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Chen, Jun
Publications (10 of 22) Show all publications
Li, L., Milesi, P., Tiret, M., Chen, J., Sendrowski, J., Baison, J., . . . Lascoux, M. (2022). Teasing apart the joint effect of demography and natural selection in the birth of a contact zone. New Phytologist, 236(5), 1976-1987
Open this publication in new window or tab >>Teasing apart the joint effect of demography and natural selection in the birth of a contact zone
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2022 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 236, no 5, p. 1976-1987Article in journal (Refereed) Published
Place, publisher, year, edition, pages
John Wiley & SonsWiley, 2022
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-492295 (URN)10.1111/nph.18480 (DOI)000861973200001 ()36093739 (PubMedID)
Funder
Swedish Foundation for Strategic Research, RBP14‐0040
Available from: 2023-01-03 Created: 2023-01-03 Last updated: 2024-01-15Bibliographically approved
Chen, Z.-Q., Zan, Y., Milesi, P., Zhou, L., Chen, J., Li, L., . . . Wu, H. X. (2021). Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis. Genome Biology, 22(1), Article ID 179.
Open this publication in new window or tab >>Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis
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2021 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 22, no 1, article id 179Article in journal (Refereed) Published
Abstract [en]

Background: Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees.

Results: We identify 55 novel quantitative trait loci (QTLs) that are associated with phenotypic variation. The largest number of QTLs is associated with the budburst stage, followed by diameter at breast height, wood quality, and frost damage. Two QTLs with the largest effect have a pleiotropic effect for budburst stage, frost damage, and diameter and are associated with MAP3K genes. Genotype data called from exome capture, recently developed SNP array and gene expression data indirectly support this discovery.

Conclusion: Several important QTLs associated with growth and frost damage have been verified in several southern and northern progeny plantations, indicating that these loci can be used in QTL-assisted genomic selection. Our study also demonstrates that existing heterogeneous phenotypic data from breeding programs, collected over several decades, is an important source for GWAS and that such integration into GWAS should be a major area of inquiry in the future.

Place, publisher, year, edition, pages
BioMed Central (BMC)BMC, 2021
Keywords
Norway spruce, Frost damage, Genome-wide association study, Wood quality, Budburst stage, MAP3K gene
National Category
Genetics and Breeding in Agricultural Sciences
Identifiers
urn:nbn:se:uu:diva-449209 (URN)10.1186/s13059-021-02392-1 (DOI)000664094600002 ()34120648 (PubMedID)
Funder
Swedish Foundation for Strategic Research , RBP14-0040
Note

Correction in: Genome Biology, Volume: 22, Issue: 1, Article Number: 210, DOI:10.1186/s13059-021-02421-z

Available from: 2021-07-19 Created: 2021-07-19 Last updated: 2024-01-15Bibliographically approved
Chen, J., Glemin, S. & Lascoux, M. (2020). From Drift to Draft: How Much Do Beneficial Mutations Actually Contribute to Predictions of Ohta's Slightly Deleterious Model of Molecular Evolution?. Genetics, 214(4), 1005-1018
Open this publication in new window or tab >>From Drift to Draft: How Much Do Beneficial Mutations Actually Contribute to Predictions of Ohta's Slightly Deleterious Model of Molecular Evolution?
2020 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 214, no 4, p. 1005-1018Article in journal (Refereed) Published
Abstract [en]

Since its inception in 1973, the slightly deleterious model of molecular evolution, also known as the nearly neutral theory of molecular evolution, remains a central model to explain the main patterns of DNA polymorphism in natural populations. This is not to say that the quantitative fit to data are perfect. A recent study used polymorphism data from Drosophila melanogaster to test whether, as predicted by the nearly neutral theory, the proportion of effectively neutral mutations depends on the effective population size (N-e). It showed that a nearly neutral model simply scaling with N-e variation across the genome could not alone explain the data, but that consideration of linked positive selection improves the fit between observations and predictions. In the present article, we extended the work in two main directions. First, we confirmed the observed pattern on a set of 59 species, including high-quality genomic data from 11 animal and plant species with different mating systems and effective population sizes, hence a priori different levels of linked selection. Second, for the 11 species with high-quality genomic data we also estimated the full distribution of fitness effects (DFE) of mutations, and not solely the DFE of deleterious mutations. Both N-e and beneficial mutations contributed to the relationship between the proportion of effectively neutral mutations and local N-e across the genome. In conclusion, the predictions of the slightly deleterious model of molecular evolution hold well for species with small N-e, but for species with large N-e, the fit is improved by incorporating linked positive selection to the model.

