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Changes in RNA Splicing in Developing Soybean (Glycine max) Embryos
Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061, USA
Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
* Author to whom correspondence should be addressed.
Received: 20 September 2013; in revised form: 6 November 2013 / Accepted: 12 November 2013 / Published: 21 November 2013
Abstract: Developing soybean seeds accumulate oils, proteins, and carbohydrates that are used as oxidizable substrates providing metabolic precursors and energy during seed germination. The accumulation of these storage compounds in developing seeds is highly regulated at multiple levels, including at transcriptional and post-transcriptional regulation. RNA sequencing was used to provide comprehensive information about transcriptional and post-transcriptional events that take place in developing soybean embryos. Bioinformatics analyses lead to the identification of different classes of alternatively spliced isoforms and corresponding changes in their levels on a global scale during soybean embryo development. Alternative splicing was associated with transcripts involved in various metabolic and developmental processes, including central carbon and nitrogen metabolism, induction of maturation and dormancy, and splicing itself. Detailed examination of selected RNA isoforms revealed alterations in individual domains that could result in changes in subcellular localization of the resulting proteins, protein-protein and enzyme-substrate interactions, and regulation of protein activities. Different isoforms may play an important role in regulating developmental and metabolic processes occurring at different stages in developing oilseed embryos.
Keywords: abscisic acid; alternative splicing; auxin; central carbon and nitrogen metabolism; desiccation tolerance; dormancy induction; post-transcriptional regulation; seed and embryo development; soybean
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Aghamirzaie, D.; Nabiyouni, M.; Fang, Y.; Klumas, C.; Heath, L.S.; Grene, R.; Collakova, E. Changes in RNA Splicing in Developing Soybean (Glycine max) Embryos. Biology 2013, 2, 1311-1337.
Aghamirzaie D, Nabiyouni M, Fang Y, Klumas C, Heath LS, Grene R, Collakova E. Changes in RNA Splicing in Developing Soybean (Glycine max) Embryos. Biology. 2013; 2(4):1311-1337.
Aghamirzaie, Delasa; Nabiyouni, Mahdi; Fang, Yihui; Klumas, Curtis; Heath, Lenwood S.; Grene, Ruth; Collakova, Eva. 2013. "Changes in RNA Splicing in Developing Soybean (Glycine max) Embryos." Biology 2, no. 4: 1311-1337.