Improved method for isolation of high-quality total RNA from Agave tequilana Weber roots

Maceda-López, Luis F.; Villalpando-Aguilar, José Luis; García-Hernández, Eleazar; Dios, Emmanuel Ávila de; Andrade‐Canto, Silvia B.; Morán-Velázquez, Dalia C.; Rodríguez‐López, Lorena; Hernández-Díaz, Demetrio; Chable-Vega, Manuel A.; Trejo, Laura; Góngora-Castillo, Elsa; López-Rosas, Itzel; Simpson, June; Alatorre‐Cobos, Fulgencio

doi:10.1007/s13205-020-02620-8

Cited by 4 publications

(2 citation statements)

References 34 publications

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“…Likewise, Pgm1 , UDP-Glucose Pyrophosphorylase1 ( UGP1 ), and four Cellulose Synthase ( CESA ) isoforms, AtqCESA1 , AtqCESA3 , AtqCESA4 , and AtqCESA8 , showed a medium expression, fairly uniform, in all the tissues tested ( Figure 1 ; Table S3 ). Contrary to most of the CESAs retrieved, AtqCESA5 and AtqCESA7 were found to be expressed only in roots and leaves, which are samples enriched with lignocellulosic cell walls [ 10 , 35 ], suggesting that these two CESA orthologous may have a functional role during secondary cell wall biosynthesis in Agave plants.…”

Section: Resultsmentioning

confidence: 99%

Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber

Maceda-López

Góngora-Castillo

Ibarra-Laclette

et al. 2022

Plants

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Resilience of growing in arid and semiarid regions and a high capacity of accumulating sugar-rich biomass with low lignin percentages have placed Agave species as an emerging bioenergy crop. Although transcriptome sequencing of fiber-producing agave species has been explored, molecular bases that control wall cell biogenesis and metabolism in agave species are still poorly understood. Here, through RNAseq data mining, we reconstructed the cellulose biosynthesis pathway and the phenylpropanoid route producing lignin monomers in A. tequilana, and evaluated their expression patterns in silico and experimentally. Most of the orthologs retrieved showed differential expression levels when they were analyzed in different tissues with contrasting cellulose and lignin accumulation. Phylogenetic and structural motif analyses of putative CESA and CAD proteins allowed to identify those potentially involved with secondary cell wall formation. RT-qPCR assays revealed enhanced expression levels of AtqCAD5 and AtqCESA7 in parenchyma cells associated with extraxylary fibers, suggesting a mechanism of formation of sclerenchyma fibers in Agave similar to that reported for xylem cells in model eudicots. Overall, our results provide a framework for understanding molecular bases underlying cell wall biogenesis in Agave species studying mechanisms involving in leaf fiber development in monocots.

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Section: Resultsmentioning

confidence: 99%

Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber

Maceda-López

Góngora-Castillo

Ibarra-Laclette

et al. 2022

Plants

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“…Because, plants possess multifarious tissue types, each has specific challenges in RNA extraction compared to other organisms. Even though several protocols and commercial kits were available, high-quality RNA extraction protocols are keep updating and modifying to meet the specific challenges in plant tissues due to its diverse chemical profiles (Jaakola et al 2001;Daohong et al 2004;Wang et al 2009;Kalinowska et al 2012;de Lima et al 2016;Maceda-López et al 2021). The optimized CTAB based RNA extraction method resulted in good quality RNA with higher yields from all the cinnamon tissues collected from the field (Fig.…”

Section: Resultsmentioning

confidence: 99%

A CTAB protocol for obtaining high-quality total RNA from cinnamon (Cinnamomum zeylanicum Blume)

2021

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Cinnamomum zeylanicum Blume is an endemic Sri Lankan species commonly known as Ceylon cinnamon or true cinnamon. It is considered the king of spices in addition to its medicinal benefits. Despite recent scientific evidence on its medicinal properties and the industrial demand, cinnamon breeding and crop improvement are not been improved to the expectation. It is mainly due to the limited availability of the genomic information of cinnamon, linked with technical challenges caused by abundant secondary metabolites in all plant parts. Therefore, obtaining high-quality RNA is the fundamental step of transcriptomic analysis and the gene discovery process of cinnamon. We have optimized a CTAB based protocol for high-quality RNA extraction from different cinnamon tissues at various maturity stages collected from the field. Regular pH around 8 and the presence of Polyvinylpyrrolidone (PVP) in CTAB buffer increased the viscosity of the cinnamon lysate. Adjusting the pH of the lysis buffer to 6-6.5 reduced the viscosity of lysate while chloroform precipitates protein efficiently at the adjusted pH with no phenol. Therefore, this protocol excludes PVP and phenol extraction steps. Nanodrop spectrophotometer, gel electrophoresis, and bioanalyzer readings confirmed the quality of extracted RNA. RNA-seq libraries prepared were sequenced with Illumina Sequencing by synthesis technology and obtained good quality data to be used for transcriptomic analysis.

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Improving AOX1 promoter efficiency by overexpression of Mit1 transcription factor

et al. 2022

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Improved method for isolation of high-quality total RNA from Agave tequilana Weber roots

Cited by 4 publications

References 34 publications

Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber

Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber

A CTAB protocol for obtaining high-quality total RNA from cinnamon (Cinnamomum zeylanicum Blume)

Improving AOX1 promoter efficiency by overexpression of Mit1 transcription factor

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