| 1. |
- Hillier, Ladeana W, et al.
(författare)
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
- 2004
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 432:7018, s. 695-716
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Tidskriftsartikel (refereegranskat)abstract
- We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
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| 2. |
- Mikkelsen, Tarjei, et al.
(författare)
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Initial sequence of the chimpanzee genome and comparison with the human genome
- 2005
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 437:7055, s. 69-87
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Tidskriftsartikel (refereegranskat)abstract
- Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.
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| 3. |
- Tomaszkiewicz, Marta, et al.
(författare)
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Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes
- 2023
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Ingår i: Genome Biology and Evolution. - 1759-6653. ; 15:11
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Tidskriftsartikel (refereegranskat)abstract
- Y chromosomal ampliconic genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and expression levels of these multicopy gene families has been studied in great apes; however, the diversity of splicing variants remains unexplored. Here, we deciphered the sequences of polyadenylated transcripts of all nine YAG families (BPY2, CDY, DAZ, HSFY, PRY, RBMY, TSPY, VCY, and XKRY) from testis samples of six great ape species (human, chimpanzee, bonobo, gorilla, Bornean orangutan, and Sumatran orangutan). To achieve this, we enriched YAG transcripts with capture probe hybridization and sequenced them with long (Pacific Biosciences) reads. Our analysis of this data set resulted in several findings. First, we observed evolutionarily conserved alternative splicing patterns for most YAG families except for BPY2 and PRY. Second, our results suggest that BPY2 transcripts and proteins originate from separate genomic regions in bonobo versus human, which is possibly facilitated by acquiring new promoters. Third, our analysis indicates that the PRY gene family, having the highest representation of noncoding transcripts, has been undergoing pseudogenization. Fourth, we have not detected signatures of selection in the five YAG families shared among great apes, even though we identified many species-specific protein-coding transcripts. Fifth, we predicted consensus disorder regions across most gene families and species, which could be used for future investigations of male infertility. Overall, our work illuminates the YAG isoform landscape and provides a genomic resource for future functional studies focusing on infertility phenotypes in humans and critically endangered great apes.
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| 4. |
- Weissensteiner, Matthias H.
(författare)
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Evolutionary genomics in Corvids : – From single nucleotides to structural variants
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Heritable genetic variation is the raw material of evolution and can occur in many different forms, from altering single nucleotides to rearranging stretches of millions at once. DNA mutations that result in phenotypic differences are the basis upon which natural selection can act, leading to a shift of the frequency of those mutations.In this thesis I aim to comprehensively characterize and quantify genetic variation in a natural system, the songbird genus Corvus. First, we expand on previous work from a hybrid zone of different populations of Eurasian crows. All black carrion crows and black-and-grey hooded crows meet in a narrow hybrid zone in central Europe, and also in central and Southeast Asia. Comparing population genetic data acquired from these three hybrid zones yielded no single genetic region as a candidate responsible for phenotypic divergence, yet a parallelism in sets of genes and gene networks was evident.Second, we capitalize on varying evolutionary timescales to investigate the driver of the heterogeneous genetic differentiation landscape observed in multiple avian species. Genetic diversity, and thus differentiation, seems to be correlated both between populations within single species and between species which diverged 50 million years ago. This pattern is best explained by conserved broad-scale recombination rate variation, which is in turn likely associated with chromosomal features such as centromeres and telomeres.Third, we introduce a de-novo assembly of the hooded crow based on long-read sequencing and optical mapping. The use of this technology allowed a glimpse into previously hidden regions of the genome, and uncovered large-scale tandem repeat arrays consisting of a 14-kbp satellite repeat or its 1.2-kpb subunit. Furthermore, these tandem repeat arrays are associated with regions of reduced recombination rate.Lastly, we extend the population genetic analysis to structural genomic variation, such as insertions and deletions. A large-scale population re-sequencing data set based on short-read and long-read technologies, spread across the entire genus is the foundation of a fine-scale genome-wide map of structural variation. A differentiation outlier approach between all-black carrion and black-and-grey hooded crows identified a 2.25-kilobase LTR retrotransposon inserted 20-kb upstream of the NDP gene. The element, which is fixed in the hooded crow population, is associated with decreased expression of NDP and may be responsible for differences in plumage color.
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