ArticleNature communications2019
Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
- R-loops and D-loops: a delicate balance in genomic stability and instability.Cell communication and signaling : CCS · 2026Review
- Comparative Analysis of Full-Length Reference Gene Stability inPlants (Basel, Switzerland) · 2026Article
- The entireAntimicrobial agents and chemotherapy · 2026Article
- Phylogenomic profile of exon-intron organization across angiosperms, their relationships with protein domains, and functional implications.Nature communications · 2026Article
- Global atlas of enhancer-promoter interactome in cotton genome revealed by profiling RNA-RNA spatial interactions.Genome biology · 2026Article
- A comprehensive landscape of theFrontiers in plant science · 2026Article
- Multi-omics integration identifies diverse transcripts and chromatin accessibility profiles in Monopterus albus gonads.Scientific data · 2025Article
- MEPDB: Database of microExons in plants.The New phytologist · 2025Article
- Morphogenesis, starvation, and light responses in a mushroom-forming fungus revealed by long-read sequencing and extensive expression profiling.Cell genomics · 2025Article
- Comparative Transcriptome Reveals Conserved Gene Expression in Reproductive Organs in Solanaceae.International journal of molecular sciences · 2025Article
- The nuclear exosome co-factor MTR4 shapes the transcriptome for meiotic initiation.Nature communications · 2025Article
- Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Characterization of the mitochondrial genomes forIMA fungus · 2025Article
- Epigenomic and 3D genomic mapping reveals developmental dynamics and subgenomic asymmetry of transcriptional regulatory architecture in allotetraploid cotton.Nature communications · 2024Article
- Noncanonical transcription initiation is primarily tissue specific and epigenetically tuned in paleopolyploid plants.The Plant cell · 2024Article
- GhATL68b regulates cotton fiber cell development by ubiquitinating the enzyme required for β-oxidation of polyunsaturated fatty acids.Plant communications · 2024Article
- A Genome-Wide Alternative Splicing Analysis ofPlants (Basel, Switzerland) · 2024Article
- Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae.bioRxiv : the preprint server for biology · 2024Article
- Integrating Iso-seq and RNA-seq data for the reannotation of the greater amberjack genome.Scientific data · 2024Article
- Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice.The Plant cell · 2024Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cotton is an important natural fiber crop, however, its comprehensive and high-resolution gene map is lacking. Here we integrate four complementary high-throughput techniques, including Pacbio long read Iso-seq, strand-specific RNA-seq, CAGE-seq, and PolyA-seq, to systematically explore the transcription landscape across 16 tissues or different organ types in Gossypium arboreum. We devise a computational pipeline, named IGIA, to reconstruct accurate gene structures from the integrated data. Our results reveal a dynamic and diverse transcriptional map in cotton: tissue-specific gene expression, alternative usage of TSSs and polyadenylation sites, hotspot of alternative splicing, and transcriptional read-through. These regulated events affect many genes in various aspects such as gain or loss of functional RNA motifs and protein domains, fine-tuning of DNA binding activity, and co-regulation for genes in the same complex or pathway. The methods and findings provide valuable resources for further functional genomic studies such as understanding natural SNP variations for plant community.
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