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Publications (10 of 21) Show all publications
Arnqvist, G., Westerberg, I., Galbraith, J., Sayadi, A., Scofield, D. G., Olsen, R.-A., . . . Suh, A. (2024). A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements. G3: Genes, Genomes, Genetics, 14(2), Article ID jkad266.
Open this publication in new window or tab >>A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements
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2024 (English)In: G3: Genes, Genomes, Genetics, E-ISSN 2160-1836, Vol. 14, no 2, article id jkad266Article in journal (Refereed) Published
Abstract [en]

Callosobruchus maculatus is a major agricultural pest of legume crops worldwide and an established model system in ecology and evolution. Yet, current molecular biological resources for this species are limited. Here, we employ Hi-C sequencing to generate a greatly improved genome assembly and we annotate its repetitive elements in a dedicated in-depth effort where we manually curate and classify the most abundant unclassified repeat subfamilies. We present a scaffolded chromosome-level assembly, which is 1.01 Gb in total length with 86% being contained within the 9 autosomes and the X chromosome. Repetitive sequences accounted for 70% of the total assembly. DNA transposons covered 18% of the genome, with the most abundant superfamily being Tc1-Mariner (9.75% of the genome). This new chromosome-level genome assembly of C. maculatus will enable future genetic and evolutionary studies not only of this important species but of beetles more generally. 

Keywords
Chrysomelidae, chromosome conformation capture, X chromosome assembly, transposable elements, Tc1-Mariner
National Category
Genetics
Identifiers
urn:nbn:se:su:diva-225411 (URN)10.1093/g3journal/jkad266 (DOI)001123598000001 ()38092066 (PubMedID)2-s2.0-85184664621 (Scopus ID)
Available from: 2024-01-16 Created: 2024-01-16 Last updated: 2024-02-21Bibliographically approved
Höglund, J., Dias, G., Olsen, R.-A., Soares, A., Bunikis, I., Talla, V. & Backström, N. (2024). A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern. Genome Biology and Evolution, 16(2), Article ID evae031.
Open this publication in new window or tab >>A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern
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2024 (English)In: Genome Biology and Evolution, E-ISSN 1759-6653, Vol. 16, no 2, article id evae031Article in journal (Refereed) Published
Abstract [en]

The clouded apollo (Parnassius mnemosyne) is a palearctic butterfly distributed over a large part of western Eurasia, but population declines and fragmentation have been observed in many parts of the range. The development of genomic tools can help to shed light on the genetic consequences of the decline and to make informed decisions about direct conservation actions. Here, we present a high-contiguity, chromosome-level genome assembly of a female clouded apollo butterfly and provide detailed annotations of genes and transposable elements. We find that the large genome (1.5 Gb) of the clouded apollo is extraordinarily repeat rich (73%). Despite that, the combination of sequencing techniques allowed us to assemble all chromosomes (nc = 29) to a high degree of completeness. The annotation resulted in a relatively high number of protein-coding genes (22,854) compared with other Lepidoptera, of which a large proportion (21,635) could be assigned functions based on homology with other species. A comparative analysis indicates that overall genome structure has been largely conserved, both within the genus and compared with the ancestral lepidopteran karyotype. The high-quality genome assembly and detailed annotation presented here will constitute an important tool for forthcoming efforts aimed at understanding the genetic consequences of fragmentation and decline, as well as for assessments of genetic diversity, population structure, inbreeding, and genetic load in the clouded apollo butterfly.

