ArticlePloS one2015
Genome-wide identification, characterization and evolutionary analysis of long intergenic noncoding RNAs in cucumber.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Genome-wide identification of long non-coding RNAs revealing their regulatory roles under seed development in ricebean (Vigna umbellata).BMC plant biology · 2026Article
- Diversity of lncRNAs in the pan-transcriptome of maize inbred lines.BMC genomics · 2026Article
- RNA sequencing and histology analysis provide insights into the formation of hollow fruits in cucumber.BMC genomics · 2025Article
- Identification and characterization of long non-coding RNA (lncRNA) in wild and semi-wild cucumbers.BMC plant biology · 2025Article
- The miR3367-lncRNA67-GhCYP724B module regulates male sterility by modulating brassinosteroid biosynthesis and interacting with Aorf27 in Gossypium hirsutum.Journal of integrative plant biology · 2025Article
- A long noncoding RNA functions in pumpkin fruit development through S-adenosyl-L-methionine synthetase.Plant physiology · 2024Article
- Emerging roles and mechanisms of lncRNAs in fruit and vegetables.Horticulture research · 2024Review
- Long noncoding RNA from Betula platyphylla, BplncSIR1, confers salt tolerance by regulating BpNAC2 to mediate reactive oxygen species scavenging and stomatal movement.Plant biotechnology journal · 2024Article
- Identification and functional prediction of lncRNAs associated with intramuscular lipid deposition in Guangling donkeys.Frontiers in veterinary science · 2024Article
- Genome-wide identification and characterization ofFrontiers in plant science · 2023Article
- Article
- Comprehensive transcriptomic analysis of two RIL parents with contrasting salt responsiveness identifies polyadenylated and non-polyadenylated flower lncRNAs in chickpea.Plant biotechnology journal · 2022Article
- Genome wide identification of lncRNAs and circRNAs having regulatory role in fruit shelf life in health crop cucumber (Frontiers in plant science · 2022Article
- Integrative mRNA and Long Noncoding RNA Analysis Reveals the Regulatory Network of Floral Bud Induction in Longan (Frontiers in plant science · 2022Article
- Whole-Transcriptome Analysis Reveals Long Noncoding RNAs Involved in Female Floral Development of Hickory (Frontiers in genetics · 2022Article
- Article
- Identification and Functional Analysis of lncRNAs Responsive to Hypoxia inCurrent issues in molecular biology · 2021Article
- Genome-wide identification and functional prediction of salt- stress related long non-coding RNAs (lncRNAs) in chickpea (Physiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation.BMC plant biology · 2020Review
- Long non-coding RNAs in the alkaline stress response in sugar beet (Beta vulgaris L.).BMC plant biology · 2020Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Long intergenic noncoding RNAs (lincRNAs) are intergenic transcripts with a length of at least 200 nt that lack coding potential. Emerging evidence suggests that lincRNAs from animals participate in many fundamental biological processes. However, the systemic identification of lincRNAs has been undertaken in only a few plants. We chose to use cucumber (Cucumis sativus) as a model to analyze lincRNAs due to its importance as a model plant for studying sex differentiation and fruit development and the rich genomic and transcriptome data available. The application of a bioinformatics pipeline to multiple types of gene expression data resulted in the identification and characterization of 3,274 lincRNAs. Next, 10 lincRNAs targeted by 17 miRNAs were also explored. Based on co-expression analysis between lincRNAs and mRNAs, 94 lincRNAs were annotated, which may be involved in response to stimuli, multi-organism processes, reproduction, reproductive processes, and growth. Finally, examination of the evolution of lincRNAs showed that most lincRNAs are under purifying selection, while 16 lincRNAs are under natural selection. Our results provide a rich resource for further validation of cucumber lincRNAs and their function. The identification of lincRNAs targeted by miRNAs offers new clues for investigations into the role of lincRNAs in regulating gene expression. Finally, evaluation of the lincRNAs suggested that some lincRNAs are under positive and balancing selection.
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