Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa

Kalluri, Udaya C.; DiFazio, Stephen P.; Brunner, Amy M.; Tuskan, Gerald A.

doi:10.1186/1471-2229-7-59

Cited by 236 publications

(209 citation statements)

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“…On a genome-wide scale, approximately one third of predicted genes are retained in duplications resulting from the salicoid duplication event [5]. The high retention rate of duplicated genes was also previously reported in other Populus gene families [70,71]. These findings are also in consistency with the previous studies demonstrating that genes involved in transcription regulation and signal transduction are preferentially retained [73-75].…”

Section: Resultssupporting

confidence: 87%

“…The tandem duplication ratio of NAC genes in this study is relatively lower compared to some other gene families in Populus , which was represented in a considerable higher proportion [71,72]. Interestingly, a similar low retention rate of tandem duplicates was also observed for Populus ARF gene family [71].…”

Section: Resultssupporting

confidence: 66%

“…Interestingly, a similar low retention rate of tandem duplicates was also observed for Populus ARF gene family [71]. …”

Section: Resultssupporting

confidence: 61%

“…Among them, the segmental duplication associated with the salicoid duplication event that occurred 65 million years (Ma) ago significantly contribute to the amplification of many multi-gene families [61,69-71]. To determine the possible relationship between the NAC genes and potential segmental duplications, we mapped Populus NACs to the duplicated blocks established in the previous studies [5].…”

Section: Resultsmentioning

confidence: 99%

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Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

et al. 2010

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BackgroundNAC (NAM, ATAF1/2 and CUC2) domain proteins are plant-specific transcriptional factors known to play diverse roles in various plant developmental processes. NAC transcription factors comprise of a large gene family represented by more than 100 members in Arabidopsis, rice and soybean etc. Recently, a preliminary phylogenetic analysis was reported for NAC gene family from 11 plant species. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, conserved motifs, and expression profiling analysis has been presented thus far for the model tree species Populus.ResultsIn the present study, a comprehensive analysis of NAC gene family in Populus was performed. A total of 163 full-length NAC genes were identified in Populus, and they were phylogeneticly clustered into 18 distinct subfamilies. The gene structure and motif compositions were considerably conserved among the subfamilies. The distributions of 120 Populus NAC genes were non-random across the 19 linkage groups (LGs), and 87 genes (73%) were preferentially retained duplicates that located in both duplicated regions. The majority of NACs showed specific temporal and spatial expression patterns based on EST frequency and microarray data analyses. However, the expression patterns of a majority of duplicate genes were partially redundant, suggesting the occurrence of subfunctionalization during subsequent evolutionary process. Furthermore, quantitative real-time RT-PCR (RT-qPCR) was performed to confirm the tissue-specific expression patterns of 25 NAC genes.ConclusionBased on the genomic organizations, we can conclude that segmental duplications contribute significantly to the expansion of Populus NAC gene family. The comprehensive expression profiles analysis provides first insights into the functional divergence among members in NAC gene family. In addition, the high divergence rate of expression patterns after segmental duplications indicates that NAC genes in Populus are likewise to have been retained by substantial subfunctionalization. Taken together, our results presented here would be helpful in laying the foundation for functional characterization of NAC gene family and further gaining an understanding of the structure-function relationship between these family members.

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Section: Resultssupporting

confidence: 87%

Section: Resultssupporting

confidence: 66%

“…Interestingly, a similar low retention rate of tandem duplicates was also observed for Populus ARF gene family [71]. …”

Section: Resultssupporting

confidence: 61%

Section: Resultsmentioning

confidence: 99%

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Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

et al. 2010

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“…These contained early auxin-responsive genes involved in transcriptional regulation (AUX/IAA) and auxin conjugation (GH3) as well as cell cycle regulators. A focus was made on the regulation of members of auxin signaling-related (PtaIAA) and homeostasis-related (PtaGH3) gene families.Six out of the 35 poplar auxin-responsive transcription factors Aux/IAA were identified as being differentially expressed: PtaIAA28.1, PtaIAA33.2, PtaIAA3.3, PtaIAA3.4, PtaIAA19.3, and PtaIAA34 (names refer to Kalluri et al, 2007). Within these six PtaIAA family members, transcripts of PtIAA28.1 were the most abundant in control roots, and PtIAA28.1 was the only family member to be down-regulated upon contact with L. bicolor.…”

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confidence: 99%

The Ectomycorrhizal FungusLaccaria bicolorStimulates Lateral Root Formation in Poplar and Arabidopsis through Auxin Transport and Signaling

et al. 2009

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The early phase of the interaction between tree roots and ectomycorrhizal fungi, prior to symbiosis establishment, is accompanied by a stimulation of lateral root (LR) development. We aimed to identify gene networks that regulate LR development during the early signal exchanges between poplar (Populus tremula 3 Populus alba) and the ectomycorrhizal fungus Laccaria bicolor with a focus on auxin transport and signaling pathways. Our data demonstrated that increased LR development in poplar and Arabidopsis (Arabidopsis thaliana) interacting with L. bicolor is not dependent on the ability of the plant to form ectomycorrhizae. LR stimulation paralleled an increase in auxin accumulation at root apices. Blocking plant polar auxin transport with 1-naphthylphthalamic acid inhibited LR development and auxin accumulation. An oligoarray-based transcript profile of poplar roots exposed to molecules released by L. bicolor revealed the differential expression of 2,945 genes, including several components of polar auxin transport (PtaPIN and PtaAUX genes), auxin conjugation (PtaGH3 genes), and auxin signaling (PtaIAA genes). Transcripts of PtaPIN9, the homolog of Arabidopsis AtPIN2, and several PtaIAAs accumulated specifically during the early interaction phase. Expression of these rapidly induced genes was repressed by 1-naphthylphthalamic acid. Accordingly, LR stimulation upon contact with L. bicolor in Arabidopsis transgenic plants defective in homologs of these genes was decreased or absent. Furthermore, in Arabidopsis pin2, the root apical auxin increase during contact with the fungus was modified. We propose a model in which fungus-induced auxin accumulation at the root apex stimulates LR formation through a mechanism involving PtaPIN9-dependent auxin redistribution together with PtaIAA-based auxin signaling.Most temperate forest trees develop a mutualistic root symbiosis with ectomycorrhizal soil fungi. During the establishment of ectomycorrhiza (ECM), fungal hyphae invade the root from root cap cells in and upwards to the epidermis (Horan et al., 1988). After attachment to epidermal cells, hyphae multiply to form a series of layers that differentiate to establish a mantle structure around the root (Horan et al., 1988). An internal network of hyphae between the epidermis and root cortex cells forms the Hartig net (Blasius et al., 1986), while extraradical hyphae prospect throughout the surrounding soil and gather nutrients. Morphological observations of forming ECMs have shown that in the vicinity of the fungus the root architecture of the host plant is profoundly modified. Interaction with hyphae stimulates lateral root (LR) formation, dichotomy of the root apical meristem in conifer species, and cytodifferentiation of root cells (radial elongation and root hair decay; Horan et al., 1988;Dexheimer and Pargney, 1991;. Even though several studies have focused on LR stimulation during ECM formation, it still remains unclear what the molecular mechanisms are that modify root development during contact with the fungus.In the ...

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Genomics of Root Development

Parizot¹,

Beeckman²

2012

Root Genomics and Soil Interactions

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Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa

Cited by 236 publications

References 65 publications

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

The Ectomycorrhizal FungusLaccaria bicolorStimulates Lateral Root Formation in Poplar and Arabidopsis through Auxin Transport and Signaling

Genomics of Root Development

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