Keywords
Parnassius mnemosyne, clouded apollo butterfly, genome assembly, gene annotation, repeat annotation, genome size
National Category
Genetics
Identifiers
urn:nbn:se:su:diva-228186 (URN)10.1093/gbe/evae031 (DOI)001177618400001 ()38368625 (PubMedID)2-s2.0-85186489278 (Scopus ID)
Available from: 2024-04-10 Created: 2024-04-10 Last updated: 2024-07-04Bibliographically approved
Llinàs-Arias, P., Ensenyat-Méndez, M., Orozco, J. I. J., Íñiguez-Muñoz, S., Valdez, B., Wang, C., . . . Marzese, D. M. (2023). 3-D chromatin conformation, accessibility, and gene expression profiling of triple-negative breast cancer. BMC Genomic Data, 24(1), Article ID 61.
Open this publication in new window or tab >>3-D chromatin conformation, accessibility, and gene expression profiling of triple-negative breast cancer
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2023 (English)In: BMC Genomic Data, ISSN 2730-6844, Vol. 24, no 1, article id 61Article in journal (Refereed) Published
Abstract [en]

Objectives Triple-negative breast cancer (TNBC) is a highly aggressive breast cancer subtype with limited treatment options. Unlike other breast cancer subtypes, the scarcity of specific therapies and greater frequencies of distant metastases contribute to its aggressiveness. We aimed to find epigenetic changes that aid in the understanding of the dissemination process of these cancers.

Data description Using CRISPR/Cas9, our experimental approach led us to identify and disrupt an insulator element, IE8, whose activity seemed relevant for cell invasion. The experiments were performed in two well-established TNBC cellular models, the MDA-MB-231 and the MDA-MB-436. To gain insights into the underlying molecular mechanisms of TNBC invasion ability, we generated and characterized high-resolution chromatin interaction (Hi-C) and chromatin accessibility (ATAC-seq) maps in both cell models and complemented these datasets with gene expression profiling (RNA-seq) in MDA-MB-231, the cell line that showed more significant changes in chromatin accessibility. Altogether, our data provide a comprehensive resource for understanding the spatial organization of the genome in TNBC cells, which may contribute to accelerating the discovery of TNBC-specific alterations triggering advances for this devastating disease.

Keywords
Epigenetic profiling, Chromatin accessibility, Long-range interactions, RNA levels, ATAC-seq, Hi-C, RNA-seq, MDA-MB-436, MDA-MB-231
National Category
Cancer and Oncology Cell and Molecular Biology
Identifiers
urn:nbn:se:su:diva-223863 (URN)10.1186/s12863-023-01166-x (DOI)001092189200001 ()37919672 (PubMedID)2-s2.0-85175719906 (Scopus ID)
Available from: 2023-11-22 Created: 2023-11-22 Last updated: 2023-11-22Bibliographically approved
Peona, V., Palacios-Gimenez, O. M., Lutgen, D., Olsen, R. A., Kakhki, N. A., Andriopoulos, P., . . . Burri, R. (2023). An annotated chromosome-scale reference genome for Eastern black-eared wheatear (Oenanthe melanoleuca). G3: Genes, Genomes, Genetics, 13(6), Article ID jkad088.
Open this publication in new window or tab >>An annotated chromosome-scale reference genome for Eastern black-eared wheatear (Oenanthe melanoleuca)
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2023 (English)In: G3: Genes, Genomes, Genetics, E-ISSN 2160-1836, Vol. 13, no 6, article id jkad088Article in journal (Refereed) Published
Abstract [en]

Pervasive convergent evolution and in part high incidences of hybridization distinguish wheatears (songbirds of the genus Oenanthe) as a versatile system to address questions at the forefront of research on the molecular bases of phenotypic and species diversification. To prepare the genomic resources for this venture, we here generated and annotated a chromosome-scale assembly of the Eastern black-eared wheatear (Oenanthe melanoleuca). This species is part of the Oenanthe hispanica complex that is characterized by convergent evolution of plumage coloration and high rates of hybridization. The long-read-based male nuclear genome assembly comprises 1.04 Gb in 32 autosomes, the Z chromosome, and the mitogenome. The assembly is highly contiguous (contig N50, 12.6 Mb; scaffold N50, 70 Mb), with 96% of the genome assembled at the chromosome level and 95.5% benchmarking universal single-copy orthologs (BUSCO) completeness. The nuclear genome was annotated with 18,143 protein-coding genes and 31,333 mRNAs (annotation BUSCO completeness, 98.0%), and about 10% of the genome consists of repetitive DNA. The annotated chromosome-scale reference genome of Eastern black-eared wheatear provides a crucial resource for research into the genomics of adaptation and speciation in an intriguing group of passerines.