Place, publisher, year, edition, pages
GENETICS SOCIETY AMERICA, 2020
Keywords
nearly neutral theory, distribution of fitness effects, beneficial mutations, linked selection
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-411425 (URN)10.1534/genetics.119.302869 (DOI)000527690300017 ()32015019 (PubMedID)
Funder
Swedish Research CouncilSwedish Foundation for Strategic Research
Available from: 2020-06-03 Created: 2020-06-03 Last updated: 2020-06-03Bibliographically approved
Milesi, P., Berlin, M., Chen, J., Orsucci, M., Li, L., Jansson, G., . . . Lascoux, M. (2019). Assessing the potential for assisted gene flow using past introduction of Norway spruce in southern Sweden: Local adaptation and genetic basis of quantitative traits in trees. Evolutionary Applications, 12(10), 1946-1959
Open this publication in new window or tab >>Assessing the potential for assisted gene flow using past introduction of Norway spruce in southern Sweden: Local adaptation and genetic basis of quantitative traits in trees
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2019 (English)In: Evolutionary Applications, E-ISSN 1752-4571, Vol. 12, no 10, p. 1946-1959Article in journal (Refereed) Published
Abstract [en]

Norway spruce (Picea abies) is a dominant conifer species of major economic importance in northern Europe. Extensive breeding programs were established to improve phenotypic traits of economic interest. In southern Sweden, seeds used to create progeny tests were collected on about 3,000 trees of outstanding phenotype (‘plus’ trees) across the region. In a companion paper, we showed that some were of local origin but many were recent introductions from the rest of the natural range. The mixed origin of the trees together with partial sequencing of the exome of >1,500 of these trees and phenotypic data retrieved from the Swedish breeding program offered a unique opportunity to dissect the genetic basis of local adaptation of three quantitative traits (height, diameter and bud-burst) and assess the potential of assisted gene flow. Through a combination of multivariate analyses and genome-wide association studies, we showed that there was a very strong effect of geographical origin on growth (height and diameter) and phenology (bud-burst) with trees from southern origins outperforming local provenances. Association studies revealed that growth traits were highly polygenic and bud-burst somewhat less. Hence, our results suggest that assisted gene flow and genomic selection approaches could help to alleviate the effect of climate change on P. abies breeding programs in Sweden.

Place, publisher, year, edition, pages
John Wiley & Sons, 2019
Keywords
assisted gene flow, breeding strategy, climate change, exome capture, Picea abies, quantitative traits architecture
National Category
Ecology Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-396250 (URN)10.1111/eva.12855 (DOI)000493919200007 ()31700537 (PubMedID)
Funder
Swedish Research Council FormasSwedish Foundation for Strategic Research
Available from: 2019-10-31 Created: 2019-10-31 Last updated: 2023-10-24Bibliographically approved
Li, L., Chen, J. & Lascoux, M. (2019). Clinal variation in growth cessation and FTL2 expression in Siberian spruce. Tree Genetics & Genomes, 15(82)
Open this publication in new window or tab >>Clinal variation in growth cessation and FTL2 expression in Siberian spruce
2019 (English)In: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 15, no 82Article in journal (Refereed) Published
Abstract [en]

Forest trees exhibit strong patterns of local adaptation in phenological traits along latitudinal gradients. Previous studies in spruce have shown that variation at genes from the photoperiodic pathway and the circadian clock are associated to these clines but it has been difficult to find solid evidence of selection for some of these genes. Here, we used growth cessation, gene expression, and single nucleotide polymorphism (SNP) data at two major candidate loci, FLOWERING LOCUS T/TERMINAL FLOWER1-Like2 (FTL2) and GIGANTEA (GI), as well as at background loci from a latitudinal gradient in Siberian spruce (Picea obovata) populations along the Ob River to test for clinal variation in growth cessation and at the two candidate genes. As in previous studies, there was a strong latitudinal cline in growth cessation that was accompanied by a significant cline in the expression of FTL2. Expression of FTL2 was significantly associated with allele frequencies at some of the GI’s SNPs. However, the cline in allele frequency at candidate genes was not as steep as in a Norway spruce cline and in a parallel Siberian spruce cline studied previously and nonsignificant when a correction for population structure was applied. A McDonald-Kreitman test did not detect decisive evidence of selection on GI (p value = 0.07) and could not be applied to FTL2 because of limited polymorphism. Nonetheless, polymorphisms contributed more to the increased neutrality index of PoGI than to that of control loci. Finally, comparing the results of two previously published studies to our new dataset led to the identification of strong candidate SNPs for local adaptation in FTL2 promoter and GI.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-399146 (URN)10.1007/s11295-019-1389-7 (DOI)000500761100002 ()
Funder
Swedish Research Council Formas
Available from: 2019-12-13 Created: 2019-12-13 Last updated: 2020-01-30Bibliographically approved
Chen, J., Li, L., Milesi, P., Jansson, G., Berlin, M., Karlsson, B., . . . Lascoux, M. (2019). Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce. Evolutionary Applications, 12(8), 1539-1551
Open this publication in new window or tab >>Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce
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2019 (English)In: Evolutionary Applications, E-ISSN 1752-4571, Vol. 12, no 8, p. 1539-1551Article in journal (Refereed) Published
Abstract [en]

