Phylogenomics and comparative transcriptomic analyses of the monocots
Open Access
- Author:
- Timilsena, Prakash Raj
- Graduate Program:
- Biology
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- April 17, 2020
- Committee Members:
- Claude Walker Depamphilis, Dissertation Advisor/Co-Advisor
Kateryna Dmytrivna Makova, Committee Chair/Co-Chair
Heather M Hines, Committee Member
John Edward Carlson, Outside Member
Tracy Langkilde, Program Head/Chair - Keywords:
- Phylogenomics
Plant Biology
Taxonomy
Systematics
Monocots
Genomics
Bioinformatics
Botany
Evolution
Comparative Genomics
Evolutionary Genomics
Transcriptomics
RNASeq
Gene Annotation - Abstract:
- Monocotyledons, which first evolved at least 140 million years ago, are one of most economically important, morphologically diverse, and dominant groups of plants, and understanding their evolutionary history is of great importance. Morphological classifications of this group in the past have been augmented mostly by plastid and, more recently, plastome-level phylogenetic analyses, which have helped to resolve the evolutionary relationships of most monocot lineages to the tribal level. However, uncertainties remain, and a higher level nuclear phylogenomic level analysis including all major families has not yet been attempted. Monocots are also home to a special group of plants, called mycoheterotrophs. Mycoheterotrophs are groups of plants that obtain their sugars and other nutrients by parasitizing fungi that are associated with other green plants, rather than using photosynthetic processes for carbohydrate acquisition. Mycoheterotrophy, like direct hasutorial parasitism, has evolved multiple times, and the monocots are hot spots of such lifestyles within the flowering plants. The consequences of mycoheterotrophy on plastid genomes has been understood relatively well, yet the dynamics of nuclear genome evolution in these plants remain poorly studied. To address both these problems, we conducted phylogenomic analyses of hundreds of single copy nuclear genes from genomes and transcriptomes across all monocot orders and most monocot families. A first detailed study analyzed genomes and transcriptomes from 37 species across all monocot orders, and included five mycoheterotrophic species from Orchidaceae, Triuridaceae, and Burmanniaceae. The transcriptome data for related mycoheterotrophic and autotrophic monocot species we compared to quantify the degree of reduction or loss in nuclear-encoded photosynthetic and chlorophyll biosynthesis gene expression, and to test whether these patterns of loss are similar to the dramatic losses of genes in the plastomes of these plants. Phylogenetically-grounded comparative analyses of gene expression profiles in mycoheterotrophic and non-mycoheterotrophic lineages elucidated parallel but distinct trajectories of reduction (or loss) in expression of chlorophyll synthesis and photosynthetic pathway genes in mycoheterotrophs of different ages. In contrast, heme biosynthesis genes were present and transcribed across all examined autotrophic and mycoheterotrophic species, consistent with essential heme functions in all plants. Reduction and loss of photosynthetic gene expression corresponded to the age of mycoheterotrophy in the plant lineage. A second study focused on phylogenomic analyses of single copy genes from genomes and transcriptomes from representing all monocot orders as well as Dasypogonaceae and most other monocot families. We recovered highly consistent and robust ordinal-level relationships of all 11 monocot orders, as well as the family Dasypogonaceae, using 602 highly conserved single copy nuclear genes. The phylogenetic trees were strongly supported and highly concordant between concatenation and coalescent-based analyses. It was found that Asparagales and Liliales are sister clades which together is sister to the rest of the large commelinid clade of ((Poales, (Commelinales, Zingiberales)), (Arecales, Dasypogonaceae)). Previous phylogenomic analyses with plastid genes and genomes have suggested that Liliales are grades with Asparagales and other Commelinid clades. However, in this study we present a very robust genomic-scale nuclear phylogeny, which places them together, irrespective of the set of nuclear genes, method of analysis, or completeness of the taxon or gene sampling. In addition, the position of order Arecales and families of Alismatales, Typhaceae and Araceae as grades at the base of the phylogenetic trees supports the possibility that the monocots initially evolved as aquatic plants before radiating and dominating nearly all geographical and ecological niches of the world.