Keywords
birds, open-habitat chats, Oenanthe melanoleuca, Oenanthe hispanica complex, transcriptome, repeat content, transposable elements
National Category
Genetics
Identifiers
urn:nbn:se:su:diva-218034 (URN)10.1093/g3journal/jkad088 (DOI)000983146000001 ()37097035 (PubMedID)2-s2.0-85164440594 (Scopus ID)
Available from: 2023-07-26 Created: 2023-07-26 Last updated: 2024-01-17Bibliographically approved
Dussex, N., Kurland, S., Olsen, R.-A., Spong, G., Ericsson, G., Ekblom, R., . . . Laikre, L. (2023). Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose. Communications Biology, 6(1), Article ID 1035.
Open this publication in new window or tab >>Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose
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2023 (English)In: Communications Biology, E-ISSN 2399-3642, Vol. 6, no 1, article id 1035Article in journal (Refereed) Published
Abstract [en]

Ungulate species have experienced severe declines over the past centuries through overharvesting and habitat loss. Even if many game species have recovered thanks to strict hunting regulation, the genome-wide impacts of overharvesting are still unclear. Here, we examine the temporal and geographical differences in genome-wide diversity in moose (Alces alces) over its whole range in Sweden by sequencing 87 modern and historical genomes. We found limited impact of the 1900s near-extinction event but local variation in inbreeding and load in modern populations, as well as suggestion of a risk of future reduction in genetic diversity and gene flow. Furthermore, we found candidate genes for local adaptation, and rapid temporal allele frequency shifts involving coding genes since the 1980s, possibly due to selective harvesting. Our results highlight that genomic changes potentially impacting fitness can occur over short time scales and underline the need to track both deleterious and selectively advantageous genomic variation.

National Category
Genetics Ecology
Identifiers
urn:nbn:se:su:diva-224297 (URN)10.1038/s42003-023-05385-x (DOI)001097463800001 ()37848497 (PubMedID)2-s2.0-85174459749 (Scopus ID)
Available from: 2023-12-07 Created: 2023-12-07 Last updated: 2023-12-07Bibliographically approved
Le Duc, D., Velluva, A., Cassatt-Johnstone, M., Olsen, R.-A., Baleka, S., Lin, C.-C., . . . Schöneberg, T. (2022). Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow. Science Advances, 8(5), Article ID eabl6496.
Open this publication in new window or tab >>Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow
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2022 (English)In: Science Advances, E-ISSN 2375-2548, Vol. 8, no 5, article id eabl6496Article in journal (Refereed) Published
Abstract [en]

Steller's sea cow, an extinct sirenian and one of the largest Quaternary mammals, was described by Georg Steller in 1741 and eradicated by humans within 27 years. Here, we complement Steller's descriptions with paleogenomic data from 12 individuals. We identified convergent evolution between Steller's sea cow and cetaceans but not extant sirenians, suggesting a role of several genes in adaptation to cold aquatic (or marine) environments. Among these are inactivations of lipoxygenase genes, which in humans and mouse models cause ichthyosis, a skin disease characterized by a thick, hyperkeratotic epidermis that recapitulates Steller's sea cows' reportedly bark-like skin. We also found that Steller's sea cows' abundance was continuously declining for tens of thousands of years before their description, implying that environmental changes also contributed to their extinction. 

