| 1. |
- Bensch, Staffan, et al.
(author)
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The genome of Haemoproteus tartakovskyi and its relationship to human malaria parasites
- 2016
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In: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 8:5, s. 73-1361
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Journal article (peer-reviewed)abstract
- The phylogenetic relationships among hemosporidian parasites, including the origin of Plasmodium falciparum, the most virulent malaria parasite of humans, have been heavily debated for decades. Studies based on multiple-gene sequences have helped settle many of these controversial phylogenetic issues. However, denser taxon sampling and genome-wide analyses are needed to confidently resolve the evolutionay relationships among hemosporidian parasites. Genome sequences of several Plasmodium parasites are available but only for species infecting primates and rodents. To root the phylogenetic tree of Plasmodium, genomic data from related parasites of birds or reptiles are required. Here, we use a novel approach to isolate parasite DNA from microgametes and describe the first genome of a bird parasite in the sister genus to Plasmodium, Haemoproteus tartakovskyi Similar to Plasmodium parasites, H. tartakovskyi has a small genome (23.2 Mb, 5,990 genes) and a GC content (25.4%) closer to P. falciparum (19.3%) than to Plasmodium vivax (42.3%). Combined with novel transcriptome sequences of the bird parasite Plasmodium ashfordi, our phylogenomic analyses of 1,302 orthologous genes demonstrate that mammalian-infecting malaria parasites are monophyletic, thus rejecting the repeatedly proposed hypothesis that the ancestor of Laverania parasites originated from a secondary host shift from birds to humans. Genes and genomic features previously found to be shared between P. falciparum and bird malaria parasites, but absent in other mammal malaria parasites, are therefore signatures of maintained ancestral states. We foresee that the genome of H. tartakovskyi will open new directions for comparative evolutionary analyses of malarial adaptive traits.
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| 2. |
- Brylka, Karolina, et al.
(author)
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Gene Duplication, Shifting Selection, and Dosage Balance of Silicon Transporter Proteins in Marine and Freshwater Diatoms
- 2023
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In: Genome Biology and Evolution. - 1759-6653. ; 15:12
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Journal article (peer-reviewed)abstract
- Numerous factors shape the evolution of protein-coding genes, including shifts in the strength or type of selection followinggene duplications or changes in the environment. Diatoms and other silicifying organisms use a family of silicon transporters(SITs) to import dissolved silicon from the environment. Freshwaters contain higher silicon levels than oceans, and marinediatoms have more efficient uptake kinetics and less silicon in their cell walls, making them better competitors for a scarceresource. We compiled SITs from 37 diatom genomes to characterize shifts in selection following gene duplications and marine–freshwater transitions. A deep gene duplication, which coincided with a whole-genome duplication, gave rise to twogene lineages. One of them (SIT1–2) is present in multiple copies in most species and is known to actively import silicon.These SITs have evolved under strong purifying selection that was relaxed in freshwater taxa. Episodic diversifying selectionwas detected but not associated with gene duplications or habitat shifts. In contrast, genes in the second SIT lineage (SIT3)were present in just half the species, the result of multiple losses. Despite conservation of SIT3 in some lineages for the past90–100 million years, repeated losses, relaxed selection, and low expression highlighted the dispensability of SIT3, consistentwith a model of deterioration and eventual loss due to relaxed selection on SIT3 expression. The extensive but relatively balancedhistory of duplications and losses, together with paralog-specific expression patterns, suggest diatoms continuouslybalance gene dosage and expression dynamics to optimize silicon transport across major environmental gradients.
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| 3. |
- Cīrulis, Aivars, et al.
