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Publications (10 of 34) Show all publications
Zhao, W., Gao, J., Hall, D., Andersson, B., Bruxaux, J., Tomlinson, K. W., . . . Wang, X.-R. (2024). Evolutionary radiation of the Eurasian Pinus species under pervasive gene flow. New Phytologist
Open this publication in new window or tab >>Evolutionary radiation of the Eurasian Pinus species under pervasive gene flow
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2024 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137Article in journal (Refereed) Epub ahead of print
Abstract [en]

Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers with (Formula presented.) 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited. Using exome capture sequencing and a fossil-calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic. We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species. Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages.

Place, publisher, year, edition, pages
Wiley-Blackwell Publishing Inc., 2024
Keywords
demographic history, divergent adaptation, ecological gradients, introgression, phylogeny, Pinus evolution, selection
National Category
Botany Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-222889 (URN)10.1111/nph.19694 (DOI)001188798500001 ()2-s2.0-85188811775 (Scopus ID)
Funder
Swedish Research Council, 2017-04686Swedish Research Council Formas, 2021-02155
Available from: 2024-04-08 Created: 2024-04-08 Last updated: 2024-04-08
Gao, J., Tomlinson, K. W., Zhao, W., Wang, B., Lapuz, R. S., Liu, J.-X., . . . Wang, X.-R. (2024). Phylogeography and introgression between Pinus kesiya and Pinus yunnanensis in Southeast Asia. Journal of Systematics and Evolution, 62(1), 120-134
Open this publication in new window or tab >>Phylogeography and introgression between Pinus kesiya and Pinus yunnanensis in Southeast Asia
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2024 (English)In: Journal of Systematics and Evolution, ISSN 1674-4918, E-ISSN 1759-6831, Vol. 62, no 1, p. 120-134Article in journal (Refereed) Published
Abstract [en]

Southeast Asia (SEA) has seen strong climatic oscillations and fluctuations in sea levels during the Quaternary. The impact of past climate changes on the evolution and distribution of local flora in SEA is still poorly understood. Here we aim to infer how the Quaternary climate change affects the evolutionary process and range shifts in two pine species. We investigated the population genetic structure and diversity using cytoplasmic DNA markers, and performed ecological niche modeling to reconstruct the species past distribution and to project range shift under future climates. We found substantial gene flow across the continuous distribution of the subtropical Pinus yunnanensis. In contrast, the tropical Pinus kesiya showed a strong population structure in accordance with its disjunct distribution across montane islands in Indochina and the Philippines. A broad hybrid zone of the two species occurs in southern Yunnan. Asymmetric introgression from the two species was detected in this zone with dominant mitochondrial gene flow from P. yunnanensis and chloroplast gene flow from P. kesiya. The observed population structure suggests a typical postglaciation expansion in P. yunnanensis, and a glacial expansion and interglacial contraction in P. kesiya. Ecological niche modeling supports the inferred demographic history and predicts a decrease in range size for P. kesiya under future climates. Our results suggest that tropical pine species in SEA have undergone evolutionary trajectories different from high latitude species related to their Quaternary climate histories. We also illustrate the need for urgent conservation actions in this fragmented landscape.

Place, publisher, year, edition, pages
John Wiley & Sons, 2024
Keywords
cpDNA, introgression, mtDNA capture, phylogeography, Pinus kesiya, Pinus yunnanensis
National Category
Ecology Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-206205 (URN)10.1111/jse.12949 (DOI)000945788000001 ()2-s2.0-85150507847 (Scopus ID)
Available from: 2023-04-03 Created: 2023-04-03 Last updated: 2024-05-07Bibliographically approved
Tian, X.-C., Chen, Z.-Y., Nie, S., Shi, T.-L., Yan, X.-M., Bao, Y.-T., . . . Mao, J.-F. (2024). Plant-LncPipe: a computational pipeline providing significant improvement in plant lncRNA identification. Horticulture Research, 11(4), Article ID uhae041.
Open this publication in new window or tab >>Plant-LncPipe: a computational pipeline providing significant improvement in plant lncRNA identification
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2024 (English)In: Horticulture Research, ISSN 2662-6810, Vol. 11, no 4, article id uhae041Article in journal (Refereed) Published
Abstract [en]

Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, such as chromatin remodeling, post-transcriptional regulation, and epigenetic modifications. Despite their critical functions in regulating plant growth, root development, and seed dormancy, the identification of plant lncRNAs remains a challenge due to the scarcity of specific and extensively tested identification methods. Most mainstream machine learning-based methods used for plant lncRNA identification were initially developed using human or other animal datasets, and their accuracy and effectiveness in predicting plant lncRNAs have not been fully evaluated or exploited. To overcome this limitation, we retrained several models, including CPAT, PLEK, and LncFinder, using plant datasets and compared their performance with mainstream lncRNA prediction tools such as CPC2, CNCI, RNAplonc, and LncADeep. Retraining these models significantly improved their performance, and two of the retrained models, LncFinder-plant and CPAT-plant, alongside their ensemble, emerged as the most suitable tools for plant lncRNA identification. This underscores the importance of model retraining in tackling the challenges associated with plant lncRNA identification. Finally, we developed a pipeline (Plant-LncPipe) that incorporates an ensemble of the two best-performing models and covers the entire data analysis process, including reads mapping, transcript assembly, lncRNA identification, classification, and origin, for the efficient identification of lncRNAs in plants. The pipeline, Plant-LncPipe, is available at: https://github.com/xuechantian/Plant-LncRNA-pipline.

National Category
Botany Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-224124 (URN)10.1093/hr/uhae041 (DOI)001204616600001 ()38638682 (PubMedID)2-s2.0-85191036612 (Scopus ID)
Available from: 2024-05-14 Created: 2024-05-14 Last updated: 2024-05-14Bibliographically approved
Tian, X.-C., Chen, Z.-Y., Nie, S., Shi, T.-L., Yan, X.-M., Bao, Y.-T., . . . Mao, J.-F. (2024). Plant-LncPipe: a computational pipeline providing significant improvement in plant lncRNA identification. Horticulture Research, 11(4), Article ID uhae041.
Open this publication in new window or tab >>Plant-LncPipe: a computational pipeline providing significant improvement in plant lncRNA identification
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2024 (English)In: Horticulture Research, ISSN 2662-6810, Vol. 11, no 4, article id uhae041Article in journal (Refereed) Published
Abstract [en]

Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, such as chromatin remodeling, post-transcriptional regulation, and epigenetic modifications. Despite their critical functions in regulating plant growth, root development, and seed dormancy, the identification of plant lncRNAs remains a challenge due to the scarcity of specific and extensively tested identification methods. Most mainstream machine learning-based methods used for plant lncRNA identification were initially developed using human or other animal datasets, and their accuracy and effectiveness in predicting plant lncRNAs have not been fully evaluated or exploited. To overcome this limitation, we retrained several models, including CPAT, PLEK, and LncFinder, using plant datasets and compared their performance with mainstream lncRNA prediction tools such as CPC2, CNCI, RNAplonc, and LncADeep. Retraining these models significantly improved their performance, and two of the retrained models, LncFinder-plant and CPAT-plant, alongside their ensemble, emerged as the most suitable tools for plant lncRNA identification. This underscores the importance of model retraining in tackling the challenges associated with plant lncRNA identification. Finally, we developed a pipeline (Plant-LncPipe) that incorporates an ensemble of the two best-performing models and covers the entire data analysis process, including reads mapping, transcript assembly, lncRNA identification, classification, and origin, for the efficient identification of lncRNAs in plants. The pipeline, Plant-LncPipe, is available at: https://github.com/xuechantian/Plant-LncRNA-pipline.

Place, publisher, year, edition, pages
Oxford University Press, 2024
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-224237 (URN)10.1093/hr/uhae041 (DOI)001204616600001 ()38638682 (PubMedID)2-s2.0-85191036612 (Scopus ID)
Available from: 2024-05-15 Created: 2024-05-15 Last updated: 2024-05-15Bibliographically approved
Bruxaux, J., Zhao, W., Hall, D., Curtu, A. L., Androsiuk, P., Drouzas, A. D., . . . Wang, X.-R. (2024). Scots pine – panmixia and the elusive signal of genetic adaptation. New Phytologist
Open this publication in new window or tab >>Scots pine – panmixia and the elusive signal of genetic adaptation
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2024 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137Article in journal (Refereed) Epub ahead of print
Abstract [en]

Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them.

To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation.

We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients.

The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.

Place, publisher, year, edition, pages
John Wiley & Sons, 2024
Keywords
conifer, demography, gene flow, genetic diversity, genetic-environmental association, Pinus sylvestris, population structure
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-221025 (URN)10.1111/nph.19563 (DOI)001155409000001 ()2-s2.0-85184157884 (Scopus ID)
Funder
Swedish Research Council Formas, 2018-00842Swedish Research Council Formas, 2021-02155Carl Tryggers foundation
Available from: 2024-03-06 Created: 2024-03-06 Last updated: 2024-03-06
Nie, S., Zhao, S.-W., Shi, T.-L., Zhao, W., Zhang, R.-G., Tian, X.-C., . . . Mao, J.-F. (2023). Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color. Horticulture Research, 10(1), Article ID uhac241.
Open this publication in new window or tab >>Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color
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2023 (English)In: Horticulture Research, ISSN 2662-6810, Vol. 10, no 1, article id uhac241Article in journal (Refereed) Published
Abstract [en]

The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.

