Long noncoding <scp>RNA</scp> transcriptome of plants

Li, Jun; Wang, Huan; Chua, Nam‐Hai

doi:10.1111/pbi.12336

Cited by 271 publications

(217 citation statements)

References 172 publications

(223 reference statements)

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“…This may not be due only to the fact that most plant lncRNAs are expressed at low levels and their expression may be confined to specific cell types or specific conditions, but also to the fact that plant lncRNAs are not evolutionarily conserved in general (Liu et al, 2012(Liu et al, , 2015a(Liu et al, , 2015b.…”

Section: Drir Is a Novel Lncrna Regulating Plant Tolerance To Droughtmentioning

confidence: 99%

“…The dual transcription of APOLO regulates the formation of a chromatin loop encompassing the promoter of PID and, thus, affects auxin transport . Liu et al (2015b) suggested that lncRNAs may participate in ABA-induced complex assembly and the relocalization of RNA-BINDING PROTEIN. However, lncRNAs involved in the ABAmediated stress response are still unknown.…”

Section: Drir Regulates Aba-mediated Responses To Drought and Salt Stmentioning

confidence: 99%

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A Nucleus-Localized Long Non-Coding RNA Enhances Drought and Salt Stress Tolerance

Qin¹,

et al. 2017

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Long noncoding RNAs (lncRNAs) affect gene expression through a wide range of mechanisms and are considered as important regulators in many essential biological processes. A large number of lncRNA transcripts have been predicted or identified in plants in recent years. However, the biological functions for most of them are still unknown. In this study, we identified an Arabidopsis (Arabidopsis thaliana) lncRNA, DROUGHT INDUCED lncRNA (DRIR), as a novel positive regulator of the plant response to drought and salt stress. DRIR was expressed at a low level under nonstress conditions but can be significantly activated by drought and salt stress as well as by abscisic acid (ABA) treatment. We identified a T-DNA insertion mutant, drir D , which had higher expression of the DRIR gene than the wild-type plants. The drir D mutant exhibits increased tolerance to drought and salt stress. Overexpressing DRIR in Arabidopsis also increased tolerance to drought and salt stress of the transgenic plants. The drir D mutant and the overexpressing seedlings are more sensitive to ABA than the wild type in stomata closure and seedling growth. Genome-wide transcriptome analysis demonstrated that the expression of a large number of genes was altered in drir D and the overexpressing plants. These include genes involved in ABA signaling, water transport, and other stress-relief processes. Our study reveals a mechanism whereby DRIR regulates the plant response to abiotic stress by modulating the expression of a series of genes involved in the stress response.

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Section: Drir Is a Novel Lncrna Regulating Plant Tolerance To Droughtmentioning

confidence: 99%

Section: Drir Regulates Aba-mediated Responses To Drought and Salt Stmentioning

confidence: 99%

A Nucleus-Localized Long Non-Coding RNA Enhances Drought and Salt Stress Tolerance

Qin¹,

et al. 2017

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“…It could also be due to the great depth of reads used for assembly (a total 1,015,845,414 reads). Even though the PacBio data included the same internodal RNAs as the de novo dataset, it has been through different library preparation, where the cDNA were produced from only polyA RNAs, which should be mostly mRNA and long non-coding RNAs with a polyA tail (Liu et al, 2015). The comparison of transcripts between the two assemblies suggests that the common transcripts between the two assemblies would mostly be polyA RNAs, while the transcripts unique to PacBio (38%) could be rare transcripts that come from the normalization process and wider tissue coverage, and those unique to de novo assembly (33%) could be attributed to other types of RNAs in the samples.…”

Section: Discussionmentioning

confidence: 99%

“…It has been proposed that de novo transcript contigs could be a good resource for studying the diversity of non-coding RNAs (Lv et al, 2016). Long non-coding RNAs are RNAs, longer than 300bp, that do not encode proteins (do not have ORF ≥100 aa) potentially play important roles in gene regulation of eukaryotic cells (Liu et al, 2015). Their numbers, characteristics and genetic patterns in the genome still remain unclear.…”

Section: Discussionmentioning

confidence: 99%

Analysis of genes controlling biomass traits in the genome of sugarcane (Saccharum spp. hybrids)

Hoang¹

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Sugarcane (Saccharum spp. hybrids) is a leading industrial crop in tropical and subtropical regions worldwide. More recently, sugarcane has been selected as a key feedstock for biofuels due to its rapid growth, high fiber content and favorable energy input/output ratio.Breeding sugarcane varieties with biomass for efficient conversion to biofuels can be optimized by understanding the genetic control of biomass composition. However, the genetic analysis of these traits is hindered by the genomic complexity, and the limited availability of a reference genome. The aims of this project were: the development of a high-throughput profiling method for rapid screening of the key biomass traits in a sugarcane population; the construction of a new full-length transcriptome reference database; and the identification of transcripts associated with sugar and fiber accumulation in sugarcane.For the screening of genotypes, newly developed predictive models employing nearinfrared (NIR) spectral analysis, coupled with the high performance liquid chromatography (HPLC), were shown to allow high-throughput profiling of major components in the fiber and sugar fractions in sugarcane biomass. Contrasting genotypes of low fiber and high fiber (minimum of ~29% and maximum of 61% total dry biomass) were identified amongst 331 samples from 186 sugarcane genotypes. The population studied exhibited a wide range of fiber/sugar ratio, from 0.4 (as low as that of the typical commercial sugarcane variety) to 2.2 (similar to that of energy-cane). In addition, the lignin content (the central factor in the biomass recalcitrance) ranged from 6 to 14% of the total dry biomass. To aid genotyping, a new sugarcane transcriptome (termed as SUGIT database) was constructed using PacBio full-length isoform sequencing (Iso-Seq), and a cDNA library derived from 22 diverse sugarcane genotypes, of the key tissues (leaf, internode and root), at different developmental stages (from immature to mature). Comparative analysis showed that this new SUGIT database included more full-length transcripts, longer predicted transcripts, and higher average length of the largest 1,000 proteins, compared to a de novo assembly from Illumina RNA-Seq short-read data from the same sample set. The annotation suggested that the majority (~94%) of the SUGIT database was from coding RNAs, while a very small proportion (~2%) could be long non-coding RNAs. About 70-82% of the RNASeq reads from different tissues mapped back to the SUGIT database, suggesting that it represented well the targeted tissues, while about 69% of this database was aligned with the sorghum genome, confirming the high conservation of orthologs in the genic regions of ii the two genomes. Applying the SUGIT database to differential expression analysis (FDR, false discovery rate corrected p-value <0.05), 1,649 transcript isoforms were identified as being differentially expressed between the young and mature tissues in the sugarcane plant, while 555 transcript isoforms were differentially expressed between th...

