Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna.

Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

Original Publication: London : Nature Publishing Group, copyright 2011-

Daphnia magna*/embryology ; Daphnia magna*/genetics ; Protein Isoforms*/genetics ; Protein Isoforms*/metabolism; Animals ; Female ; Male ; Embryo, Nonmammalian/metabolism ; Gene Expression Regulation, Developmental ; Parthenogenesis/genetics ; Sex Determination Processes/genetics

The cladoceran crustacean Daphnia exhibits phenotypic plasticity, a phenomenon that leads to diverse phenotypes from one genome. Alternative usage of gene isoforms has been considered a key gene regulation mechanism for controlling different phenotypes. However, to understand the phenotypic plasticity of Daphnia, gene isoforms have not been comprehensively analyzed. Here we identified 25,654 transcripts derived from the 9710 genes expressed during environmental sex determination of Daphnia magna using the long-read RNA-Seq with PacBio Iso-Seq. We found that 14,924 transcripts were previously unidentified and 5713 genes produced two or more isoforms. By a combination of Illumina short-read RNA-Seq, we detected 824 genes that implemented switching of the highest expressed isoform between females and males. Among the 824 genes, we found isoform switching of an ortholog of CREB-regulated transcription coactivator, a major regulator of carbohydrate metabolism in animals, and a correlation of this switching event with the sexually dimorphic expression of carbohydrate metabolic genes. These results suggest that a comprehensive catalog of isoforms may lead to understanding the molecular basis for environmental sex determination of Daphnia. We also infer the applicability of the full-length isoform analyses to the elucidation of phenotypic plasticity in Daphnia.
(© 2024. The Author(s).)

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JP22H02701 MEXT | Japan Society for the Promotion of Science (JSPS); JP22H05598 MEXT | Japan Society for the Promotion of Science (JSPS); JP21K19298 MEXT | Japan Society for the Promotion of Science (JSPS); JP20H04923 MEXT | Japan Society for the Promotion of Science (JSPS); JP18H04884 MEXT | Japan Society for the Promotion of Science (JSPS); JP16H06279 (PAGS) MEXT | Japan Society for the Promotion of Science (JSPS); 21H03602 MEXT | Japan Society for the Promotion of Science (JSPS)

0 (Protein Isoforms)

Date Created: 20240430 Date Completed: 20240430 Latest Revision: 20240718

20240719

PMC11061156

10.1038/s41598-024-59774-1

38688940