Identification and expression analysis of twenty ARF genes in Populus

Yang, Chunxia; Xu, Meng; Liu, Xuan; Xiangmei, Jiang; Huang, Minren

doi:10.1016/j.gene.2014.04.067

Cited by 21 publications

(16 citation statements)

References 38 publications

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“…Under exogenous auxin treatment, the expression patterns of CitARF, CitGH3 and CitAUX/IAA family genes were remarkably varied. Of 59 genes investigated in this study, 10 genes including 2 CitARFs, 4 CitGH3s and 4 CitAUX/IAAs were up-or down-regulated by auxin, which was consistent with previous results (Wang et al 2007;Shen et al 2014;Yang et al 2014a). While the expression levels of remaining genes were stable during the time course.…”

Section: Discussionsupporting

confidence: 92%

The ARF, AUX/IAA and GH3 gene families in citrus: genome-wide identification and expression analysis during fruitlet drop from abscission zone A

Xie

Pang

et al. 2015

Mol Genet Genomics

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Completion of the whole genome sequencing of citrus enabled us to perform genome-wide identification and functional analysis of the gene families involved in agronomic traits and morphological diversity of citrus. In this study, 22 CitARF, 11 CitGH3 and 26 CitAUX/IAA genes were identified in citrus, respectively. Phylogenetic analysis revealed that all the genes of each gene family could be subdivided into three groups and showed strong evolutionary conservation. The GH3 and AUX/IAA gene families shrank and ARF gene family was highly conserved in the citrus genome after speciation from Arabidopsis thaliana. Tissue-specific expression profiles revealed that 54 genes were expressed in at least one tissue while just 5 genes including CitARF07, CitARF20, CitGH3.04, CitAUX/IAA25 and CitAUX/IAA26 with very low expression level in all tissues tested, suggesting that the CitARF, CitGH3 and CitAUX/IAA gene families played important roles in the development of citrus organs. In addition, our data found that the expression of 2 CitARF, 4 CitGH3 and 4 AUX/IAA genes was affected by IAA treatment, and 7 genes including, CitGH3.04, CitGH3.07, CitAUX/IAA03, CitAUX/IAA04, CitAUX/IAA18, CitAUX/IAA19 and CitAUX/IAA23 were related to fruitlet abscission. This study provides a foundation for future studies on elucidating the precise role of citrus ARF, GH3 and AUX/IAA genes in early steps of auxin signal transduction and open up a new opportunity to uncover the molecular mechanism underlying citrus fruitlet abscission.

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Section: Discussionsupporting

confidence: 92%

The ARF, AUX/IAA and GH3 gene families in citrus: genome-wide identification and expression analysis during fruitlet drop from abscission zone A

Xie

Pang

et al. 2015

Mol Genet Genomics

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“…Arabidopsis ARFs were divided into four subgroups, which is in accordance with the phylogenetic classifications of ARFs in rice [ 18 ], banana ( Musa acuminata L.) [ 23 ] and Salvia miltiorrhiza [ 24 ]. Maize and poplar ARFs are classified to six subgroups [ 25 ], whereas Medicago ARFs were divided into eight subgroups [ 20 ]. In general, the wide variety of ARF phylogenetic grouping patterns are based on the diversification of its gene structure and motif locations, which may be the result of gene truncation or alternative splicing [ 22 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification, Phylogeny, and Expression Analysis of ARF Genes Involved in Vegetative Organs Development in Switchgrass

Wang

Shen³

et al. 2018

International Journal of Genomics

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Auxin response factors (ARFs) have been reported to play vital roles during plant growth and development. In order to reveal specific functions related to vegetative organs in grasses, an in-depth study of the ARF gene family was carried out in switchgrass (Panicum virgatum L.), a warm-season C4 perennial grass that is mostly used as bioenergy and animal feedstock. A total of 47 putative ARF genes (PvARFs) were identified in the switchgrass genome (2n = 4x = 36), 42 of which were anchored to the seven pairs of chromosomes and found to be unevenly distributed. Sixteen PvARFs were predicted to be potential targets of small RNAs (microRNA160 and 167). Phylogenetically speaking, PvARFs were divided into seven distinct subgroups based on the phylogeny, exon/intron arrangement, and conserved motif distribution. Moreover, 15 pairs of PvARFs have different temporal-spatial expression profiles in vegetative organs (2nd, 3rd, and 4th internode and leaves), which implies that different PvARFs have specific functions in switchgrass growth and development. In addition, at least 14 pairs of PvARFs respond to naphthylacetic acid (NAA) treatment, which might be helpful for us to study on auxin response in switchgrass. The comprehensive analysis, described here, will facilitate the future functional analysis of ARF genes in grasses.

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“…Broad genetic variation exists for adventitious rooting in Populus (Zalesny et al ), which provides the potential for realizing substantial selection gains. In recent years, some genes and signaling pathways associated with adventitious rooting have been identified in Populus (Ramírez‐Carvajal et al , Rigal et al , Xu et al , Xuan et al , Yang et al ).…”

Section: Introductionmentioning

confidence: 99%

Two WUSCHEL‐related HOMEOBOX genes, PeWOX11a and PeWOX11b, are involved in adventitious root formation of poplar

Xie

Huang

2015

Physiologia Plantarum

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The plant-specific WUSCHEL-related HOMEOBOX (WOX) transcription factors play important roles in key developmental processes, but knowledge regarding functional characterization of WOX genes in poplar remains limited. To reveal genes and signaling pathways associated with adventitious rooting in poplar, here we isolated and characterized two WOX genes through the rapid amplification of cDNA ends (RACE), sequence aligning, expression profiling, protoplast transfection and poplar transformation. Detailed information about the sequence similarity, structural features, evolutionary relationships, expression patterns and subcellular localization of the two genes were revealed. Overexpression of either PeWOX11a or PeWOX11b not only increased the number of adventitious roots on the cuttings but also induced ectopic roots in the aerial parts of transgenic poplars. Meanwhile, their overexpression in transgenic poplars affected axillary bud and leaf development. These results suggest that PeWOX11a and PeWOX11b were involved in multiple developmental processes of poplar, especially in adventitious root formation. Our results provide new insights into the molecular mechanisms underlying adventitious root formation of poplar.

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Identification and expression analysis of twenty ARF genes in Populus

Cited by 21 publications

References 38 publications

The ARF, AUX/IAA and GH3 gene families in citrus: genome-wide identification and expression analysis during fruitlet drop from abscission zone A

The ARF, AUX/IAA and GH3 gene families in citrus: genome-wide identification and expression analysis during fruitlet drop from abscission zone A

Genome-Wide Identification, Phylogeny, and Expression Analysis of ARF Genes Involved in Vegetative Organs Development in Switchgrass

Two WUSCHEL‐related HOMEOBOX genes, PeWOX11a and PeWOX11b, are involved in adventitious root formation of poplar

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