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      An Integrated Transcriptome and Proteome Analysis Reveals Putative Regulators of Adventitious Root Formation in Taxodium ‘Zhongshanshan’

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          Abstract

          Adventitious root (AR) formation from cuttings is the primary manner for the commercial vegetative propagation of trees. Cuttings is also the main method for the vegetative reproduction of Taxodium ‘Zhongshanshan’, while knowledge of the molecular mechanisms regulating the processes is limited. Here, we used mRNA sequencing and an isobaric tag for relative and absolute quantitation-based quantitative proteomic (iTRAQ) analysis to measure changes in gene and protein expression levels during AR formation in Taxodium ‘Zhongshanshan’. Three comparison groups were established to represent the three developmental stages in the AR formation process. At the transcript level, 4743 genes showed an expression difference in the comparison groups as detected by RNA sequencing. At the protein level, 4005 proteins differed in their relative abundance levels, as indicated by the quantitative proteomic analysis. A comparison of the transcriptome and proteome data revealed regulatory aspects of metabolism during AR formation and development. In summary, hormonal signal transduction is different at different developmental stages during AR formation. Other factors related to carbohydrate and energy metabolism and protein degradation and some transcription factor activity levels, were also correlated with AR formation. Studying the identified genes and proteins will provide further insights into the molecular mechanisms controlling AR formation.

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          TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.

          TGICL is a pipeline for analysis of large Expressed Sequence Tags (EST) and mRNA databases in which the sequences are first clustered based on pairwise sequence similarity, and then assembled by individual clusters (optionally with quality values) to produce longer, more complete consensus sequences. The system can run on multi-CPU architectures including SMP and PVM.
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            Methods of integrating data to uncover genotype-phenotype interactions.

            Recent technological advances have expanded the breadth of available omic data, from whole-genome sequencing data, to extensive transcriptomic, methylomic and metabolomic data. A key goal of analyses of these data is the identification of effective models that predict phenotypic traits and outcomes, elucidating important biomarkers and generating important insights into the genetic underpinnings of the heritability of complex traits. There is still a need for powerful and advanced analysis strategies to fully harness the utility of these comprehensive high-throughput data, identifying true associations and reducing the number of false associations. In this Review, we explore the emerging approaches for data integration - including meta-dimensional and multi-staged analyses - which aim to deepen our understanding of the role of genetics and genomics in complex outcomes. With the use and further development of these approaches, an improved understanding of the relationship between genomic variation and human phenotypes may be revealed.
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              MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development.

              Although several plant microRNAs (miRNAs) have been shown to play a role in plant development, no phenotype has yet been associated with a reduction or loss of expression of any plant miRNA. Arabidopsis thaliana miR164 was predicted to target five NAM/ATAF/CUC (NAC) domain-encoding mRNAs, including NAC1, which transduces auxin signals for lateral root emergence. Here, we show that miR164 guides the cleavage of endogenous and transgenic NAC1 mRNA, producing 3'-specific fragments. Cleavage was blocked by NAC1 mutations that disrupt base pairing with miR164. Compared with wild-type plants, Arabidopsis mir164a and mir164b mutant plants expressed less miR164 and more NAC1 mRNA and produced more lateral roots. These mutant phenotypes can be complemented by expression of the appropriate MIR164a and MIR164b genomic sequences. By contrast, inducible expression of miR164 in wild-type plants led to decreased NAC1 mRNA levels and reduced lateral root emergence. Auxin induction of miR164 was mirrored by an increase in the NAC1 mRNA 3' fragment, which was not observed in the auxin-insensitive mutants auxin resistant1 (axr1-12), axr2-1, and transport inhibitor response1. Moreover, the cleavage-resistant form of NAC1 mRNA was unaffected by auxin treatment. Our results indicate that auxin induction of miR164 provides a homeostatic mechanism to clear NAC1 mRNA to downregulate auxin signals.
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                Author and article information

                Journal
                Int J Mol Sci
                Int J Mol Sci
                ijms
                International Journal of Molecular Sciences
                MDPI
                1422-0067
                11 March 2019
                March 2019
                : 20
                : 5
                : 1225
                Affiliations
                [1 ]Jiangsu Engineering Research Center for Taxodium Rich. Germplasm Innovation and Propagation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, Jiangsu, China; zhiquanjiejie@ 123456163.com (Z.W.); jfhua2009@ 123456gmail.com (J.H.); yinyl066@ 123456sina.com (Y.Y.); chunsungu@ 123456126.com (C.G.); yucg168@ 123456sina.com (C.Y.); 455244921@ 123456139.com (Q.S.); guojb0113@ 123456163.com (J.G.)
                [2 ]Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, Jiangsu, China
                [3 ]Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
                Author notes
                [* ]Correspondence: 13851991791@ 123456163.com (L.X.); fyyu@ 123456njfu.com.cn (F.Y.)
                Author information
                https://orcid.org/0000-0002-9182-8692
                Article
                ijms-20-01225
                10.3390/ijms20051225
                6429173
                30862088
                eb71f923-35ec-4a33-be55-0dd2385cf502
                © 2019 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 30 January 2019
                : 07 March 2019
                Categories
                Article

                Molecular biology
                adventitious root formation,morphology,proteome,taxodium,transcriptome
                Molecular biology
                adventitious root formation, morphology, proteome, taxodium, transcriptome

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