| 1. |
- Peona, Valentina, et al.
(författare)
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Satellite DNA evolution in Corvides inferred from short and long reads
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Satellite DNA (satDNA) is a fast-evolving portion of eukaryotic genomes. The homogeneous and repetitive nature of such satellitomes causes problems during the assembly of genomes, and therefore it is still difficult to study satDNA in detail in non-model organisms as well as across broad evolutionary timescales. Here, we combined the use of short-read and long-read data to explore the diversity and evolution of satDNA between individuals of the same species and between genera of birds spanning ~40 millions of years of bird evolution using birds-of-paradise and Corvus species. These avian species highlighted the presence of a GC-rich Corvides satellitome composed of 61 satellite families and provided a set of candidates satDNA monomers for being centromeric on the basis of length, abundance, homogeneity and transcription. Surprisingly, we found that the satellitome of Corvus spp. rapidly diverged between closely related species while the satellitome appeared more similar between birds-of-paradise species belonging to different genera.
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| 2. |
- Peona, Valentina, 1990-
(författare)
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The exploration and evolution of the avian genomic dark matter
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The development and improvement of genome sequencing technologies in the last decade revolutionised the entire field of biology with genome assemblies of virtually any organism. Despite this tremendous progress, complex genomic regions are systematically missing from genome assemblies and form the so-called "genomic dark matter". The presence of genomic dark matter entails that such regions cannot be fully studied and the effects and/or functions thereof (if any) on the organisms remain hidden. Therefore, it is key to be able to explore those dark genomic corners to fully understand the evolution and physiology of organisms without biasing the interpretations. In this thesis, I contribute to the understanding of the use of new sequencing technologies to assemble complex genomic regions and to investigate the evolution of such regions throughout the avian phylogeny. First, I assessed the best combination of technologies and assembly methods to maximise the resolution of genomic dark matter using genomic data from the paradise crow. This included testing for the presence of repetitive elements, GC-rich regions, G-quadruplex motifs, non-recombining sex chromosomes, and microchromosomes. Then, the high-quality assemblies for the paradise crow and other birds allowed the discovery that the avian W chromosome features more than half of potentially active transposable elements (TEs), especially endogenous retroviruses, of the genome. This characteristic makes the W chromosome potentially "toxic" for females. The female-biased accumulation of active TEs could also play a role in the origin of genetic incompatibilities and be an explanatory variable for Haldane’s rule in birds. Next, I investigated the genetic variability of birds-of-paradise chromosomes originating from structural rearrangements with a special focus on the W chromosome. The analysis revealed more genetic variability than previously reported suggesting that all sources of genetic variability should be considered to understand the evolution of sex-limited chromosomes. Finally, I explored the evolution of another main component of avian genomic dark matter, satellite DNA, throughout the phylogeny of birds-of-paradise and closely related crow species. I found that the avian satellitome evolves in different modes in the two groups and a more comprehensive species sampling is necessary to establish which evolutionary mode is the most prevalent in birds. Altogether, the results of this thesis provide a case study for how to investigate the most complex genomic regions, highlight their possible evolutionary roles, and therefore showcase the necessity for the field to shed light into the dark corners of genomes. Mind the gap!
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| 3. |
- Peona, Valentina, et al.
(författare)
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The hidden structural variability in avian genomes
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Structural variants (SVs) are DNA mutations that can have relevant effects at the micro- and macro-evolutionary scales. The detection of SVs is largely limited by the type and quality of sequencing technologies adopted, therefore genetic variability linked to SVs may remain undiscovered especially in complex repetitive regions. In this study, we used a combination of long-read and linked-read genome assemblies to explore the occurrence of insertions and deletions across the chromosomes of 14 species birds-of-paradise and two species of estrildid finches. The species sampling encompasses all genera of birds-of-paradise, allowing comparisons between individuals of the same species, genus, and family. Interestingly, we found the highest densities of SVs to be located on the microchromosomes and on the female-specific W chromosome. Genome assemblies of multiple individuals from the same species allowed us to compare the levels of genetic variability linked to SVs and single nucleotide polymorphisms (SNPs) on the W and other chromosomes. Our results demonstrate that the avian W chromosome harbours more genetic variability than previously thought and that its structure is shaped by the continuous accumulation and turnover of transposable element insertions, especially endogenous retroviruses.
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| 4. |
- Segami, Carolina, et al.
(författare)
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Rapid GRC-linked gene expression divergence in Ficedula flycatchers and implications for spermatogenesis
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Since the discovery of the maternally inherited Germline Restricted Chromosome (GRC) in the songbird clade, the function of this chromosome has been highly debated. Whether it is a parasitic element or has an essential adaptive role needs to be unveiled. Here, we use a combination of linked reads DNA sequencing and single cell RNA sequencing to examine the gene content of the GRC in pied and collared flycatchers and the expression pattern of these genes during spermatogenesis. We found 157 paralogs on the GRC of which only 46 were shared between the two species. We also found that the identities of the genes that were expressed during spermatogenesis differed between these species. We found important genes for meiosis, germline maintenance and sex-determination. These finding suggest a possible essential role of the GRC during spermatogenesis. This evidence together with the rapid gene content and gene expression evolution suggests that GRCs could also contribute to the appearance of genetic incompatibilities between closely related species.
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