Large-scale transcriptional profiling of lignified tissues in Tectona grandis

Galeano, Esteban; Vasconcelos, Tarcísio Sales; Vidal, Mabel; Mejía‐Guerra, Maria Katherine; Carrer, Helaine

doi:10.1186/s12870-015-0599-x

Cited by 30 publications

(26 citation statements)

References 90 publications

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“…The RAW RNASeq data from T. grandis were accessed in the Sequence Read Archive (SRA-NCBI) under the accession number SRP059970. These data were previously generated by our group [36] and comprise various plant tissues in three plant developmental stages. The teak RAW RNASeq data were processed with BBDuk2 [52] in order to remove low-quality regions from the reads, remainders of adapter sequences, and ribosomal RNA.…”

Section: In Silico Gene Expression Profilingmentioning

confidence: 99%

“…Teak's secondary xylem biosynthesis is a complex molecular process that involves several genes and environmental factors. Recent genomic and transcriptomic analyses of T. grandis have allowed to improve the understanding of the xylogenesis role in biomass increase and wood quality [35][36][37][38], even though T. grandis NAC transcription factors have not yet been identified. The identification and characterization of teak NAC TFs are fundamental to elucidate their regulation role in vascular tissue differentiation and wood formation, as well as future biotechnological studies aiming to improve biomass and wood quality.…”

Section: Introductionmentioning

confidence: 99%

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Analysis of NAC Domain Transcription Factor Genes of Tectona grandis L.f. Involved in Secondary Cell Wall Deposition

Hurtado

Pinto

Oliveira

et al. 2019

Genes

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NAC proteins are one of the largest families of plant-specific transcription factors (TFs). They regulate diverse complex biological processes, including secondary xylem differentiation and wood formation. Recent genomic and transcriptomic studies of Tectona grandis L.f. (teak), one of the most valuable hardwood trees in the world, have allowed identification and analysis of developmental genes. In the present work, T. grandis NAC genes were identified and analyzed regarding to their evolution and expression profile during wood formation. We analyzed the recently published T. grandis genome, and identified 130 NAC proteins that are coded by 107 gene loci. These proteins were classified into 23 clades of the NAC family, together with Populus, Eucalyptus, and Arabidopsis. Data on transcript expression revealed specific temporal and spatial expression patterns for the majority of teak NAC genes. RT-PCR indicated expression of VND genes (Tg11g04450-VND2 and Tg15g08390-VND4) related to secondary cell wall formation in xylem vessels of 16-year-old juvenile trees. Our findings open a way to further understanding of NAC transcription factor genes in T. grandis wood biosynthesis, while they are potentially useful for future studies aiming to improve biomass and wood quality using biotechnological approaches.

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Section: In Silico Gene Expression Profilingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Analysis of NAC Domain Transcription Factor Genes of Tectona grandis L.f. Involved in Secondary Cell Wall Deposition

Hurtado

Pinto

Oliveira

et al. 2019

Genes

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“…Other tree-specific processes approached by transcriptomic studies include wood quality traits, secondary cell wall formation and lignin synthesis, performed mostly in Populus (Chen et al, 2015), Eucalyptus (Thavamanikumar et al, 2014), Acacia (Wong et al, 2011), and Tectona (Galeano et al, 2015) genera.…”

Section: Deep Sequencing Of Transcriptomes: Rna-seqmentioning

confidence: 99%

Application of Genomic Technologies to the Breeding of Trees

et al. 2016

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The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the former gap of genetic tools between trees and annual species.

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“…Natural populations of teak have been found in Laos, Myanmar, Thailand, Java Islands and India, with a worldwide planted area and natural forest of 33,381 ha (2.5 million m 3 of wood) (Kollert and Cherubini 2012). Unfortunately, despite its importance, there is a lack of genetic studies regarding gene expression and characterization (Alcântara and Veasey 2013;Galeano et al 2014;Galeano et al 2015). Consequently, to obtain CAD members related to lignin biosynthesis in teak, this study amplified, cloned and characterized three partial CAD genes (TgCAD2, TgCAD3 and TgCAD4) and a complete bona fide CAD gene (TgCAD1).…”

Section: Introductionmentioning

confidence: 99%

Characterization of Cinnamyl Alcohol Dehydrogenase gene family in lignifying tissues of Tectona grandis L.f.

2018

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The cinnamyl alcohol dehydrogenase (CAD) enzyme catalyzes the last step of monolignols synthesis in the lignin pathway. Tectona grandis (teak) is a tropical tree with high valuable timber. As there is few genetic information about lignin formation in teak, the purpose of this study is to characterize members of CAD family in this species. As methodology, PCR amplification using cDNA samples, vector cloning, sequencing, bioinformatics analyses and gene expression studies using real time RTqPCR were performed. As results, four members (TgCAD1-TgCAD4) were obtained. Comparative analyses showed that all of them have conserved residues for catalytic zinc action, structural zinc ligation, NADPH binding and substrate specificity, consistent with the mechanism of alcohol dehydrogenases. Phylogenetic analysis showed that TgCADs are present in three main classes and seven groups. Expression analyses revealed that TgCAD1 was highly expressed in leaves and could be related with pathogen defense. TgCAD2 was more expressed in branches and roots. Differently, TgCAD3 and TgCAD4 were highly expressed in juvenile and mature sapwood, suggesting a crucial role in wood development and lignin biosynthesis, with tissue-specialized expression profiles. Furthermore, TgCAD4 could be related with teak maturation for being more expressed in sapwood of mature teak trees. As conclusion, this work is the first to characterize genes of CAD family in Tectona grandis. These genes could be interesting to develop transgenic plants for basic research and field applications.

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Large-scale transcriptional profiling of lignified tissues in Tectona grandis

Cited by 30 publications

References 90 publications

Analysis of NAC Domain Transcription Factor Genes of Tectona grandis L.f. Involved in Secondary Cell Wall Deposition

Analysis of NAC Domain Transcription Factor Genes of Tectona grandis L.f. Involved in Secondary Cell Wall Deposition

Application of Genomic Technologies to the Breeding of Trees

Characterization of Cinnamyl Alcohol Dehydrogenase gene family in lignifying tissues of Tectona grandis L.f.

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