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

Kato, Yasuhiko; Nitta, Joel H.; Perez Christelle Alexa Garcia; Adhitama, Nikko; Religia, Pijar; Toyoda, Atsushi; Iwasaki, Wataru; Watanabe, Hajime

doi:https://doi.org/10.1038/s41598-024-59774-1

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

Kato, Yasuhiko; Nitta, Joel H.; Perez Christelle Alexa Garcia et al.

Scientific Reports, 2024, 14, 9407

Number of Access:1,064（2025-07-27 03:02 Counts）

Identifier to cite or link to this item: https://hdl.handle.net/11094/97214

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Title	Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna
Creator	NRID 1000060415932 1000060415932 ORCID 0000-0002-1041-1044 0000-0002-1041-1044 researchmap permalink 03082710 03082710 Scopus Author ID 55363323700 55363323700 CreatorName Kato, Yasuhiko
	NRID 1000050901443 1000050901443 CreatorName Nitta, Joel H.
	CreatorName Perez Christelle Alexa Garcia
	NRID 1000000905953 1000000905953 ORCID 0000-0001-7864-7654 0000-0001-7864-7654 researchmap permalink adhitamanikko adhitamanikko Scopus Author ID 57202986462 57202986462 CreatorName Adhitama, Nikko
	ORCID 0000-0002-9349-2993 0000-0002-9349-2993 researchmap permalink pijar_religia pijar_religia CreatorName Religia, Pijar
	NRID 1000010267495 1000010267495 CreatorName Toyoda, Atsushi
	NRID 1000050545019 1000050545019 CreatorName Iwasaki, Wataru
	NRID 1000080212322 1000080212322 ORCID 0000-0001-9657-6554 0000-0001-9657-6554 researchmap permalink read0052409 read0052409 Scopus Author ID 35466703500 35466703500 CreatorName Watanabe, Hajime
Description	Kato Y., Nitta J.H., Perez C.A.G., et al. Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna. Scientific Reports 14, 9407 (2024); https://doi.org/10.1038/s41598-024-59774-1.
Abstract	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.
Publisher	Nature Research
Source Title	Scientific Reports
Volume (Issue)	14
Page	9407
Date of Issued	2024-04-30
Language	English
Handle URL	https://hdl.handle.net/11094/97214
eISSN	20452322
Relation.isIdenticalTo	DOI (Publisher Version) https://doi.org/10.1038/s41598-024-59774-1
Access Rights	open access
CopyRight	This article is licensed under a Creative Commons Attribution 4.0 International License.
oaire:version	Version of Record
Category	学術雑誌論文 Journal Article

Resource Type	journal article
Local Type	Journal Article
DCTERMS.bibliographicCitation	Scientific Reports. 2024, 14, p. 9407
DC.title	Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna
DC.creator	Kato, Yasuhiko
	Nitta, Joel H.
	Perez Christelle Alexa Garcia
	Adhitama, Nikko
	Religia, Pijar
	Toyoda, Atsushi
	Iwasaki, Wataru
	Watanabe, Hajime
DC.publisher	Nature Research
DC.language' scheme='DCTERMS.RFC1766	English
DCTERMS.issued' scheme='DCTERMS.W3CDTF	2024-04-30
DC.identifier	https://doi.org/10.1038/s41598-024-59774-1
DC.description	Kato Y., Nitta J.H., Perez C.A.G., et al. Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna. Scientific Reports 14, 9407 (2024); https://doi.org/10.1038/s41598-024-59774-1.
DCTERMS.abstract	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.
DC.rights	This article is licensed under a Creative Commons Attribution 4.0 International License.
DC.format	97214
citation_title	Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna
citation_author	Kato, Yasuhiko
	Nitta, Joel H.
	Perez Christelle Alexa Garcia
	Adhitama, Nikko
	Religia, Pijar
	Toyoda, Atsushi
	Iwasaki, Wataru
	Watanabe, Hajime
citation_publisher	Nature Research
citation_language	English
citation_date	2024-04-30
citation_journal_title	Scientific Reports
citation_volume	14
citation_firstpage	9407
citation_doi	https://doi.org/10.1038/s41598-024-59774-1
citation_public_url	https://hdl.handle.net/11094/97214

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

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