Keywords
Mammals, Aquatic environments, Convergent evolution, Environmental change, Genomics, Human modelling, Lipoxygenases, Marine environment, Mice models, Skin disease, Genes, animal, bovine, Dugong, female, mammal, mouse, phenotype, Animals, Cattle, Mice
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-206281 (URN)10.1126/sciadv.abl6496 (DOI)000799992000012 ()35119923 (PubMedID)2-s2.0-85124159826 (Scopus ID)
Available from: 2022-07-04 Created: 2022-07-04 Last updated: 2022-09-26Bibliographically approved
von Seth, J., van der Valk, T., Lord, E., Sigeman, H., Olsen, R.-A., Knapp, M., . . . Dussex, N. (2022). Genomic trajectories of a near-extinction event in the Chatham Island black robin. BMC Genomics, 23, Article ID 747.
Open this publication in new window or tab >>Genomic trajectories of a near-extinction event in the Chatham Island black robin
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2022 (English)In: BMC Genomics, E-ISSN 1471-2164, Vol. 23, article id 747Article in journal (Refereed) Published
Abstract [en]

Background: Understanding the micro-­evolutionary response of populations to demographic declines is a major goal in evolutionary and conservation biology. In small populations, genetic drift can lead to an accumulation of deleterious mutations, which will increase the risk of extinction. However, demographic recovery can still occur after extreme declines, suggesting that natural selection may purge deleterious mutations, even in extremely small populations. The Chatham Island black robin (Petroica traversi) is arguably the most inbred bird species in the world. It avoided imminent extinction in the early 1980s and after a remarkable recovery from a single pair, a second population was established and the two extant populations have evolved in complete isolation since then. Here, we analysed 52 modern and historical genomes to examine the genomic consequences of this extreme bottleneck and the subsequent translocation.

Results: We found evidence for two-fold decline in heterozygosity and three- to four-fold increase in inbreeding in modern genomes. Moreover, there was partial support for temporal reduction in total load for detrimental variation. In contrast, compared to historical genomes, modern genomes showed a significantly higher realised load, reflecting the temporal increase in inbreeding. Furthermore, the translocation induced only small changes in the frequency of deleterious alleles, with the majority of detrimental variation being shared between the two populations.

Conclusion: Our results highlight the dynamics of mutational load in a species that recovered from the brink of extinction, and show rather limited temporal changes in mutational load. We hypothesise that ancestral purging may have been facilitated by population fragmentation and isolation on several islands for thousands of generations and may have already reduced much of the highly deleterious load well before human arrival and introduction of pests to the archipelago. The majority of fixed deleterious variation was shared between the modern populations, but translocation of individuals with low mutational load could possibly mitigate further fixation of high-frequency deleterious variation.

Keywords
Mutational load, Inbreeding, Genomics, Bottleneck, Near-extinction, Translocation
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-211679 (URN)10.1186/s12864-022-08963-1 (DOI)000881730600001 ()36357860 (PubMedID)2-s2.0-85141614528 (Scopus ID)
Available from: 2022-11-25 Created: 2022-11-25 Last updated: 2024-01-17Bibliographically approved
Peña-Pérez, L., Frengen, N., Hauenstein, J., Gran, C., Gustafsson, C., Eisfeldt, J., . . . Månsson, R. (2022). Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma. Blood Advances, 6(17), 5009-5023
Open this publication in new window or tab >>Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma
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2022 (English)In: Blood Advances, ISSN 2473-9529 , E-ISSN 2473-9537, Vol. 6, no 17, p. 5009-5023Article in journal (Refereed) Published
Abstract [en]

