In the fern Ceratopteris richardii, every spore has the potential to develop as either a male or hermaphroditic gametophyte. Gametophyte sex is determined by a GA-like pheromone (ACE) that is secreted by hermaphrodites approximately 6 days after spore inoculation and induces male development in other juvenile gametophytes. Our goal is to better understand the genetic and molecular mechanisms involved in sex determination and to identify sex determination genes in Ceratopteris. RNA-Seq was used to create de novotranscriptome assemblies from gametophytes grown, with or without ACE, during the time that their sex is determined, and from male gametophytes in early development. We found that ACE alters the expression of 1,163 genes, including those involved in epigenetic reprogramming of the genome. This suggests that epigenetics plays an important role in the early establishment of the male program of expression. We also found that a large number of transcripts are stored in the dormant spore (18,437) and that the transcriptomes of male gametophytes early in development are incredibly dynamic. The research presented in this thesis was used to generate easily testable hypotheses and to identify candidate sex-determining genes that had been genetically characterized previously. We propose that theHERMAPHRODITIC gene encodes GID1, the ACE receptor, that theTRANSFORMER gene encodes a DELLA protein, and that the FEMINIZATION(FEM) gene encodes a MYB transcription factor. We also propose that FEM directly or indirectly blocks ACE synthesis in the male by down-regulating the expression of a gene (CPS/KS) that is essential for GA biosynthesis.
","abstract_html":"<p>In the fern Ceratopteris richardii, every spore has the potential to develop as either a male or hermaphroditic gametophyte. Gametophyte sex is determined by a GA-like pheromone (ACE) that is secreted by hermaphrodites approximately 6 days after spore inoculation and induces male development in other juvenile gametophytes. Our goal is to better understand the genetic and molecular mechanisms involved in sex determination and to identify sex determination genes in Ceratopteris. RNA-Seq was used to create <em>de novo</em>transcriptome assemblies from gametophytes grown, with or without ACE, during the time that their sex is determined, and from male gametophytes in early development. We found that ACE alters the expression of 1,163 genes, including those involved in epigenetic reprogramming of the genome. This suggests that epigenetics plays an important role in the early establishment of the male program of expression. We also found that a large number of transcripts are stored in the dormant spore (18,437) and that the transcriptomes of male gametophytes early in development are incredibly dynamic. The research presented in this thesis was used to generate easily testable hypotheses and to identify candidate sex-determining genes that had been genetically characterized previously. We propose that the<em>HERMAPHRODITIC</em> gene encodes GID1, the ACE receptor, that the<em>TRANSFORMER</em> gene encodes a DELLA protein, and that the <em>FEMINIZATION</em>(<em>FEM</em>) gene encodes a MYB transcription factor. We also propose that FEM directly or indirectly blocks A<sub>CE</sub> synthesis in the male by down-regulating the expression of a gene (<em>CPS/KS</em>) that is essential for GA biosynthesis.</p>","abstract_has_math":false,"creators":["Atallah, Nadia"],"institution":null,"degree_name":"Doctor of Philosophy (PhD)","degree_level":"Dissertation","degree_discipline":"Botany and Plant Pathology","degree_department":null,"school":null,"contributors":["Jo Ann Banks","Joseph Ogas","Michael Gribskov","Peter B. Goldsbrough","Olga Vitek","Milos Tanurdzic"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2015,"date_issued":"2015-04-01T07:00:00Z","date_published":"2015-04-01T07:00:00Z","updated_at":"2026-07-24T03:53:22Z","subjects":["Bioinformatics","Developmental Biology","Plant Sciences"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://docs.lib.purdue.edu/open_access_dissertations/417","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Jo Ann Banks","Joseph Ogas","Michael Gribskov","Peter B. 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Gametophyte sex is determined by a GA-like pheromone (ACE) that is secreted by hermaphrodites approximately 6 days after spore inoculation and induces male development in other juvenile gametophytes. Our goal is to better understand the genetic and molecular mechanisms involved in sex determination and to identify sex determination genes in Ceratopteris. RNA-Seq was used to create de novotranscriptome assemblies from gametophytes grown, with or without ACE, during the time that their sex is determined, and from male gametophytes in early development. We found that ACE alters the expression of 1,163 genes, including those involved in epigenetic reprogramming of the genome. This suggests that epigenetics plays an important role in the early establishment of the male program of expression. We also found that a large number of transcripts are stored in the dormant spore (18,437) and that the transcriptomes of male gametophytes early in development are incredibly dynamic. The research presented in this thesis was used to generate easily testable hypotheses and to identify candidate sex-determining genes that had been genetically characterized previously. We propose that theHERMAPHRODITIC gene encodes GID1, the ACE receptor, that theTRANSFORMER gene encodes a DELLA protein, and that the FEMINIZATION(FEM) gene encodes a MYB transcription factor. We also propose that FEM directly or indirectly blocks ACE synthesis in the male by down-regulating the expression of a gene (CPS/KS) that is essential for GA biosynthesis.
"]},{"key":"dc:title","label":"Title","values":["Profiling gene expression during early gametophyte development and sex determination in Ceratopteris richardii"]}]}],"canonical_facts":{"dc:contributor":["Jo Ann Banks","Joseph Ogas","Michael Gribskov","Peter B. Goldsbrough","Olga Vitek","Milos Tanurdzic"],"dc:creator":["Atallah, Nadia"],"dc:description.abstract":["In the fern Ceratopteris richardii, every spore has the potential to develop as either a male or hermaphroditic gametophyte. Gametophyte sex is determined by a GA-like pheromone (ACE) that is secreted by hermaphrodites approximately 6 days after spore inoculation and induces male development in other juvenile gametophytes. Our goal is to better understand the genetic and molecular mechanisms involved in sex determination and to identify sex determination genes in Ceratopteris. RNA-Seq was used to create de novotranscriptome assemblies from gametophytes grown, with or without ACE, during the time that their sex is determined, and from male gametophytes in early development. We found that ACE alters the expression of 1,163 genes, including those involved in epigenetic reprogramming of the genome. This suggests that epigenetics plays an important role in the early establishment of the male program of expression. We also found that a large number of transcripts are stored in the dormant spore (18,437) and that the transcriptomes of male gametophytes early in development are incredibly dynamic. The research presented in this thesis was used to generate easily testable hypotheses and to identify candidate sex-determining genes that had been genetically characterized previously. We propose that theHERMAPHRODITIC gene encodes GID1, the ACE receptor, that theTRANSFORMER gene encodes a DELLA protein, and that the FEMINIZATION(FEM) gene encodes a MYB transcription factor. We also propose that FEM directly or indirectly blocks ACE synthesis in the male by down-regulating the expression of a gene (CPS/KS) that is essential for GA biosynthesis.
"],"dc:identifier":["https://docs.lib.purdue.edu/open_access_dissertations/417"],"dc:subject":["Bioinformatics","Developmental Biology","Plant Sciences"],"dc:title":["Profiling gene expression during early gametophyte development and sex determination in Ceratopteris richardii"],"thesis:degree_discipline":["Botany and Plant Pathology"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Doctor of Philosophy (PhD)"]},"updated_at":"2026-07-24T03:53:22Z"}