Genome-wide characterization and expression analysis of the auxin response factor (ARF) gene family during melon (Cucumis melo L.) fruit development

Protoplasma - ARFs in plants mediate auxin signaling transduction and regulate growth process. To determine genome-wide characterization of ARFs family in melon (Cucumis melo L.), ARFs were...     

Genome-wide identification of auxin response factor (ARF) family in kiwifruit (Actinidia chinensis) and analysis of their inducible involvements in abiotic stresses

Auxin response factor (ARF) acts as a vital component of auxin signaling and participates in growth, development, and stress responses in plants. In the present study, we comprehensively analyzed kiwifruit’s (Actinidia chinensis) ARF genes (AcARFs) and their involvement in abiotic stress response. We identified a total of 41 AcARFs encoding ARFs in the A. chinensis genome. AcARF genes were characterized by the classic ARF_resp and a B3 domain and primarily localized on the cytoplasm and nucleus. AcARFs were categorized into eight subgroups as per the phylogenetic analysis. Synteny analysis showed that 35 gene pairs in AcARF family underwent segmental and whole genome duplication events. Promoter cis-element prediction revealed that AcARFs might be involved in abiotic factors related to stress response, which was later assessed and validated by qRT-PCR based expression analysis. Additionally, AcARFs showed tissue-specific expression. These findings extend our understanding of the functional roles of AcARFs in stress responses. Taken together, the systematic annotation of the AcARF family genes provides a platform for the functional and evolutionary study, which might help in elucidating the precise roles of the AcARFs in stress responses.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-01011-4.     

Expression analysis of the auxin efflux carrier family in tomato fruit development

Auxin transport network, which is important in the integration of plant developmental signals, depends on differential expression of the auxin efflux carrier PIN gene family. We cloned three tomato PIN (referred as SlPIN) cDNAs and examined their expression patterns in fruit and other organs. The expression of SlPIN1 and SlPIN2 was highest in very young fruit immediately after anthesis, whereas the expression of SlPIN3 was low at this same stage of fruit development. SlPIN2::GUS was expressed in ovules at anthesis and in young developing seeds at 4 days after anthesis, while SlPIN1::GUS was expressed in whole fruit. The DR5::GUS auxin-responsive reporter gene was expressed in the fruit and peduncle at anthesis and was higher in the peduncle 4 days after anthesis. These studies suggest that auxin is likely transported from young seeds by SlPIN1 and SlPIN2 and accumulated in peduncles where SlPIN gene expression is low in tomato. The possible role of SlPINs in fruit set was discussed.     

Genome-wide analysis of the auxin response factor (ARF) gene family in maize (<Emphasis Type="Italic">Zea mays</Emphasis>)

Auxin response factors (ARFs) are an important family involved in auxin-mediated response through specific binding to auxin response elements (AuxREs). A few members of the ARF family have been functionally characterized in Arabidopsis, rice (Oryza sativa), Poplar (Populous trichocarpa). However, little is known about ARF genes in maize (Zea mays). We performed a comprehensive bioinformatics analysis of the maize ARF gene family including analysis of the genome sequence, conserved domains, chromosomal locations, phylogenetic relationships, gene duplication, and expression profiles. 35 ZmARF genes were identified and categorized into four groups (Class I, II, III, and IV). In addition, a segmental ZmARF duplication event was shown to play an important role in maize ARF gene expansion. 7 ZmARF genes had no expression in specific tissues we obtained, but presented in mixed tissues according to the NCBI EST database, respectively. These studies have laid the theoretical foundation for further functional verification of these ZmARF genes.     

Genome-wide identification and expression analysis of peach auxin response factor gene families

Plant auxin response factors (ARFs) are involved in plant growth, development and multiple other processes. In this study, the ARF gene family in the peach genome was identified by bioinformatics software and RT-PCR. In total, 18 PpARF candidate genes were found in the peach genome. The DNA-binding and ARF domains, as well as motif III and IV of the PpARF gene family were highly conserved. The phylogenetic analysis revealed that PpARF gene family was divided into five classes: Class I (three members), Class II (four members), Class III (five members), Class IV (three members) and Class V (three members). The results of an intron-exon structure analysis indicated that PpARF gene family members were composed of 2–15 exons. A chromosome mapping analysis revealed that PpARF genes were distributed with different densities over eight chromosomes, with the largest number of PpARF genes on chromosome 1 (four genes), followed by chromosome 4 and 6 (three genes each). Only one gene was located on each of chromosome 3, 7 and 8. A conserved motif analysis revealed that the DNA-binding and ARF domains were observed in all PpARF proteins (except for PpARF18). Class I contained no motifs III or IV (except for PpARF7). RT-PCR results indicated that all of the PpARF genes, with the exception of PpARF15 and PpARF17, were expressed in at least one of the tissues (roots, stems, leaves, flowers and five stages of fruit development). These results suggested that the PpARF gene family members are highly and structurally conserved, and are involved in various aspects of peach growth and development, especially in fruit development.     