(author)
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Sex-limited experimental evolution drives transcriptomic divergence in a hermaphrodite
- 2024
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In: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 16:1
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Journal article (peer-reviewed)abstract
- The evolution of gonochorism from hermaphroditism is linked with the formation of sex chromosomes, as well as the evolution of sex-biased and sex-specific gene expression to allow both sexes to reach their fitness optimum. There is evidence that sexual selection drives the evolution of male-biased gene expression in particular. However, previous research in this area in animals comes from either theoretical models or comparative studies of already old sex chromosomes. We therefore investigated changes in gene expression under 3 different selection regimes for the simultaneous hermaphrodite Macrostomum lignano subjected to sex-limited experimental evolution (i.e. selection for fitness via eggs, sperm, or a control regime allowing both). After 21 and 22 generations of selection for male-specific or female-specific fitness, we characterized changes in whole-organism gene expression. We found that female-selected lines had changed the most in their gene expression. Although annotation for this species is limited, gene ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analyses suggest that metabolic changes (e.g. biosynthesis of amino acids and carbon metabolism) are an important adaptive component. As predicted, we found that the expression of genes previously identified as testis-biased candidates tended to be downregulated in the female-selected lines. We did not find any significant expression differences for previously identified candidates of other sex-specific organs, but this may simply reflect that few transcripts have been characterized in this way. In conclusion, our experiment suggests that changes in testis-biased gene expression are important in the early evolution of sex chromosomes and gonochorism.
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| 4. |
- Dyrhage, Karl, et al.
(author)
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Genome Evolution of a Symbiont Population for Pathogen Defense in Honeybees
- 2022
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In: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 14:11
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Journal article (peer-reviewed)abstract
- The honeybee gut microbiome is thought to be important for bee health, but the role of the individual members is poorly understood. Here, we present closed genomes and associated mobilomes of 102 Apilactobacillus kunkeei isolates obtained from the honey crop (foregut) of honeybees sampled from beehives in Helsingborg in the south of Sweden and from the islands Gotland and angstrom land in the Baltic Sea. Each beehive contained a unique composition of isolates and repeated sampling of similar isolates from two beehives in Helsingborg suggests that the bacterial community is stably maintained across bee generations during the summer months. The sampled bacterial population contained an open pan-genome structure with a high genomic density of transposons. A subset of strains affiliated with phylogroup A inhibited growth of the bee pathogen Melissococcus plutonius, all of which contained a 19.5 kb plasmid for the synthesis of the antimicrobial compound kunkecin A, while a subset of phylogroups B and C strains contained a 32.9 kb plasmid for the synthesis of a putative polyketide antibiotic. This study suggests that the mobile gene pool of A. kunkeei plays a key role in pathogen defense in honeybees, providing new insights into the evolutionary dynamics of defensive symbiont populations.
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| 5. |
- Feiner, Nathalie, et al.
(author)
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Saltatory Evolution of the Ectodermal Neural Cortex Gene Family at the Vertebrate Origin
- 2013
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In: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 5:8, s. 1485-1502
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Journal article (peer-reviewed)abstract
- The ectodermal neural cortex (ENC) gene family, whose members are implicated in neurogenesis, is part of the kelch repeat superfamily. To date, ENC genes have been identified only in osteichthyans, although other kelch repeat-containing genes are prevalent throughout bilaterians. The lack of elaborate molecular phylogenetic analysis with exhaustive taxon sampling has obscured the possible link of the establishment of this gene family with vertebrate novelties. In this study, we identified ENC homologs in diverse vertebrates by means of databasemining and polymerase chain reaction screens. Our analysis revealed that the ENC3 ortholog was lost in the basal eutherian lineage through single-gene deletion and that the triplication between ENC1, -2, and -3 occurred early in vertebrate evolution. Including our original data on the catshark and the zebrafish, our comparison revealed high conservation of thepleiotropic expression pattern of ENC1 and shuffling of expression domains between ENC1, -2, and -3. Compared withmany other gene families including developmental key regulators, the ENC gene family is unique in that conventional molecular phylogenetic inference could identifynoobvious invertebrateortholog. This suggests a composite nature of the vertebrate-specificgene repertoire, consistingnot onlyofdenovogenes introducedat thevertebrateorigin but alsoof long-standinggenes withnoapparent invertebrateorthologs. Some of the latter, including the ENC gene family, may be too rapidly evolving to provide sufficient phylogenetic signals marking orthology to their invertebrate counterparts. Such gene families that experienced saltatory evolution likely remain to be explored and might also have contributed to phenotypic evolution of vertebrates.
