ArticleBMC genomics2015
Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Global transcriptome analysis of allopolyploidization reveals large-scale repression of the D-subgenome in synthetic hexaploid wheat.Communications biology · 2023Article
- Genome-wide analysis of R2R3-MYB genes in cultivated peanut (Frontiers in plant science · 2023Article
- Molecular evolutionary analysis of theFrontiers in plant science · 2022Article
- Temporal regulation of alternative splicing events in rice memory under drought stress.Plant diversity · 2022Article
- Genome-wide differences in gene expression and alternative splicing in developing embryo and endosperm, and between F1 hybrids and their parental pure lines in sorghum.Plant molecular biology · 2022Article
- Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms.BMC genomics · 2021Article
- Comparative transcriptome analyses revealed different heat stress responses in pigeonpea (Cajanus cajan) and its crop wild relatives.Plant cell reports · 2021Article
- The emergence and evolution of intron-poor and intronless genes in intron-rich plant gene families.The Plant journal : for cell and molecular biology · 2021Article
- The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns.Frontiers in plant science · 2021Article
- Article
- Genome-Wide Identification and Characterization of the Vacuolar HInternational journal of molecular sciences · 2019Article
- Article
- Genome-Wide Identification, Expression Profile, and Alternative Splicing Analysis of the Brassinosteroid-Signaling Kinase (BSK) Family Genes inInternational journal of molecular sciences · 2019Article
- Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane.Frontiers in plant science · 2019Article
- Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato.Frontiers in plant science · 2019Article
- The kinome of pineapple: catalog and insights into functions in crassulacean acid metabolism plants.BMC plant biology · 2018Article
- Transcriptome analysis of alternative splicing in peanut (Arachis hypogaea L.).BMC plant biology · 2018Article
- Position-specific intron retention is mediated by the histone methyltransferase SDG725.BMC biology · 2018Article
- Transcriptome analysis of Brachypodium during fungal pathogen infection reveals both shared and distinct defense responses with wheat.Scientific reports · 2017Article
- Alternative splicing in tomato pollen in response to heat stress.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
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6 authors.
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Abstract
backgroundProtein functional diversity at the post-transcriptional level is regulated through spliceosome mediated pre-mRNA alternative splicing (AS) events and that has been widely demonstrated to be a key player in regulating the functional diversity in plants. Identification and analysis of AS genes in cereal crop plants are critical for crop improvement and understanding regulatory mechanisms.
resultsWe carried out the comparative analyses of the functional landscapes of the AS using the consensus assembly of expressed sequence tags and available mRNA sequences in four cereal plants. We identified a total of 8,734 in Oryza sativa subspecies (ssp) japonica, 2,657 in O. sativa ssp indica, 3,971 in Sorghum bicolor, and 10,687 in Zea mays AS genes. Among the identified AS events, intron retention remains to be the dominant type accounting for 23.5 % in S. bicolor, and up to 55.8 % in O. sativa ssp indica. We identified a total of 887 AS genes that were conserved among Z. mays, S. bicolor, and O. sativa ssp japonica; and 248 AS genes were found to be conserved among all four studied species or ssp. Furthermore, we identified 53 AS genes conserved with Brachypodium distachyon. Gene Ontology classification of AS genes revealed functional assignment of these genes in many biological processes with diverse molecular functions.
conclusionsAS is common in cereal plants. The AS genes identified in four cereal crops in this work provide the foundation for further studying the roles of AS in regulation of cereal plant growth and development. The data can be accessed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/).
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