CANTATAdb 2.0: Expanding the Collection of Plant Long Noncoding RNAs

Szcześniak, Michał Wojciech; Bryzghalov, Oleksii; Ciomborowska-Basheer, Joanna; Makałowska, Izabela

doi:10.1007/978-1-4939-9045-0_26

Cited by 79 publications

(74 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Based on this lncRNA were then classified into TE-lncRNA, intergenic lncRNA (cuffcompare class code u), intronic lncRNA (cuffcompare class code i), sense lncRNA (cuffcompare class code o), antisense lncRNA (cuffcompare class code x) and other lncRNA (remaining cuffcompare class codes). Conservation of BAnTr lncRNA transcripts was assessed by alignment using BLAST ( Altschul et al, 1990 ) to: RiceLncPedia transcripts ( Zhang Z. et al, 2020 ); Arabidopsis non-code v5 transcripts ( Zhao et al, 2016 ); maize, wheat, and Brachypodium GreeNC transcripts ( Paytuví Gallart et al, 2016 ); and barley CANTATAdb v2.0 transcripts ( Szcześniak et al, 2019 ).…”

Section: Methodsmentioning

confidence: 99%

Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I

et al. 2021

View full text Add to dashboard Cite

In flowering plants, successful germinal cell development and meiotic recombination depend upon a combination of environmental and genetic factors. To gain insights into this specialized reproductive development program we used short- and long-read RNA-sequencing (RNA-seq) to study the temporal dynamics of transcript abundance in immuno-cytologically staged barley (Hordeum vulgare) anthers and meiocytes. We show that the most significant transcriptional changes in anthers occur at the transition from pre-meiosis to leptotene–zygotene, which is followed by increasingly stable transcript abundance throughout prophase I into metaphase I–tetrad. Our analysis reveals that the pre-meiotic anthers are enriched in long non-coding RNAs (lncRNAs) and that entry to meiosis is characterized by their robust and significant down regulation. Intriguingly, only 24% of a collection of putative meiotic gene orthologs showed differential transcript abundance in at least one stage or tissue comparison. Argonautes, E3 ubiquitin ligases, and lys48 specific de-ubiquitinating enzymes were enriched in prophase I meiocyte samples. These developmental, time-resolved transcriptomes demonstrate remarkable stability in transcript abundance in meiocytes throughout prophase I after the initial and substantial reprogramming at meiosis entry and the complexity of the regulatory networks involved in early meiotic processes.

show abstract

Section: Methodsmentioning

confidence: 99%

Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I

et al. 2021

View full text Add to dashboard Cite

show abstract

“…To address these shortcomings, several web-based resources and databases have been developed, viz., NONCODE provides the comprehensive biological functions of lncRNAs [ 143 – 145 ], PLNlncRbase contains information on 1187 plant lncRNAs from more than 40 species [ 146 ], and Plant Long non-coding RNA Database (PLncDB) offers information on 6480 lncRNAs in Arabidopsis [ 147 ]. Likewise, the Plant Natural Antisense Transcripts Database (PlantNATsDB) provides information on plant NATs controlling various physiological and development processes [ 148 ], Plant ncRNA Database (PNRD) maintains records of 25,739 non-coding RNAs including lncRNAs [ 149 ], CANTATAdb maintains 45,117 lncRNAs from 10 plant species [ 16 ], CANTATAdb 2.0. annotates plant lncRNAs [ 155 ] and PLncPRO provides information on abiotic stress-responsive lncRNAs in rice and chickpea [ 72 ]. A detailed list of plant lncRNA databases is in Table 3 .…”

Section: Introductionmentioning

confidence: 99%

“… PlaNC-TE Provide insights about the relationship between ncRNA and TEs in plants Information on overlapping of ncRNA and transposon elements from 40 plant genomes [ 151 ] http://planc-te.cp.utfpr.edu.br EVLncRNAs It contains lncRNA information on various species including plant 1543 lncRNAs from 77 species and also 428 plant lncRNAs from 44 plant species [ 152 , 153 ] http://biophy.dzu.edu.cn/EVLncRNAs . CRISPRlnc Database for validated CRISPR/Cas9 sgRNAs for lncRNAs from variousspecies including plants 305 lncRNAs and 2102 validated sgRNAs on eight species including plant [ 154 ] http://www.crisprlnc.org or http://crisprlnc.xtbg.ac.cn CANTATAdb 2.0 It provides information on annotation of plant lncRNAs Covers information on lnc RNA on 39 plant species [ 155 ] http://cantata.amu.edu.pl , http://yeti.amu.edu.pl/CANTATA/ PLIT Used for investigating of plant lncRNAs from RNA seq data. Provides information on lncRNA from 8 plant species [ 156 ] PLncDB Detail information on plant lncRNAs Provides plant lincRNAs and lncNATs information [ 157 ] – The table is updated version of [ 17 , 61 , 143 ] …”

