Development of a high-quality annotated reference genome and evolutionary genomics analysis of chromosomal inversions in drosophila subobscura
- Autores: Charikleia Karageorgiou
- Directores de la Tesis: Rosa M. Tarrio Fernandez (dir. tes.), Francisco Rodríguez Trelles Astruga (codir. tes.)
- Lectura: En la Universitat Autònoma de Barcelona ( España ) en 2022
- Idioma: inglés
- Tribunal Calificador de la Tesis: Aurora Ruiz-Herrera Moreno (presid.), Josefa González Pérez (secret.), Pavlos Pavlidis (voc.)
- Programa de doctorado: Programa de Doctorado en Genética por la Universidad Autónoma de Barcelona
- Materias:
- Enlaces
- Tesis en acceso abierto en: TDX
- Resumen
Drosophila subobscura belongs to the obscura species group, which is one of the known ten species groups of the subgenus Sophophora of the genus Drosophila. Originally endemic from the Palearctic region, it has recently colonized North and South America. The chromosomal inversion system of D. subobscura represents one of the most interesting models to investigate the evolution of this type of genome rearrangement, because i) it shows extremely high levels of polymorphism, exhibiting inversions of all kinds regarding length and chromosomal location; and ii) it has been identified to be involved in the species' adaptation to contemporary global climate warming. The lack of a reference genome for the species has, however, stood as a major obstacle to its study. To overcome this limitation, here we have tackled a de novo assembly of the genome of D. subobscura using PacBio long-read technology. Raw PacBio reads were assembled using the Canu assembler. A semi-automated pipeline for assessing the quality of the contigs and scaffolding the genome has been developed that combined both synteny information from previously assembled genomes of D. melanogaster and D. pseudoobscura, and published data from 560 genetic markers derived from in situ hybridization experiments and genetic linkage analyses. Canu assembled contigs were then scaffolded resulting in 186 scaffolds with a N50 of approximately 6Mb. Chromosomal assignment, ordering and orientation of the scaffolds resulted in six pseudochromosomes, one for each of the six D. subobscura chromosomes. A total of 13,939 protein-coding genes were predicted, and 13% of the species genome was found to consist of repetitive sequences. Finally, the amounts of genome rearrangement between D. subobscura, D. guanche, D. melanogaster and D. pseudoobscura was assessed. The breakpoints of the fixed inversions between D. subobscura and D. guanche were determined and characterized. Here we illustrate that genome structure evolution in D. subobscura is driven indirectly, through the inversions' recombination-suppression effects in maintaining sets of adaptive alleles together in the face of gene flow.
Presently, D. subobscura is experiencing a rapid replacement of high-latitude by low-latitude inversions associated with global warming. However, not all low-latitude inversions are correlated with the secular warming trend. The mixed behavior of O7 inversion across components of the ambient temperature suggests that it is driven by selective factors other than temperature alone. Research into this question has been hindered by lacking knowledge of the genomic breakpoint sequences of the inversion. To tackle this limitation, we generated a PacBio long read-based chromosome-scale genome assembly, from an O3+4+7 isogenic line. The complete continuous sequence of O7 was isolated using synteny analysis with the reference genome. Inversion O7 was shown to stretch 9.936 Mb, containing over 1,000 annotated genes. We illustrate that inversion O7 had a complex origin, involving multiple breaks associated with non-B DNA motifs, formation of a microinversion, and ectopic repair in trans with the two homologous chromosomes. Our findings support that inversion O7 breakpoints carry a pre-inversion record of fragility, including a sequence insertion, and transposition with later inverted duplication of an Attacin immunity gene. The O7 inversion was found to have relocated the major insulin signaling forkhead box subgroup O (foxo) gene bringing it in tight linkage with its antagonistic regulatory partner serine/threonine-protein kinase B (Akt1). Further, its distal breakpoint disrupted concerted evolution of the two inverted Attacin duplicates, reattaching them to dFOXO metabolic enhancers. We suggest that O7 exerts antagonistic pleiotropic effects on reproduction and immunity, setting a framework to understand its relationship with climate change. Our findings have general implications for current theories on the molecular mechanisms of formation of inversions and the contribution of breakage versus repair in shaping inversion-breakpoint junctions.