Primeval forests are today exceedingly rare in Europe, and transfer of forest reproductive material for afforestation and improvement has been very common, especially over the last two centuries. This can be a serious impediment when inferring past population movements in response to past climate changes such as the last glacial maximum (LGM), some 18,000 years ago. In the present study, we genotyped 1,672 individuals from three Picea species (P. abies, P. obovata, and P. omorika) at 400K SNPs using exome capture to infer the past demographic history of Norway spruce (P. abies) and estimate the amount of recent introduction used to establish the Norway spruce breeding program in southern Sweden. Most of these trees belong to P. abies and originate from the base populations of the Swedish breeding program. Others originate from populations across the natural ranges of the three species. Of the 1,499 individuals stemming from the breeding program, a large proportion corresponds to recent introductions from mainland Europe. The split of P. omorika occurred 23 million years ago (mya), while the divergence between P. obovata and P. abies began 17.6 mya. Demographic inferences retrieved the same main clusters within P. abies than previous studies, that is, a vast northern domain ranging from Norway to central Russia, where the species is progressively replaced by Siberian spruce (P. obovata) and two smaller domains, an Alpine domain and a Carpathian one, but also revealed further subdivision and gene flow among clusters. The three main domains divergence was ancient (15 mya), and all three went through a bottleneck corresponding to the LGM. Approximately 17% of P. abies Nordic domain migrated from P. obovata ~103K years ago, when both species had much larger effective population sizes. Our analysis of genomewide polymorphism data thus revealed the complex demographic history of Picea genus in Western Europe and highlighted the importance of material transfer in Swedish breeding program.

Place, publisher, year, edition, pages
WILEY, 2019
Keywords
demographic inferences, forest management, Picea abies, population transfer
National Category
Botany
Identifiers
urn:nbn:se:uu:diva-395853 (URN)10.1111/eva.12801 (DOI)000484471100004 ()31462913 (PubMedID)
Available from: 2019-10-25 Created: 2019-10-25 Last updated: 2023-10-24Bibliographically approved
Kryvokhyzha, D., Salcedo, A., Eriksson, M. C., Duan, T., Tawari, N., Chen, J., . . . Lascoux, M. (2019). Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae). PLOS Genetics, 15(2), Article ID e1007949.
Open this publication in new window or tab >>Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)
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2019 (English)In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 15, no 2, article id e1007949Article in journal (Refereed) Published
Abstract [en]

Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species nor how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe, and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (Cbp(Cg)) and the other one from the selfing and genetically depauperate Capsella orientalis (Cbp(Co)). For each subgenome, we assessed its relationship with the diploid relatives, temporal changes of effective population size (N-e), signatures of positive and negative selection, and gene expression patterns. In all three regions, N-e of the two subgenomes decreased gradually over time and the Cbp(Co) subgenome accumulated more deleterious changes than Cbp(Cg). There were signs of widespread admixture between C. bursa-pastoris and its diploid relatives. The two subgenomes were impacted differentially depending on geographic region suggesting either strong interploidy gene flow or multiple origins of C. bursa-pastoris. Selective sweeps were more common on the Cbp(Cg) subgenome in Europe and the Middle East, and on the Cbp(Co) subgenome in Asia. In contrast, differences in expression were limited with the Cbp(Cg) subgenome slightly more expressed than Cbp(Co) in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy but their evolutionary trajectory strongly varied across geographic regions. Author summary Allopolyploid species have two or more sets of chromosomes that originate from hybridization of different species. It remains largely unknown how the two genomes evolve in the same organism and how strongly their evolutionary trajectory depends on the initial differences between the two parental species and the specific demographic history of the newly formed allopolyploid species. To address these questions, we analyzed the genomic and gene expression variation of the shepherd's purse, a recent allopolyploid species, in three regions of its natural range. After approximate to 100,000 generations of co-existence within the same species, the two subgenomes had still retained part of the initial difference between the two parental species in the number of deleterious mutations reflecting a history of mating system differences. This difference, as well as differences in patterns of positive selection and levels of gene expression, also strongly depended on the specific histories of the three regions considered. Most strikingly, and unexpectedly, the allopolyploid species showed signs of hybridization with different diploid relatives or multiple origins in different parts of its range. Regardless if it was hybridization or multiple origins, this profoundly altered the relationship between the two subgenomes in different regions. Hence, our study illustrates how both the genomic structure and ecological arena interact to determine the evolutionary trajectories of allopolyploid species.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-379946 (URN)10.1371/journal.pgen.1007949 (DOI)000459970100033 ()30768594 (PubMedID)
Funder
Swedish Research Council, 2012-04999Swedish Research Council, 2015-03797
Note

De 2 första författarna delar förstaförfattarskapet.