Place, publisher, year, edition, pages
Oxford University Press, 2023
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-213600 (URN)10.1093/hr/uhac241 (DOI)000913472300006 ()36643737 (PubMedID)2-s2.0-85146799427 (Scopus ID)
Available from: 2023-08-29 Created: 2023-08-29 Last updated: 2023-08-29Bibliographically approved
Guo, J.-F., Zhao, W., Andersson, B., Mao, J.-F. & Wang, X.-R. (2023). Genomic clines across the species boundary between a hybrid pine and its progenitor in the eastern Tibetan Plateau. Plant Communications, 4(4), Article ID 100574.
Open this publication in new window or tab >>Genomic clines across the species boundary between a hybrid pine and its progenitor in the eastern Tibetan Plateau
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2023 (English)In: Plant Communications, E-ISSN 2590-3462, Vol. 4, no 4, article id 100574Article in journal (Refereed) Published
Abstract [en]

Most species have clearly defined distribution ranges and ecological niches. The genetic and ecological causes of species differentiation and the mechanisms that maintain species boundaries between newly evolved taxa and their progenitors are, however, less clearly defined. This study investigated the genetic structure and clines in Pinus densata, a pine of hybrid origin on the southeastern Tibetan Plateau, to gain an understanding of the contemporary dynamics of species barriers. We analyzed genetic diversity in a range-wide collection of P. densata and representative populations of its progenitors, Pinus tabuliformis and Pinus yunnanensis, using exome capture sequencing. We detected four distinct genetic groups within P. densata that reflect its migration history and major gene-flow barriers across the landscape. The demographies of these genetic groups in the Pleistocene were associated with regional glaciation histories. Interestingly, population sizes rebounded rapidly during interglacial periods, suggesting persistence and resilience of the species during the Quaternary ice age. In the contact zone between P. densata and P. yunnanensis, 3.36% of the analyzed loci (57 849) showed exceptional patterns of introgression, suggesting their potential roles in either adaptive introgression or reproductive isolation. These outliers showed strong clines along critical climate gradients and enrichment in a number of biological processes relevant to high-altitude adaptation. This indicates that ecological selection played an important role in generating genomic heterogeneity and a genetic barrier across a zone of species transition. Our study highlights the forces that operate to maintain species boundaries and promote speciation in the Qinghai-Tibetan Plateau and other mountain systems.

Place, publisher, year, edition, pages
Cell Press, 2023
Keywords
demographic history, ecological selection, genomic cline, introgression outliers, reproductive isolation, species boundary
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-208078 (URN)10.1016/j.xplc.2023.100574 (DOI)2-s2.0-85153500172 (Scopus ID)
Funder
Swedish Research Council, 2017-04686
Available from: 2023-05-17 Created: 2023-05-17 Last updated: 2024-01-10Bibliographically approved
Zhao, S.-W., Guo, J.-F., Kong, L., Nie, S., Yan, X.-M., Shi, T.-L., . . . Mao, J.-F. (2023). Haplotype-resolved genome assembly of Coriaria nepalensis a non-legume nitrogen-fixing shrub. Scientific Data, 10(1), Article ID 259.
Open this publication in new window or tab >>Haplotype-resolved genome assembly of Coriaria nepalensis a non-legume nitrogen-fixing shrub
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2023 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 10, no 1, article id 259Article in journal (Refereed) Published
Abstract [en]

Coriaria nepalensis Wall. (Coriariaceae) is a nitrogen-fixing shrub which forms root nodules with the actinomycete Frankia. Oils and extracts of C. nepalensis have been reported to be bacteriostatic and insecticidal, and C. nepalensis bark provides a valuable tannin resource. Here, by combining PacBio HiFi sequencing and Hi-C scaffolding techniques, we generated a haplotype-resolved chromosome-scale genome assembly for C. nepalensis. This genome assembly is approximately 620 Mb in size with a contig N50 of 11 Mb, with 99.9% of the total assembled sequences anchored to 40 pseudochromosomes. We predicted 60,862 protein-coding genes of which 99.5% were annotated from databases. We further identified 939 tRNAs, 7,297 rRNAs, and 982 ncRNAs. The chromosome-scale genome of C. nepalensis is expected to be a significant resource for understanding the genetic basis of root nodulation with Frankia, toxicity, and tannin biosynthesis.

