍和60倍。用10%PEG处理实验材料6 h后,VvNHX05的表达量明显增加,是对照的5倍。【结论】VvNHX05和VvNHX06基因与植物耐盐和抗旱性有密切关系,可为葡萄的逆境胁迫机制研究提供参考。     

鸭梨多酚氧化酶基因CDS区的克隆及表达

以鸭梨(Pyrus bretschneideri Rehd.)果皮基因组DNA为模板,根据已经发表的多酚氧化酶(polyphenol oxidase,PPO)基因保守序列设计引物,利用PCR技术,克隆得到鸭梨多酚氧化酶编码区序列,将此核酸序列克隆到载体pGEM-T,酶切鉴定后测序,结果表明该段序列含有1782个核苷酸,编码593个氨基酸。对鸭梨多酚氧化酶基因片段的一致性分析和进化树分析表明,该片段与沙梨(Pyrus pyrifolia,AB056680)、苹果(Malus domestica,L29450)、李(Prunuss alicina,AY866432)以及杏(Prunus armeniaca,AF020786)的一致性分别为99%、96.3%、82%和51.4%,绘制的进化树和形态学分类地位相一致。将该片段连接到表达载体pET39b上,获得的重组子命名为pET39b-PPO,热激法转化表达受体大肠杆菌BL21(DE3)菌株,用IPTG进行诱导。SDS-PAGE分析表明,PPO基因在大肠杆菌中被诱导表达蛋白质相对分子质量约66ku,检测表明具有多酚氧化酶的活性。