Plastid genomes (plastomes) serve as valuable and cost-effective genomic resources for plants and algae. More than 2,500 complete plastomes (as of December 2018) are now publicly available on GenBank, and they provide critical information on the evolution and phylogeny of plastid-bearing organisms. In this dissertation, I will focus on the plastome evolution of non-flowering seed plants (gymnosperms). Gymnosperms comprise ca. 1,000 species in five groups, including cycads, ginkgo, gnetophytes, Pinaceae (conifers I), and cupressophytes (conifers II). Cupressophytes may be further divided into five families: Cupressaceae, Taxaceae, Sciadopityaceae, Araucariaceae, and Podocarpaceae. Previous studies have highlighted that gymnosperm plastomes are highly variable. However, our understanding of the plastome evolution within gymnosperm families is incomplete because not all 12 families are equally represented. In this study, I aimed to investigate (1) the plastome evolution and plastid phylogenomics of the two largest conifer families, Pinaceae and Podocarpaceae, and (2) the evolution of acetyl-CoA carboxylase (ACCase) genes in all five groups of gymnosperms.
This dissertation has four chapters. In chapter one, I reviewed the available literature on gymnosperm plastids, plastome evolution, and ACCase. In chapter two, I reconstructed the complete plastid phylogenomics of Pinaceae by sequencing two Pinaceous genera, Pseudolarix and Tsuga. The intergeneric relationships among members of the Abietoideae subfamily were resolved with Cedrus as sister to the clade containing Pseudolarix-Tsuga and Abies-Keteleeria, which refutes previous phylogenetic studies. I also documented accD elongation in Pinaceae for the first time.
In chapter three, I examined plastome evolution in the Podocarpaceae and expanded the number of available Podocarpaceae plastomes from 5 to 13. This addition enabled me to gain more insights into plastome evolution within the family. I found an exceptionally enlarged plastome in Lagarostrobos franklinii (Huon pine), a species endemic to Tasmania. Subsequent analyses revealed that the Lagarostrobos plastome is enriched with repetitive sequences, pseudogenes, and intergenic spacers that were not observed in other Podocarpaceae. In addition, plastid phylogenomic trees were also built to resolve problematic nodes in the Podocarpaceae phylogeny.
In chapter four, I investigated the evolutionary history of ACCase genes in the five gymnosperm groups. These genes are the key regulators of fatty acid biosynthesis, and most plants have both heteromeric and homomeric ACCases in plastids and cytosol, respectively. Heteromeric ACCase is composed of four subunits: three nuclear-encoded accA–C and one plastid-encoded accD, while homomeric ACCase is only encoded by one nuclear ACC gene. This study uncovered that: (1) the ACCD subunit in all cupressophytes (except Sciadopitys) are elongated by lineage-specific tandem repeats, (2) Sciadopitys and gnetophytes have functionally transferred their accD from the plastome to the nucleus, (3) Gnetum has two accDs in their nuclear genomes, and (4) one of Gnetum’s accD dually targets plastids and mitochondria, while the other copy only targets plastoglobuli, a microcompartment within the plastid. This is the first study to report the presence of two accDs and their distinct targeting in any green plant.

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