ArticlePloS one2012
Sorting the wheat from the chaff: identifying miRNAs in genomic survey sequences of Triticum aestivum chromosome 1AL.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 64 citations in OpenAlex.
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- Identification of Known and NovelLife (Basel, Switzerland) · 2022Article
- Computational screening of miRNAs and their targets in saffron (Crocus sativus L.) by transcriptome mining.Planta · 2021Article
- Pan-Genome miRNomics inPlants (Basel, Switzerland) · 2021Article
- Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat.GigaScience · 2019Article
- Hotspots in the genomic architecture of field drought responses in wheat as breeding targets.Functional & integrative genomics · 2019Article
- Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides.Plant biotechnology journal · 2018Article
- High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans).BMC plant biology · 2018Article
- Identification and functional characterization of intermediate-size non-coding RNAs in maize.BMC genomics · 2018Article
- TaMIR1139: a wheat miRNA responsive to Pi-starvation, acts a critical mediator in modulating plant tolerance to Pi deprivation.Plant cell reports · 2018Article
- A large-scale multiomics analysis of wheat stem solidness and the wheat stem sawfly feeding response, and syntenic associations in barley, Brachypodium, and rice.Functional & integrative genomics · 2018Article
- RNA Sequencing and Co-expressed Long Non-coding RNA in Modern and Wild Wheats.Scientific reports · 2017Article
- Identification and characterization of durum wheat microRNAs in leaf and root tissues.Functional & integrative genomics · 2017Article
- MicroRNAs in model and complex organisms.Functional & integrative genomics · 2017Article
- Wheat miRNA ancestors: evident by transcriptome analysis of A, B, and D genome donors.Functional & integrative genomics · 2017Article
- Abiotic stress miRNomes in the Triticeae.Functional & integrative genomics · 2017Review
- Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi.BMC genomics · 2017Article
- Response of microRNAs to cold treatment in the young spikes of common wheat.BMC genomics · 2017Article
- Assembly and Annotation of Transcriptome Provided Evidence of miRNA Mobility between Wheat and Wheat Stem Sawfly.Frontiers in plant science · 2017Article
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Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Individual chromosome-based studies of bread wheat are beginning to provide valuable structural and functional information about one of the world's most important crops. As new genome sequences become available, identifying miRNA coding sequences is arguably as important a task as annotating protein coding sequences, but one that is not as well developed. We compared conservation-based identification of conserved miRNAs in 1.5× coverage survey sequences of wheat chromosome 1AL with a predictive method based on pre-miRNA hairpin structure alone. In total, 42 sequences expected to encode conserved miRNAs were identified on chromosome 1AL, including members of several miRNA families that have not previously been reported to be expressed in T. aestivum. In addition, we demonstrate that a number of sequences previously annotated as novel wheat miRNAs are closely related to transposable elements, particularly Miniature Inverted Terminal repeat Elements (MITEs). Some of these TE-miRNAs may well have a functional role, but separating true miRNA coding sequences from TEs in genomic sequences is far from straightforward. We propose a strategy for annotation to minimize the risk of mis-identifying TE sequences as miRNAs.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.