Section: Introductionmentioning

confidence: 99%

Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation

et al. 2020

View full text Add to dashboard Cite

Background The immobile nature of plants means that they can be frequently confronted by various biotic and abiotic stresses during their lifecycle. Among the various abiotic stresses, water stress, temperature extremities, salinity, and heavy metal toxicity are the major abiotic stresses challenging overall plant growth. Plants have evolved complex molecular mechanisms to adapt under the given abiotic stresses. Long non-coding RNAs (lncRNAs)—a diverse class of RNAs that contain > 200 nucleotides(nt)—play an essential role in plant adaptation to various abiotic stresses. Results LncRNAs play a significant role as ‘biological regulators’ for various developmental processes and biotic and abiotic stress responses in animals and plants at the transcription, post-transcription, and epigenetic level, targeting various stress-responsive mRNAs, regulatory gene(s) encoding transcription factors, and numerous microRNAs (miRNAs) that regulate the expression of different genes. However, the mechanistic role of lncRNAs at the molecular level, and possible target gene(s) contributing to plant abiotic stress response and adaptation, remain largely unknown. Here, we review various types of lncRNAs found in different plant species, with a focus on understanding the complex molecular mechanisms that contribute to abiotic stress tolerance in plants. We start by discussing the biogenesis, type and function, phylogenetic relationships, and sequence conservation of lncRNAs. Next, we review the role of lncRNAs controlling various abiotic stresses, including drought, heat, cold, heavy metal toxicity, and nutrient deficiency, with relevant examples from various plant species. Lastly, we briefly discuss the various lncRNA databases and the role of bioinformatics for predicting the structural and functional annotation of novel lncRNAs. Conclusions Understanding the intricate molecular mechanisms of stress-responsive lncRNAs is in its infancy. The availability of a comprehensive atlas of lncRNAs across whole genomes in crop plants, coupled with a comprehensive understanding of the complex molecular mechanisms that regulate various abiotic stress responses, will enable us to use lncRNAs as potential biomarkers for tailoring abiotic stress-tolerant plants in the future.

show abstract

“…We have identified lncRNAs by performing BLASTn search within CantataDB (Szcześniak et al, 2019) in which G. max lncRNAs were queried by transcripts obtained in our experiment. As a result, 31,718 lncRNA sequences homologous to those in soybean were found and deposited in LuluDB.…”

Section: Ncrnas In Luludbmentioning

confidence: 99%

LuluDB—The Database Created Based on Small RNA, Transcriptome, and Degradome Sequencing Shows the Wide Landscape of Non-coding and Coding RNA in Yellow Lupine (Lupinus luteus L.) Flowers and Pods

et al. 2020

View full text Add to dashboard Cite

Yellow lupine (Lupinus luteus L.) belongs to a legume family that benefits from symbiosis with nitrogen-fixing bacteria. Its seeds are rich in protein, which makes it a valuable food source for animals and humans. Yellow lupine is also the model plant for basic research on nodulation or abscission of organs. Nevertheless, the knowledge about the molecular regulatory mechanisms of its generative development is still incomplete. The RNA-Seq technique is becoming more prominent in high-throughput identification and expression profiling of both coding and non-coding RNA sequences. However, the huge amount of data generated with this method may discourage other scientific groups from making full use of them. To overcome this inconvenience, we have created a database containing analysis-ready information about non-coding and coding L. luteus RNA sequences (LuluDB). LuluDB was created on the basis of RNA-Seq analysis of small RNA, transcriptome, and degradome libraries obtained from yellow lupine cv. Taper flowers, pod walls, and seeds in various stages of development, flower pedicels, and pods undergoing abscission or maintained on the plant. It contains sequences of miRNAs and phased siRNAs identified in L. luteus, information about their expression in individual samples, and their target sequences. LuluDB also contains identified lncRNAs and protein-coding RNA sequences with their organ expression and annotations to widely used databases like GO, KEGG, NCBI, Rfam, Pfam, etc. The database also provides sequence homology search by BLAST using, e.g., an unknown sequence as a query. To present the full capabilities offered by our database, we performed a case study concerning transcripts annotated as DCL 1-4 (DICER LIKE 1-4) homologs involved in small non-coding RNA biogenesis and identified miRNAs that most likely regulate DCL1 and DCL2 expression in yellow lupine. LuluDB is available at http://luluseqdb.umk.pl/ basic/web/index.php.

show abstract

CANTATAdb 2.0: Expanding the Collection of Plant Long Noncoding RNAs

Cited by 79 publications

References 26 publications

Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I

Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I

Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation

LuluDB—The Database Created Based on Small RNA, Transcriptome, and Degradome Sequencing Shows the Wide Landscape of Non-coding and Coding RNA in Yellow Lupine (Lupinus luteus L.) Flowers and Pods

Contact Info

Product

Resources

About