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“…Unfortunately at the present the ncRNA is still in their early stages and just some mammalian entries were uploaded to IncRNA database (Laurent et al, 2015). Up to now, the only plant that has received some attention is Arabidopsis thaliana where 13,000 RNAs were found transcribed from intergenic regions (Liu et al, , 2015a Gene ontology provides a systematic language in three key biological domains shared by all organisms: molecular function, biological process and cellular component to unify the representation of gene features across all species (Gousset et al, 2005). GO terms are structured as a graph and can be distributed in levels.…”

Section: Annotation Of S Incanum and S Aethiopicum Transcriptomesmentioning

confidence: 99%

Genetics and Genomics of Cultivated Eggplants and Wild Relatives

Gramazio¹

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"Nothing in life is to be feared, it is only to be understood. Now is the time to understand more, so that we may fear less." Maria Salomea Skłodowska-Curie AgradecimientosAunque parezcan mucho menos, ya siete son los años que llevo en el COMAV. Los años pasan volando cuando el ambiente de trabajo es estimulante, constructivo, apasionante, gratificante, motivador, intrigante, creativo, integrador, cooperativo, productivo, positivo, divertido…, familiar.Todo empezó aquella tarde del 10 de noviembre del 2010, cuando Lola Raigón, a quien va mi eterna gratitud, me presentó la persona que iba a cambiar mi vida, Jaime Prohens.Jaime, la admiración, el respeto y la gratitud que siento por ti no se pueden expresar en unas pocas frases. Eres la persona que más me ha enseñado, motivado y animado en estos años. Has conseguido sacar de mí unas cualidades que ni siquiera había imaginado tener. Tu inteligencia, sabiduría, humildad, paciencia, hacen de ti un verdadero líder. Gracias por estar pendiente en cada momento, espero colaborar contigo durante muchos años más. Eres un ejemplo a seguir y fuente de inspiración y guía para mi y muchas personas.Mi formación doctoral no sería completa si no hubiera sido por tí, Santi. Intelligente, simpatíco, caótico, siempre de buen humor y "runner".Gracias por todo el conocimiento, las buenas ideas, las clases de Génomica, las risas y los videos "frikis" que has compartido conmigo. Gracias por alegrar nuestros días.Mariola, aunque burocráticamente no has podido ser mi co-directora, te agradezco el apoyo, motivación y alegría de estos años. Aunque ahora pasamos todo el día en los despachos, echo de menos los primeros años de laboratorio, cuando pasábamos horas y horas hablando de lo que fuera. Junto a Jaime y Santi, eres un pilar de "Los Berenjen@s".Gracias a mi "hermano mayor" Javi, por los muchos momentos de amistad pasados juntos, por tu inteligencia, por compartir tus experiencias, por tu buen gusto musical, tu escepticismo, por ser un gran amigo."Los Berenjen@s" se han ido multiplicando y muchas son las entradas que hemos recolectado en estos años alrededor del mundo. Me hubiera gustado escribir algo sobre cada uno de vosotros, pero necesitaría otro capítulo de tesis, así que os agradeceré de forma conjuntas.Gracias Abou, Adriana, Agustín, Alba E., Alba L., Alessio, Andrea, Arantxa, Arunika, Bianca, Brice, Camil, Carolina, Celia, Celine, Cristina, Dani, David, Dionís, Dora, Edgar, Elena C., Elena R., Elisa, Francesco, Giulio, Gloria, Ioana, Irene, Isa, Juan, Juan Pablo, Judith, Lahiru, Lara, Laura, Loles, Maria, Marieta, Michael, Muditha, Nacho, Nadia, Nirasha, Noelia, Orsi, Pelin, Prashant, Ramses, Ranil, Rory, Silia, Sorin, Trong, por haber aportado vuestro granito de arena para la realización de esta tesis y de colaboraciones varias. Todos, los que todavía estáis por aquí y los que se han ido, habéis dejado una huella en el laboratorio y en mí (Pido disculpa si se me ha olvidado alguien, sois muchos los que se han pasado por el labo).Gracias también a todos mis compañeros del COMAV,...

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Long noncoding RNA transcriptome of plants

Cited by 271 publications

References 172 publications

A Nucleus-Localized Long Non-Coding RNA Enhances Drought and Salt Stress Tolerance

A Nucleus-Localized Long Non-Coding RNA Enhances Drought and Salt Stress Tolerance

Analysis of genes controlling biomass traits in the genome of sugarcane (Saccharum spp. hybrids)

Genetics and Genomics of Cultivated Eggplants and Wild Relatives

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