Multiple myeloma (MM) is an incurable and aggressive plasma cell malignancy characterized by a complex karyotype with multiple structural variants (SVs) and copy-number variations (CNVs). Linked-read whole-genome sequencing (lrWGS) allows for refined detection and reconstruction of SVs by providing long-range genetic information from standard short-read sequencing. This makes lrWGS an attractive solution for capturing the full genomic complexity of MM. Here we show that high-quality lrWGS data can be generated from low numbers of cells subjected to fluorescence-activated cell sorting (FACS) without DNA purification. Using this protocol, we analyzed MM cells after FACS from 37 patients with MM using lrWGS. We found high concordance between lrWGS and fluorescence in situ hybridization (FISH) for the detection of recurrent translocations and CNVs. Outside of the regions investigated by FISH, we identified .150 additional SVs and CNVs across the cohort. Analysis of the lrWGS data allowed for resolution of the structure of diverse SVs affecting the MYC and t(11;14) loci, causing the duplication of genes and gene regulatory elements. In addition, we identified private SVs causing the dysregulation of genes recurrently involved in translocations with the IGH locus and show that these can alter the molecular classification of MM. Overall, we conclude that lrWGS allows for the detection of aberrations critical for MM prognostics and provides a feasible route for providing comprehensive genetics. Implementing lrWGS could provide more accurate clinical prognostics, facilitate genomic medicine initiatives, and greatly improve the stratification of patients included in clinical trials.

Keywords
immunoglobulin heavy chain, Article, cancer classification, cancer genetics, cancer prognosis, cell count, clinical article, cohort analysis, controlled study, DNA purification, feasibility study, fluorescence activated cell sorting, fluorescence in situ hybridization, gene control, gene duplication, gene locus, gene structure, gene translocation, genetic variability, human, human cell, human genome, human tissue, linked read whole genome sequencing, molecular genetics, multiple myeloma, myeloma cell, oncogene myc, quality control, whole genome sequencing
National Category
Medical Genetics
Identifiers
urn:nbn:se:su:diva-211969 (URN)10.1182/bloodadvances.2021006720 (DOI)000877428400002 ()35675515 (PubMedID)2-s2.0-85138055806 (Scopus ID)
Available from: 2022-11-29 Created: 2022-11-29 Last updated: 2022-12-06Bibliographically approved
Lord, E., Marangoni, A., Baca, M., Popović, D., Goropashnaya, A. V., Stewart, J. R., . . . Dalén, L. (2022). Population dynamics and demographic history of Eurasian collared lemmings. BMC Ecology and Evolution, 22(1), Article ID 126.
Open this publication in new window or tab >>Population dynamics and demographic history of Eurasian collared lemmings
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2022 (English)In: BMC Ecology and Evolution, E-ISSN 2730-7182, Vol. 22, no 1, article id 126Article in journal (Refereed) Published
Abstract [en]

Background: Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming (Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species.

Results: Here, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest population growth and genetic diversification during the early Late Pleistocene, implying that collared lemmings may have experienced a genetic bottleneck during the warm Eemian interglacial. Furthermore, we find multiple temporally structured mitogenome clades during the Late Pleistocene, consistent with earlier results suggesting a dynamic late glacial population history. Finally, we identify a population in northeastern Siberia that maintained genetic diversity and a constant population size at the end of the Pleistocene, suggesting suitable conditions for collared lemmings in this region during the increasing temperatures associated with the onset of the Holocene.

Conclusions: This study highlights an influence of past warming, in particular the Eemian interglacial, on the evolutionary history of the collared lemming, along with spatiotemporal population structuring throughout the Late Pleistocene.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:su:diva-208528 (URN)10.1186/s12862-022-02081-y (DOI)000878677600001 ()2-s2.0-85141186681 (Scopus ID)
Available from: 2022-09-03 Created: 2022-09-03 Last updated: 2023-12-15Bibliographically approved
Liu, S., Westbury, M., Dussex, N., Mitchell, K. J., Sinding, M.-H. S., Heintzman, P. D., . . . Gilbert, M. T. (2021). Ancient and modem genomes unravel the evolutionary history of the rhinoceros family. Cell, 184(19), 4874-4885
Open this publication in new window or tab >>Ancient and modem genomes unravel the evolutionary history of the rhinoceros family
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2021 (English)In: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 184, no 19, p. 4874-4885Article in journal (Refereed) Published
Abstract [en]

Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.

National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-198860 (URN)10.1016/j.cell.2021.07.032 (DOI)000704445100006 ()34433011 (PubMedID)
Available from: 2021-11-17 Created: 2021-11-17 Last updated: 2023-05-08Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0009-0002-8357-5186

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