Outrageous orchid organellar genomes: Structural evolution and composition

Organellar genomes are remnants of more complex bacterial genomes reduced until reach the simplest and most efficient content. Regularly depicted as circular, these genomes can form other structures, like linear, ramified, or entangled chromosomes, or a combination of those. Nonetheless, their gene content is nearly constant throughout flowering plants based on the multiple plastid genomes (plastomes) and the comparatively few mitochondrial genomes (mitogenomes) sequenced to date. Here, I explored the evolution of the organellar genomes in orchids from a phylogenetic perspective. For this research, plastomes and mitogenomes were assembled from short pair-ended reads obtained using Illumina sequencing technology. I developed a workflow to confidently recover plastid and mitochondrial sequences, even for regions without references in databases (chapter 1). The comparison among taxa from all orchid subfamilies identified patterns of gain, loss and rearrangement of coding and non-coding DNA. Plastid and mitochondrial protein-coding genes present in all samples were used to reconstruct the phylogenetic history of orchids that was coincident in terms of topology (chapter 1). Plastomes can suffer degradation in heterotrophic species, however that is not true for mixotrophic species, as I discovered by comparing albino and green individuals of the orchid Epipactis helleborine. I found that albino plants did not suffer loss of any genes and that the sequence was almost identical to the photosynthetic plants (chapter 2). In contrast to what it is observed in angiosperm plastomes, for which the structure, content and size is conserved, plant mitogenomes are highly variable in size, which can increase by the acquisition of external DNA via horizontal gene transfer. In some orchids, the mitogenome hosts a sixteen-gene sequence transferred from a fungal mitogenome to a clade of epidendroid orchids 12-60 My ago, and has been fragmented, conserved, or fully lost since (chapter 3). Transfer RNA genes are variable in number and origin throughout orchid evolution. I identified that they had four different sources, three novel possible replacement events of the native genes with plastid-origin genes, seven tRNA remodeling events in orchids and three more in other angiosperms (chapter 4). Our comparative studies conclude that there are three main dynamics that shape the organellar genomes: gain, loss and rearrangement of genomic content. I presented examples of them in orchids (chapter 5). Additionally, I created two sets of genomic resources: one comprises eighteen new orchid mitogenomes and plastomes, and the second consists of a well-curated set of references of tRNA genes in mitogenomes discriminated by origin. These results contribute to increasing the knowledge of angiosperm organellar genomes and highlight the importance of comprehensive studies that allow the interpretation of the genomic changes in the light of the phylogenetic evolution