The overall aim of the project was to understand how plants reacted to environmental stress and evolved to overcome it. The land plants that we see today evolved from a green algal ancestor around 510 million years ago. Plants had to make significant changes to their cellular, morphological, regulatory and physiological processes during their adaptation to the terrestrial environment from an aquatic environment. The first part of the project was to find out how these changes were reflected on the protein makeup of the early land plants. The gene model sequence data of two early land plants, Physcomitrella patens (moss) and Chlamydomonas reinhardtii(green algae). We specifically focused on the protein family expansion of protein kinases due to their roles in various important functions that would affect the transition from water to land. We developed a gene model quality evaluation method to score the gene models of P. patens and C. reinhardtii using well-studied plants such as Arabidopsis thaliana and Oryza sativa (rice) to improve the poor quality gene models that currently exist. The resulting corrected gene models were analyzed using functional annotation methods to understand how the proteomics of the early land plants varied from modern land plants.
The second part of the project was to identify the genes responsible for herbicide resistance in Ambrosia trifida (giant ragweed). Giant ragweed is one of the most competitive annual weeds in corn and soybean production across the eastern Corn Belt in the United States. The use of glyphosate (commercial name: Roundup) and glyphosate-ready crop systems managed to keep giant ragweed populations under control. Glyphosate-ready crop systems consist of seeds that are resistant to glyphosate, which enables farmers to use glyphosate to control the population of weeds. But in the last decade, glyphosate-resistant giant ragweed populations have been reported across the world. It is a huge problem to farmers since it results in unusable glyphosate-ready cropping systems and huge yield losses. Glyphosate-resistant and sensitive plants were identified from across the Midwestern United States and a RNA-seq experiment was performed by isolating the total mRNA from leaf material, and obtaining the expressed messenger RNA sequences. The genetic makeup of the sensitive and resistant strains was thus compared based on their transcriptome data, and a list of potential genes that were differentially expressed between them was identified. We also analyzed how much the quality of the transcriptome can be improved by using the transcriptome and genome of sunflower, a closely-related plant.
","abstract_html":"<p>The overall aim of the project was to understand how plants reacted to environmental stress and evolved to overcome it. The land plants that we see today evolved from a green algal ancestor around 510 million years ago. Plants had to make significant changes to their cellular, morphological, regulatory and physiological processes during their adaptation to the terrestrial environment from an aquatic environment. The first part of the project was to find out how these changes were reflected on the protein makeup of the early land plants. The gene model sequence data of two early land plants, <em>Physcomitrella patens</em> (moss) and <em>Chlamydomonas reinhardtii</em>(green algae). We specifically focused on the protein family expansion of protein kinases due to their roles in various important functions that would affect the transition from water to land. We developed a gene model quality evaluation method to score the gene models of <em>P. patens </em>and <em>C. reinhardtii</em> using well-studied plants such as <em>Arabidopsis thaliana</em> and <em>Oryza sativa</em> (rice) to improve the poor quality gene models that currently exist. The resulting corrected gene models were analyzed using functional annotation methods to understand how the proteomics of the early land plants varied from modern land plants.</p> <p>The second part of the project was to identify the genes responsible for herbicide resistance in <em>Ambrosia trifida</em> (giant ragweed). Giant ragweed is one of the most competitive annual weeds in corn and soybean production across the eastern Corn Belt in the United States. The use of glyphosate (commercial name: Roundup) and glyphosate-ready crop systems managed to keep giant ragweed populations under control. Glyphosate-ready crop systems consist of seeds that are resistant to glyphosate, which enables farmers to use glyphosate to control the population of weeds. But in the last decade, glyphosate-resistant giant ragweed populations have been reported across the world. It is a huge problem to farmers since it results in unusable glyphosate-ready cropping systems and huge yield losses. Glyphosate-resistant and sensitive plants were identified from across the Midwestern United States and a RNA-seq experiment was performed by isolating the total mRNA from leaf material, and obtaining the expressed messenger RNA sequences. The genetic makeup of the sensitive and resistant strains was thus compared based on their transcriptome data, and a list of potential genes that were differentially expressed between them was identified. We also analyzed how much the quality of the transcriptome can be improved by using the transcriptome and genome of sunflower, a closely-related plant.</p>","abstract_has_math":false,"creators":["Padmanabhan, Karthik Ramaswamy"],"institution":null,"degree_name":"Doctor of Philosophy (PhD)","degree_level":"Dissertation","degree_discipline":"Biological Science","degree_department":null,"school":null,"contributors":["Michael R. Gribskov","Daisuke Kihara","Laurie L. Parker","Carol B. Post"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2016,"date_issued":"2016-08-01T07:00:00Z","date_published":"2016-08-01T07:00:00Z","updated_at":"2026-07-24T03:54:02Z","subjects":["Biological sciences","Gene models","Genomics","Giant ragweed","Glyphosate","Plant evolution","Protein kinases","Bioinformatics","Biology","Plant Sciences"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://docs.lib.purdue.edu/open_access_dissertations/823","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Michael R. Gribskov","Daisuke Kihara","Laurie L. Parker","Carol B. Post"]},{"key":"dc:creator","label":"Author","values":["Padmanabhan, Karthik Ramaswamy"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"thesis:degree_discipline","label":"Discipline","values":["Biological Science"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Doctor of Philosophy (PhD)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Biological sciences","Gene models","Genomics","Giant ragweed","Glyphosate","Plant evolution","Protein kinases","Bioinformatics","Biology","Plant Sciences"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://docs.lib.purdue.edu/open_access_dissertations/823"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["The overall aim of the project was to understand how plants reacted to environmental stress and evolved to overcome it. The land plants that we see today evolved from a green algal ancestor around 510 million years ago. Plants had to make significant changes to their cellular, morphological, regulatory and physiological processes during their adaptation to the terrestrial environment from an aquatic environment. The first part of the project was to find out how these changes were reflected on the protein makeup of the early land plants. The gene model sequence data of two early land plants, Physcomitrella patens (moss) and Chlamydomonas reinhardtii(green algae). We specifically focused on the protein family expansion of protein kinases due to their roles in various important functions that would affect the transition from water to land. We developed a gene model quality evaluation method to score the gene models of P. patens and C. reinhardtii using well-studied plants such as Arabidopsis thaliana and Oryza sativa (rice) to improve the poor quality gene models that currently exist. The resulting corrected gene models were analyzed using functional annotation methods to understand how the proteomics of the early land plants varied from modern land plants.