Available from: 2019-03-25 Created: 2019-03-25 Last updated: 2022-09-13Bibliographically approved
Chen, J., Yang, Y.-f., Yang, Y., Zou, P., Chen, J., He, Y., . . . Xu, J. (2018). AXL promotes Zika virus infection in astrocytes by antagonizing type I interferon signalling. Nature Microbiology, 3(3), 302-309
Open this publication in new window or tab >>AXL promotes Zika virus infection in astrocytes by antagonizing type I interferon signalling
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2018 (English)In: Nature Microbiology, E-ISSN 2058-5276, Vol. 3, no 3, p. 302-309Article in journal (Refereed) Published
Abstract [en]

Zika virus (ZIKV) is associated with neonatal microcephaly and Guillain-Barre syndrome(1,2). While progress has been made in understanding the causal link between ZIKV infection and microcephaly(3-9), the life cycle and pathogenesis of ZIKV are less well understood. In particular, there are conflicting reports on the role of AXL, a TAM family kinase receptor that was initially described as the entry receptor for ZIKV(10-22). Here, we show that while genetic ablation of AXL protected primary human astrocytes and astrocytoma cell lines from ZIKV infection, AXL knockout did not block the entry of ZIKV. We found, instead, that the presence of AXL attenuated the ZIKV-induced activation of type I interferon (IFN) signalling genes, including several type I IFNs and IFN-stimulating genes. Knocking out type I IFN receptor alpha chain (IFNAR1) restored the vulnerability of AXL knockout astrocytes to ZIKV infection. Further experiments suggested that AXL regulates the expression of SOCS1, a known type I IFN signalling suppressor, in a STAT1/STAT2-dependent manner. Collectively, our results demonstrate that AXL is unlikely to function as an entry receptor for ZIKV and may instead promote ZIKV infection in human astrocytes by antagonizing type I IFN signalling.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2018
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:uu:diva-350062 (URN)10.1038/s41564-017-0092-4 (DOI)000425846200011 ()29379210 (PubMedID)
Available from: 2018-05-03 Created: 2018-05-03 Last updated: 2018-05-03Bibliographically approved
Svedberg, J., Hosseini, S., Chen, J., Vogan, A. A., Mozgova, I., Hennig, L., . . . Johannesson, H. (2018). Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements. Nature Communications, 9, Article ID 4242.
Open this publication in new window or tab >>Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements
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2018 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 9, article id 4242Article in journal (Refereed) Published
Abstract [en]

Meiotic drive is widespread in nature. The conflict it generates is expected to be an important motor for evolutionary change and innovation. In this study, we investigated the genomic consequences of two large multi-gene meiotic drive elements, Sk-2 and Sk-3, found in the filamentous ascomycete Neurospora intermedia. Using long-read sequencing, we generated the first complete and well-annotated genome assemblies of large, highly diverged, non-recombining regions associated with meiotic drive elements. Phylogenetic analysis shows that, even though Sk-2 and Sk-3 are located in the same chromosomal region, they do not form sister clades, suggesting independent origins or at least a long evolutionary separation. We conclude that they have in a convergent manner accumulated similar patterns of tandem inversions and dense repeat clusters, presumably in response to similar needs to create linkage between genes causing drive and resistance.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2018
National Category
Genetics Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-368443 (URN)10.1038/s41467-018-06562-x (DOI)000447123000018 ()30315196 (PubMedID)
Funder
Swedish Research CouncilEU, Horizon 2020, 648143Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Available from: 2018-12-07 Created: 2018-12-07 Last updated: 2023-03-28Bibliographically approved
Plomion, C., Aury, J.-M., Amselem, J., Leroy, T., Murat, F., Duplessis, S., . . . Salse, J. (2018). Oak genome reveals facets of long lifespan. NATURE PLANTS, 4(7), 440-452
Open this publication in new window or tab >>Oak genome reveals facets of long lifespan
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2018 (English)In: NATURE PLANTS, ISSN 2055-026X, Vol. 4, no 7, p. 440-452Article in journal (Refereed) Published
Abstract [en]

Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes' but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times(2). With 450 species spread throughout Asia, Europe and America(3), oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical(4) and modelling(5) approaches have shown that intra-organismal genetic heterogeneity can be selected for(6) and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes(7). However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-364056 (URN)10.1038/s41477-018-0172-3 (DOI)000443221200016 ()29915331 (PubMedID)
Funder
EU, FP7, Seventh Framework ProgrammeEU, European Research CouncilSwedish Foundation for Strategic Research
Available from: 2018-12-07 Created: 2018-12-07 Last updated: 2018-12-07Bibliographically approved
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