Comparative Evolutionary Analysis of Organellar Genomic Diversity in Green Plants

The mitochondrial genome (mitogenome) and plastid genome (plastome) of plants vary immensely in genome size and gene content. They have also developed several eccentric features, such as the preference for horizontal gene transfer of mitochondrial genes, the reduction of the plastome in non-photosynthetic plants, and variable amounts of RNA editing affecting both genomes. Different organismal lifestyles can partially account for the highly diverse organellar genomes across the tree of green plants. For example, endosymbiotic and parasitic lifestyles can dramatically affect the genomic architectures of plant mitochondria and plastids. In this study, the organellar genomes of several green plants with atypical lifestyles were investigated and compared with the breadth of organelle genomic diversity within green plants. Next-generation sequencing and comparative evolutionary analyses were performed on organellar genomes of parasitic plants in Orobanchaceae and endosymbiotic algae in Chlorellaceae. Comparative organellar genomic analysis from endosymbiotic green algae provided no evidence for genome reduction; instead the endosymbiont genomes are generally larger in genome size and richer in intron content. Similarly, facultative hemiparasitic species in Orobanchaceae revealed minimal organellar genome degradation, but some evidence for several horizontal transferred genes. In both groups, the lack of genomic reduction may be attributed to the retention of photosynthetic ability. In addition, the extent of RNA editing was examined in the mitogenome of Welwitschia, a xerophytic plant. RNA editing sites in Welwitschia are extremely reduced compared with other gymnosperms, and may be caused by retroprocessing. Taken together, these results demonstrated that atypical lifestyle does not necessarily lead to the production of unusual genomic features and exhibited the convergence and divergence in green plants organelle genomes. Advisor: Jeffrey P. Mowe

MOTION CONTROL SIMULATION OF A HEXAPOD ROBOT

This thesis addresses hexapod robot motion control. Insect morphology and locomotion patterns inform the design of a robotic model, and motion control is achieved via trajectory planning and bio-inspired principles. Additionally, deep learning and multi-agent reinforcement learning are employed to train the robot motion control strategy with leg coordination achieves using a multi-agent deep reinforcement learning framework. The thesis makes the following contributions: First, research on legged robots is synthesized, with a focus on hexapod robot motion control. Insect anatomy analysis informs the hexagonal robot body and three-joint single robotic leg design, which is assembled using SolidWorks. Different gaits are studied and compared, and robot leg kinematics are derived and experimentally verified, culminating in a three-legged gait for motion control. Second, an animal-inspired approach employs a central pattern generator (CPG) control unit based on the Hopf oscillator, facilitating robot motion control in complex environments such as stable walking and climbing. The robot\u27s motion process is quantitatively evaluated in terms of displacement change and body pitch angle. Third, a value function decomposition algorithm, QPLEX, is applied to hexapod robot motion control. The QPLEX architecture treats each leg as a separate agent with local control modules, that are trained using reinforcement learning. QPLEX outperforms decentralized approaches, achieving coordinated rhythmic gaits and increased robustness on uneven terrain. The significant of terrain curriculum learning is assessed, with QPLEX demonstrating superior stability and faster consequence. The foot-end trajectory planning method enables robot motion control through inverse kinematic solutions but has limited generalization capabilities for diverse terrains. The animal-inspired CPG-based method offers a versatile control strategy but is constrained to core aspects. In contrast, the multi-agent deep reinforcement learning-based approach affords adaptable motion strategy adjustments, rendering it a superior control policy. These methods can be combined to develop a customized robot motion control policy for specific scenarios

Comparative Evolutionary Analysis of Organellar Genomic Diversity in Green Plants

The mitochondrial genome (mitogenome) and plastid genome (plastome) of plants vary immensely in genome size and gene content. They have also developed several eccentric features, such as the preference for horizontal gene transfer of mitochondrial genes, the reduction of the plastome in non-photosynthetic plants, and variable amounts of RNA editing affecting both genomes. Different organismal lifestyles can partially account for the highly diverse organellar genomes across the tree of green plants. For example, endosymbiotic and parasitic lifestyles can dramatically affect the genomic architectures of plant mitochondria and plastids. In this study, the organellar genomes of several green plants with atypical lifestyles were investigated and compared with the breadth of organelle genomic diversity within green plants. Next-generation sequencing and comparative evolutionary analyses were performed on organellar genomes of parasitic plants in Orobanchaceae and endosymbiotic algae in Chlorellaceae. Comparative organellar genomic analysis from endosymbiotic green algae provided no evidence for genome reduction; instead the endosymbiont genomes are generally larger in genome size and richer in intron content. Similarly, facultative hemiparasitic species in Orobanchaceae revealed minimal organellar genome degradation, but some evidence for several horizontal transferred genes. In both groups, the lack of genomic reduction may be attributed to the retention of photosynthetic ability. In addition, the extent of RNA editing was examined in the mitogenome of Welwitschia, a xerophytic plant. RNA editing sites in Welwitschia are extremely reduced compared with other gymnosperms, and may be caused by retroprocessing. Taken together, these results demonstrated that atypical lifestyle does not necessarily lead to the production of unusual genomic features and exhibited the convergence and divergence in green plants organelle genomes. Advisor: Jeffrey P. Mowe