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| 6. |
- Gounot, Jean Sébastien, et al.
(author)
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High Complexity and Degree of Genetic Variation in Brettanomyces bruxellensis Population
- 2020
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In: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 12:6, s. 795-807
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Journal article (peer-reviewed)abstract
- Genome-wide characterization of genetic variants of a large population of individuals within the same species is essential to have a deeper insight into its evolutionary history as well as the genotype-phenotype relationship. Population genomic surveys have been performed in multiple yeast species, including the two model organisms, Saccharomyces cerevisiae and Schizosaccharomyces pombe. In this context, we sought to characterize at the population level the Brettanomyces bruxellensis yeast species, which is a major cause of wine spoilage and can contribute to the specific flavor profile of some Belgium beers. We have completely sequenced the genome of 53 B. bruxellensis strains isolated worldwide. The annotation of the reference genome allowed us to define the gene content of this species. As previously suggested, our genomic data clearly highlighted that genetic diversity variation is related to ploidy level, which is variable in the B. bruxellensis species. Genomes are punctuated by multiple loss-of-heterozygosity regions, whereas aneuploidies as well as segmental duplications are uncommon. Interestingly, triploid genomes are more prone to gene copy number variation than diploids. Finally, the pangenome of the species was reconstructed and was found to be small with few accessory genes compared with S. cerevisiae. The pangenome is composed of 5,409 ORFs (open reading frames) among which 5,106 core ORFs and 303 ORFs that are variable within the population. All these results highlight the different trajectories of species evolution and consequently the interest of establishing population genomic surveys in more populations.
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| 7. |
- Harish, Ajith, et al.
(author)
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Did Viruses Evolve As a Distinct Supergroup from Common Ancestors of Cells?
- 2016
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In: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 8:8, s. 2474-2481
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Journal article (peer-reviewed)abstract
- The evolutionary origins of viruses according to marker gene phylogenies, as well as their relationships to the ancestors of host cells remains unclear. In a recent article Nasir and Caetano-Anolles reported that their genome-scale phylogenetic analyses based on genomic composition of protein structural-domains identify an ancient origin of the "viral supergroup" (Nasir et al. 2015. A phylogenomic data-driven exploration of viral origins and evolution. Sci Adv. 1(8):e1500527.). It suggests that viruses and host cells evolved independently from a universal common ancestor. Examination of their data and phylogenetic methods indicates that systematic errors likely affected the results. Reanalysis of the data with additional tests shows that small-genome attraction artifacts distort their phylogenomic analyses, particularly the location of the root of the phylogenetic tree of life that is central to their conclusions. These new results indicate that their suggestion of a distinct ancestry of the viral supergroup is not well supported by the evidence.
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| 8. |
- Khademi, S. M.Hossein, et al.
(author)
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Within-Host Adaptation Mediated by Intergenic Evolution in Pseudomonas aeruginosa
- 2019
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In: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 11:5, s. 1385-1397
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Journal article (peer-reviewed)abstract
- Bacterial pathogens evolve during the course of infection as they adapt to the selective pressures that confront them inside the host. Identification of adaptive mutations and their contributions to pathogen fitness remains a central challenge. Although mutations can either target intergenic or coding regions in the pathogen genome, studies of host adaptation have focused predominantly on molecular evolution within coding regions, whereas the role of intergenic mutations remains unclear. Here, we address this issue and investigate the extent to which intergenic mutations contribute to the evolutionary response of a clinically important bacterial pathogen, Pseudomonas aeruginosa, to the host environment, and whether intergenic mutations have distinct roles in host adaptation. We characterize intergenic evolution in 44 clonal lineages of P. aeruginosa and identify 77 intergenic regions in which parallel evolution occurs. At the genetic level, we find that mutations in regions under selection are located primarily within regulatory elements upstream of transcriptional start sites. At the functional level, we show that some of these mutations both increase or decrease transcription of genes and are directly responsible for evolution of important pathogenic phenotypes including antibiotic sensitivity. Importantly, we find that intergenic mutations facilitate essential genes to become targets of evolution. In summary, our results highlight the evolutionary significance of intergenic mutations in creating host-adapted strains, and that intergenic and coding regions have different qualitative contributions to this process.
