@phdthesis{oai:oist.repo.nii.ac.jp:00002880,
 author = {Bliznina, Aleksandra},
 month = {2023-01-11, 2023-01-11},
 note = {Larvaceans represent the second most abundant zooplankton in all the world’s oceans, with key roles in marine food chains and global carbon flux. Oikopleura dioica is a free-swimming planktonic tunicate from the group and possesses the smallest animal genome with extremely dynamic organization: multiple genomic features such as transposon diversity, intron repertoire, gene content and order are altered in Oikopleura compared with other metazoans. Intriguingly, such genome reorganization has not affected the preservation of their ancestral morphology, since O. dioica maintains a chordate-like body plan throughout its life. O. dioica can be easily distinguished from other larvaceans mainly based on separate sexes and the presence of two subchordal cells on its tail. My research is focused on the cross-genome comparison of three O. dioica populations sampled from the Northern hemisphere: one from North Atlantic (Barcelona/Bergen) and two from Pacific (Osaka/Aomori and Okinawa/Kume) Oceans. For each population, I generated high-quality genome assemblies using a combination of short- and long-read sequencing technologies, as well as chromatin conformation data, confirming preservation of three chromosome pairs. A pairwise comparison of populations revealed a striking degree of genome reshuffling that involves a vast number of synteny breaks and rearrangements. My research also shows that rearrangements mostly happen within individual chromosomes and generally preserve protein-coding features, such as genes and their constituent exons, although the gene order has been effectively randomized. O. dioica populations exhibit differences in repeats and gene content that affect even evolutionary conserved clusters, such as Hox genes. Consistent with an increased evolutionary rate, the accumulation of rearrangements in O. dioica appears to have happened much faster than in other animals and resulted in the divergence of multiple lineages of dioecious Oikopleura. The fact that their morphology stayed virtually identical makes O. dioica a perfect model to study genotype-phenotype correlation and the possible existence of unknown regulatory mechanisms.
Overall, my thesis contributes new insights into the evolution of chordate genomes and, thus, may be interesting beyond the field of Oikopleura research.},
 school = {Okinawa Institute of Science and Technology Graduate University},
 title = {ワカレオタマボヤの世界的個体群のゲノム間比較},
 year = {}
}