Place, publisher, year, edition, pages
Springer Nature, 2023
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-208944 (URN)10.1038/s41597-023-02171-6 (DOI)000983082000002 ()37156769 (PubMedID)2-s2.0-85158095885 (Scopus ID)
Available from: 2023-06-02 Created: 2023-06-02 Last updated: 2023-06-02Bibliographically approved
Andersson, B., Zhao, W., Haller, B. C., Brännström, Å. & Wang, X.-R. (2023). Inference of the distribution of fitness effects of mutations is affected by single nucleotide polymorphism filtering methods, sample size and population structure. Molecular Ecology Resources, 23(7), 1589-1603
Open this publication in new window or tab >>Inference of the distribution of fitness effects of mutations is affected by single nucleotide polymorphism filtering methods, sample size and population structure
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2023 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 23, no 7, p. 1589-1603Article in journal (Refereed) Published
Abstract [en]

The distribution of fitness effects (DFE) of new mutations has been of interest to evolutionary biologists since the concept of mutations arose. Modern population genomic data enable us to quantify the DFE empirically, but few studies have examined how data processing, sample size and cryptic population structure might affect the accuracy of DFE inference. We used simulated and empirical data (from Arabidopsis lyrata) to show the effects of missing data filtering, sample size, number of single nucleotide polymorphisms (SNPs) and population structure on the accuracy and variance of DFE estimates. Our analyses focus on three filtering methods—downsampling, imputation and subsampling—with sample sizes of 4–100 individuals. We show that (1) the choice of missing-data treatment directly affects the estimated DFE, with downsampling performing better than imputation and subsampling; (2) the estimated DFE is less reliable in small samples (<8 individuals), and becomes unpredictable with too few SNPs (<5000, the sum of 0- and 4-fold SNPs); and (3) population structure may skew the inferred DFE towards more strongly deleterious mutations. We suggest that future studies should consider downsampling for small data sets, and use samples larger than 4 (ideally larger than 8) individuals, with more than 5000 SNPs in order to improve the robustness of DFE inference and enable comparative analyses.

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
Keywords
DFE, missing-data treatment, population structure, sample size, SLiM simulation
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-211803 (URN)10.1111/1755-0998.13825 (DOI)001015493200001 ()37340611 (PubMedID)2-s2.0-85162975600 (Scopus ID)
Funder
Swedish Research CouncilSwedish National Infrastructure for Computing (SNIC)
Available from: 2023-07-11 Created: 2023-07-11 Last updated: 2024-01-10Bibliographically approved
Guo, J.-F., Wang, B., Liu, Z.-L., Mao, J.-F., Wang, X.-R. & Zhao, W. (2023). Low genetic diversity and population connectivity fuel vulnerability to climate change for the Tertiary relict pine Pinus bungeana. Journal of Systematics and Evolution, 61(1), 143-156
Open this publication in new window or tab >>Low genetic diversity and population connectivity fuel vulnerability to climate change for the Tertiary relict pine Pinus bungeana
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2023 (English)In: Journal of Systematics and Evolution, ISSN 1674-4918, E-ISSN 1759-6831, Vol. 61, no 1, p. 143-156Article in journal (Refereed) Published
Abstract [en]

Endemic species are important components of regional biodiversity and hold the key to understanding local adaptation and evolutionary processes that shape species distributions. This study investigated the biogeographic history of a relict conifer Pinus bungeana Zucc. ex Endl. confined to central China. We examined genetic diversity in P. bungeana using genotyping-by-sequencing and chloroplast and mitochondrial DNA markers. We performed spatial and temporal inference of recent genetic and demographic changes, and dissected the impacts of geography and environmental gradients on population differentiation. We then projected P. bungeana's risk of decline under future climates. We found extremely low nucleotide diversity (average π 0.0014), and strong population structure (global FST 0.234) even at regional scales, reflecting long-term isolation in small populations. The species experienced severe bottlenecks in the early Pliocene and continued to decline in the Pleistocene in the western distribution, whereas the east expanded recently. Local adaptation played a small (8%) but significant role in population diversity. Low genetic diversity in fragmented populations makes the species highly vulnerable to climate change, particularly in marginal and relict populations. We suggest that conservation efforts should focus on enhancing gene pool and population growth through assisted migration within each genetic cluster to reduce the risk of further genetic drift and extinction.

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
Keywords
climate relict, genetic diversity, genomic offset, migration barrier, Pinus bungeana, population bottleneck
National Category
Botany Genetics
Identifiers
urn:nbn:se:umu:diva-192657 (URN)10.1111/jse.12821 (DOI)000755100500001 ()2-s2.0-85124608048 (Scopus ID)
Funder
Swedish National Infrastructure for Computing (SNIC)Swedish Research Council
Available from: 2022-02-21 Created: 2022-02-21 Last updated: 2023-07-13Bibliographically approved
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Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-9437-3198

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