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| 9. |
- Laine, Veronika N., et al.
(author)
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Whole-genome Analysis Reveals Contrasting Relationships Among Nuclear and Mitochondrial Genomes Between Three Sympatric Bat Species
- 2023
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In: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 15:1
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Journal article (peer-reviewed)abstract
- Understanding mechanisms involved in speciation can be challenging, especially when hybridization or introgression blurs species boundaries. In bats, resolving relationships of some closely related groups has proved difficult due subtle interspecific variation both in morphometrics and molecular data sets. The endemic South American Histiotus bats, currently considered a subgenus of Eptesicus, harbor unresolved phylogenetic relationships and of those is a trio consisting of two closely related species: Eptesicus (Histiotus) macrotus and Eptesicus (Histiotus) montanus, and their relationship with a third, Eptesicus (Histiotus) magellanicus. The three sympatric species bear marked resemblance to each other, but can be differentiated morphologically. Furthermore, previous studies have been unable to differentiate the species from each other at a molecular level. In order to disentangle the phylogenetic relationships of these species, we examined the differentiation patterns and evolutionary history of the three Eptesicus (H.) species at the whole-genome level. The nuclear DNA statistics between the species suggest strong gene flow and recent hybridization between E. (H.) montanus and E. (H.) macrotus, whereas E. (H.) magellanicus shows a higher degree of isolation. In contrast, mitochondrial DNA shows a closer relationship between E. (H.) magellanicus and E. (H.) montanus. Opposing patterns in mtDNA and nuclear markers are often due to differences in dispersal, and here it could be both as a result of isolation in refugia during the last glacial maximum and female philopatry and male-biased dispersal. In conclusion, this study shows the importance of both the nuclear and mitochondrial DNA in resolving phylogenetic relationships and species histories.
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| 10. |
- Linde, Anna-Malin, et al.
(author)
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Genome Evolution in Plants: Complex Thalloid Liverworts (Marchantiopsida)
- 2023
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In: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 15:3
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Journal article (peer-reviewed)abstract
- Why do some genomes stay small and simple, while others become huge, and why are some genomes more stable? In contrast to angiosperms and gymnosperms, liverworts are characterized by small genomes with low variation in size and conserved chromosome numbers. We quantified genome evolution among five Marchantiophyta (liverworts), measuring gene characteristics, transposable element (TE) landscape, collinearity, and sex chromosome evolution that might explain the small size and limited variability of liverwort genomes. No genome duplications were identified among examined liverworts and levels of duplicated genes are low. Among the liverwort species, Lunularia cruciata stands out with a genome size almost twice that of the other liverwort species investigated here, and most of this increased size is due to bursts of Ty3/Gypsy retrotransposons. Intrachromosomal rearrangements between examined liverworts are abundant but occur at a slower rate compared with angiosperms. Most genes on L. cruciata scaffolds have their orthologs on homologous Marchantia polymorpha chromosomes, indicating a low degree of rearrangements between chromosomes. Still, translocation of a fragment of the female U chromosome to an autosome was predicted from our data, which might explain the uniquely small U chromosome in L. cruciata. Low levels of gene duplication, TE activity, and chromosomal rearrangements might contribute to the apparent slow rate of morphological evolution in liverworts.
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