ArticlePlant biotechnology journal2016
An RNA-Seq-based reference transcriptome for Citrus.
Article in Plant biotechnology journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 28 citations in OpenAlex.
- Physiologic, Genetic and Epigenetic Determinants of Water Deficit Tolerance in Fruit Trees.Plants (Basel, Switzerland) · 2025Review
- Citrus genomes: past, present and future.Horticulture research · 2025Article
- OrangeExpDB: an integrative gene expression database for Citrus spp.BMC genomics · 2024Article
- Comprehensive Profiling of Alternative Splicing and Alternative Polyadenylation during Fruit Ripening in Watermelon (International journal of molecular sciences · 2023Article
- Current insights into posttranscriptional regulation of fleshy fruit ripening.Plant physiology · 2023Review
- De novo transcriptome analysis and identification of defensive genes in garlic (Allium sativum L.) using high-throughput sequencing.Journal, genetic engineering & biotechnology · 2023Article
- ConservingPlants (Basel, Switzerland) · 2023Article
- Shaping the biology of citrus: II. Genomic determinants of domestication.The plant genome · 2021Article
- Shaping the biology of citrus: I. Genomic determinants of evolution.The plant genome · 2021Article
- CitrusKB: a comprehensive knowledge base for transcriptome and interactome of Citrus spp. infected by Xanthomonas citri subsp. citri at different infection stages.Database : the journal of biological databases and curation · 2020Article
- Genome sequencing and CRISPR/Cas9 gene editing of an early flowering Mini-Citrus (Fortunella hindsii).Plant biotechnology journal · 2019Article
- Transcriptome analysis of the endangeredPlant diversity · 2019Article
- Transcriptomic analysis of Citrus clementina mandarin fruits maturation reveals a MADS-box transcription factor that might be involved in the regulation of earliness.BMC plant biology · 2019Article
- Facing Climate Change: Biotechnology of Iconic Mediterranean Woody Crops.Frontiers in plant science · 2019Review
- Comparative transcriptome analysis of Poncirus trifoliata identifies a core set of genes involved in arbuscular mycorrhizal symbiosis.Journal of experimental botany · 2018Article
- The HTPmod Shiny application enables modeling and visualization of large-scale biological data.Communications biology · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Previous RNA-Seq studies in citrus have been focused on physiological processes relevant to fruit quality and productivity of the major species, especially sweet orange. Less attention has been paid to vegetative or reproductive tissues, while most Citrus species have never been analysed. In this work, we characterized the transcriptome of vegetative and reproductive tissues from 12 Citrus species from all main phylogenetic groups. Our aims were to acquire a complete view of the citrus transcriptome landscape, to improve previous functional annotations and to obtain genetic markers associated with genes of agronomic interest. 28 samples were used for RNA-Seq analysis, obtained from 12 Citrus species: C. medica, C. aurantifolia, C. limon, C. bergamia, C. clementina, C. deliciosa, C. reshni, C. maxima, C. paradisi, C. aurantium, C. sinensis and Poncirus trifoliata. Four different organs were analysed: root, phloem, leaf and flower. A total of 3421 million Illumina reads were produced and mapped against the reference C. clementina genome sequence. Transcript discovery pipeline revealed 3326 new genes, the number of genes with alternative splicing was increased to 19,739, and a total of 73,797 transcripts were identified. Differential expression studies between the four tissues showed that gene expression is overall related to the physiological function of the specific organs above any other variable. Variants discovery analysis revealed the presence of indels and SNPs in genes associated with fruit quality and productivity. Pivotal pathways in citrus such as those of flavonoids, flavonols, ethylene and auxin were also analysed in detail.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.