The second part of the project was to identify the genes responsible for herbicide resistance in Ambrosia trifida (giant ragweed). Giant ragweed is one of the most competitive annual weeds in corn and soybean production across the eastern Corn Belt in the United States. The use of glyphosate (commercial name: Roundup) and glyphosate-ready crop systems managed to keep giant ragweed populations under control. Glyphosate-ready crop systems consist of seeds that are resistant to glyphosate, which enables farmers to use glyphosate to control the population of weeds. But in the last decade, glyphosate-resistant giant ragweed populations have been reported across the world. It is a huge problem to farmers since it results in unusable glyphosate-ready cropping systems and huge yield losses. Glyphosate-resistant and sensitive plants were identified from across the Midwestern United States and a RNA-seq experiment was performed by isolating the total mRNA from leaf material, and obtaining the expressed messenger RNA sequences. The genetic makeup of the sensitive and resistant strains was thus compared based on their transcriptome data, and a list of potential genes that were differentially expressed between them was identified. We also analyzed how much the quality of the transcriptome can be improved by using the transcriptome and genome of sunflower, a closely-related plant.
"]},{"key":"dc:title","label":"Title","values":["Understanding Plant Response to Stress Using Gene Model Quality Evaluation and Transcriptome Analysis"]}]}],"canonical_facts":{"dc:contributor":["Michael R. Gribskov","Daisuke Kihara","Laurie L. Parker","Carol B. Post"],"dc:creator":["Padmanabhan, Karthik Ramaswamy"],"dc:description.abstract":["The overall aim of the project was to understand how plants reacted to environmental stress and evolved to overcome it. The land plants that we see today evolved from a green algal ancestor around 510 million years ago. Plants had to make significant changes to their cellular, morphological, regulatory and physiological processes during their adaptation to the terrestrial environment from an aquatic environment. The first part of the project was to find out how these changes were reflected on the protein makeup of the early land plants. The gene model sequence data of two early land plants, Physcomitrella patens (moss) and Chlamydomonas reinhardtii(green algae). We specifically focused on the protein family expansion of protein kinases due to their roles in various important functions that would affect the transition from water to land. We developed a gene model quality evaluation method to score the gene models of P. patens and C. reinhardtii using well-studied plants such as Arabidopsis thaliana and Oryza sativa (rice) to improve the poor quality gene models that currently exist. The resulting corrected gene models were analyzed using functional annotation methods to understand how the proteomics of the early land plants varied from modern land plants.
The second part of the project was to identify the genes responsible for herbicide resistance in Ambrosia trifida (giant ragweed). Giant ragweed is one of the most competitive annual weeds in corn and soybean production across the eastern Corn Belt in the United States. The use of glyphosate (commercial name: Roundup) and glyphosate-ready crop systems managed to keep giant ragweed populations under control. Glyphosate-ready crop systems consist of seeds that are resistant to glyphosate, which enables farmers to use glyphosate to control the population of weeds. But in the last decade, glyphosate-resistant giant ragweed populations have been reported across the world. It is a huge problem to farmers since it results in unusable glyphosate-ready cropping systems and huge yield losses. Glyphosate-resistant and sensitive plants were identified from across the Midwestern United States and a RNA-seq experiment was performed by isolating the total mRNA from leaf material, and obtaining the expressed messenger RNA sequences. The genetic makeup of the sensitive and resistant strains was thus compared based on their transcriptome data, and a list of potential genes that were differentially expressed between them was identified. We also analyzed how much the quality of the transcriptome can be improved by using the transcriptome and genome of sunflower, a closely-related plant.
"],"dc:identifier":["https://docs.lib.purdue.edu/open_access_dissertations/823"],"dc:subject":["Biological sciences","Gene models","Genomics","Giant ragweed","Glyphosate","Plant evolution","Protein kinases","Bioinformatics","Biology","Plant Sciences"],"dc:title":["Understanding Plant Response to Stress Using Gene Model Quality Evaluation and Transcriptome Analysis"],"thesis:degree_discipline":["Biological Science"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Doctor of Philosophy (PhD)"]},"updated_at":"2026-07-24T03:54:02Z"}