番茄PPR基因家族的鉴定与生物信息学分析

PPR(Pentatricopeptide repeats)基因家族在植物中广泛存在, 其在植物生长发育过程中至关重要。文章采用生物信息学方法, 利用Pfam已鉴定的PPR保守结构域序列检索番茄(Solanum lycopersicum L.)基因组计划注释的蛋白序列, 最终确定了番茄中可能存在的471个PPR编码基因; 根据拟南芥(Arabidopsis thaliana L.)中鉴定的各个结构域的特点对其进行了蛋白结构分析、分类和保守序列分析, 并对番茄PPR基因家族进行了系统进化树构建、染色体定位、亚细胞定位预测、表达和GO分析等。结果表明：番茄PPR基因家族分为P和PLS两个亚家族, 各占序列数目的一半, PLS亚家族又分为PLS、E、E+和DYW四类, 且在进化树中形成不同的分支; 各个结构域在植物中非常保守; PPR基因家族分布在番茄12条染色体上, 且多数无内含子结构; 大部分PPR蛋白具有线粒体或叶绿体定位序列, GO分析表明PPR蛋白参与RNA相关的生物学过程     

Genome-wide identification and expression analysis of MATE gene family in citrus fruit (Citrus clementina)

Multidrug and toxic compound extrusion (MATE) proteins are a class of secondary active multidrug transporters. In plants, this family has significantly expanded and is involved in numerous plant physiological processes. Although MATE proteins have been identified in an increasing number of species, the understanding about this family in citrus remains unclear. In this study, a total of 69 MATE transporters were identified in the citrus genome (Citrus clementina) and classified into four groups by phylogenetic analysis. Tandem and segmental duplication events were the main causes of the citrus MATE family expansion. RNA-seq and qRT-PCR analyses were performed during citrus fruit development. The results indicated that CitMATE genes showed specific expression profiles in citrus peels and flesh at different developmental stages. Combined with the variations of flavonoids and citrate levels in citrus fruit, we suggested that CitMATE43 and CitMATE66 may be involved in the transport process of flavonoids and citrate in citrus fruit, respectively. In addition, two flavonoids positive regulators, CitERF32 and CitERF33, both directly bind to and activated the CitMATE43 promoter. Our results provide comprehensive information on citrus MATE genes and valuable understanding for the flavonoids and citrate metabolism in citrus fruit.     

番茄B3超家族成员鉴定及生物信息学分析

B3超家族是一类含有B3功能域(与DNA结合的高度保守结构域)的转录因子,在植物生长发育过程中起重要作用。本研究采用生物信息学的方法,利用Pfam中的B3保守结构域序列检索番茄(Solanum lycopersicum L.)蛋白序列,确定了97个B3超家族基因。对番茄B3超家族成员进行了系统进化树分析、染色体定位、结构域分析、组织表达和诱导表达分析等。番茄B3超家族分为LAV、ARF、RAV和REM 4个亚家族,每个亚家族中的数量分别为4、22、9和62个,且在进化树中形成明显不同的分支,每个亚家族都进行了系统进化和结构域分析;番茄12条染色体都含有B3超家族基因;11个成员的表达模式表明,B3超家族同一亚家族成员也具有不同的时空表达模式;在干旱、盐和高温胁迫处理下,部分成员响应强烈并且响应不同的外界信号;而对于ABA处理响应非常弱。本研究将为B3基因超家族成员的生物学功能研究提供参考。     

Genome-wide analysis of tomato WIP family genes and their response to salt stress under glutathione treatment

Journal of Plant Biochemistry and Biotechnology - Cys2His2 (C2H2)-type zinc-finger proteins (ZFPs) participate in plant tolerance under various abiotic stresses. Wound-induced protein (WIP) is a...     

Genome-wide analysis of gene expression during early Arabidopsis flower development

Detailed information about stage-specific changes in gene expression is crucial for the understanding of the gene regulatory networks underlying development. Here, we describe the global gene expression dynamics during early flower development, a key process in the life cycle of a plant, during which floral patterning and the specification of floral organs is established. We used a novel floral induction system in Arabidopsis, which allows the isolation of a large number of synchronized floral buds, in conjunction with whole-genome microarray analysis to identify genes with differential expression at distinct stages of flower development. We found that the onset of flower formation is characterized by a massive downregulation of genes in incipient floral primordia, which is followed by a predominance of gene activation during the differentiation of floral organs. Among the genes we identified as differentially expressed in the experiment, we detected a significant enrichment of closely related members of gene families. The expression profiles of these related genes were often highly correlated, indicating similar temporal expression patterns. Moreover, we found that the majority of these genes is specifically up-regulated during certain developmental stages. Because co-expressed members of gene families in Arabidopsis frequently act in a redundant manner, these results suggest a high degree of functional redundancy during early flower development, but also that its extent may vary in a stage-specific manner.