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Whole Genome Based Insights Into the Phylogeny and Evolution of the Juglandaceae
Whole Genome based Insights into the Phylogeny and Evolution of the Juglandaceae Huijuan Zhou Northwest A&F University: Northwest Agriculture and Forestry University Yiheng Hu Northwestern University Aziz Ebrahimi Purdue University Peiliang Liu Northwestern University Keith Woeste Purdue University Shuoxin Zhang Northwest A&F University: Northwest Agriculture and Forestry University Peng Zhao ( [email protected] ) Northwest University https://orcid.org/0000-0003-3033-6982 Research article Keywords: Diversication, Divergence time, Genome, Juglandaceae, Phylogenomics, Plastome Posted Date: May 24th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-495294/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/23 Abstract Background: The walnut family (Juglandaceae) contains commercially important woody trees commonly called walnut, wingnut, pecan and hickory. Phylogenetic relationships in the Juglandaceae are problematic, and their historical diversication has not been claried, in part because of low phylogenetic resolution and/or insucient marker variability. Results: We reconstructed the backbone phylogenetic relationships of Juglandaceae using organelle and nuclear genome data from 27 species. The divergence time of Juglandaceae was estimated to be 78.7 Mya. The major lineages diversied in warm and dry habitats during the mid-Paleocene and early Eocene. The plastid, mitochondrial, and nuclear phylogenetic analyses all revealed three subfamilies, i.e., Juglandoideae, Engelhardioideae, Rhoipteleoideae. Five genera of Juglandoideae were strongly supported. Juglandaceae were estimated to have originated during the late Cretaceous, while Juglandoideae were estimated to have originated during the Paleocene, with evidence for rapid diversication events during several glacial and geological periods. The phylogenetic analyses of organelle sequences and nuclear genome yielded highly supported incongruence positions for J. -
Carya – Hickorynoot Sortimentsonderzoek
Carya – Hickorynoot sortimentsonderzoek Ing. G.J.J. Bolscher Carya is een geslacht dat slechts in beperkte mate in Europa voorkomt. In enkele parken, arboreta en kasteeltuinen worden soms fraaie, oude, maar zeer gezonde, exemplaren aangetroffen. Als straat- en laanboom worden ze zelden toegepast. Om Carya meer bekendheid te geven heeft de Technische Keuringscommissie van de Naktuinbouw in 2007 besloten dit geslacht te onderzoeken om het vervolgens door middel van publicatie te promoten. In het kader van dit onderzoek is een inventarisa zijn nadien soorten en hybriden, die niet in het tie uitgevoerd van de meest voorkomende soorten veldonderzoek betrokken zijn geweest, toch kort in Nederland en België. Vervolgens zijn, aan de genoemd en beschreven. hand van de beschikbare literatuur, de bomen op de verschillende locaties beoordeeld op soortecht Juglandaceae heid en beschreven ten behoeve van identificatie en Het geslacht Carya behoort tot de Juglandaceae registratie. (Nootachtigen). Deze familie, behorend tot de Aanvankelijk is alleen gekeken naar gezonde soor orde der Fagales (Eikenorde), bestaat, enigs ten die geschikt zouden kunnen zijn voor gebruik zins afhankelijk van de interpretatie, uit 8 tot 10 als straat en laanboom in Nederland. In praktijk geslachten. blijkt Carya zich moeilijk te laten vermeerderen Manos & Stone (2001) onderscheiden 2 onder en nog moeilijker is te verplanten, waardoor de families Engelhardioideae en Juglandoideae. opkweek van dit toch al traag groeiende geslacht Tot de Engelhardioideae behoren 34 geslachten; beperkt blijft. Vervolgens is besloten het keurings Engelhardia is bladverliezend tot wintergroen en onderzoek een breder, meer algemeen taxonomisch komt met 68 soorten voor in Azië, Oreomunnea karakter te geven om op deze manier dit geslacht is wintergroen en komt eveneens voor in Azië, toch meer onder de aandacht te brengen. -
Genomic Variation Among and Within Six Juglans Species
UC Davis UC Davis Previously Published Works Title Genomic Variation Among and Within Six Juglans Species. Permalink https://escholarship.org/uc/item/0xk5r0q1 Journal G3 (Bethesda, Md.), 8(7) ISSN 2160-1836 Authors Stevens, Kristian A Woeste, Keith Chakraborty, Sandeep et al. Publication Date 2018-07-02 DOI 10.1534/g3.118.200030 Peer reviewed eScholarship.org Powered by the California Digital Library University of California SOFTWARE AND DATA RESOURCES Genomic Variation Among and Within Six Juglans Species Kristian A. Stevens,*,1 Keith Woeste,† Sandeep Chakraborty,‡ Marc W. Crepeau,* Charles A. Leslie,‡ Pedro J. Martínez-García,‡ Daniela Puiu,§ Jeanne Romero-Severson,** Mark Coggeshall,† Abhaya M. Dandekar,‡ Daniel Kluepfel,†† David B. Neale,‡ Steven L. Salzberg,§,‡‡ and Charles H. Langley* *Department of Evolution and Ecology and ‡Department of Plant Sciences University of California, Davis, CA 95616, †USDA Forest Service Hardwood Tree Improvement and Regeneration Center, Department of Forestry and Natural § Resources, Purdue University, West Lafayette, IN, Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine and ‡‡Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, and **Department of Biological Sciences, University of Notre Dame, IN, ††USDA Agricultural Research Station, Davis, CA ORCID ID: 0000-0002-8859-7432 (S.L.S.) ABSTRACT Genomic analysis in Juglans (walnuts) is expected to transform the breeding and agricultural pro- KEYWORDS duction of both nuts and lumber. To that end, we report here the determination of reference sequences for six Juglans additional relatives of Juglans regia: Juglans sigillata (also from section Dioscaryon), Juglans nigra, Juglans walnut microcarpa, Juglans hindsii (from section Rhysocaryon), Juglans cathayensis (from section Cardiocaryon), and reference the closely related Pterocarya stenoptera. -
Supplementary Material
Xiang et al., Page S1 Supporting Information Fig. S1. Examples of the diversity of diaspore shapes in Fagales. Fig. S2. Cladogram of Fagales obtained from the 5-marker data set. Fig. S3. Chronogram of Fagales obtained from analysis of the 5-marker data set in BEAST. Fig. S4. Time scale of major fagalean divergence events during the past 105 Ma. Fig. S5. Confidence intervals of expected clade diversity (log scale) according to age of stem group. Fig. S6. Evolution of diaspores types in Fagales with BiSSE model. Fig. S7. Evolution of diaspores types in Fagales with Mk1 model. Fig. S8. Evolution of dispersal modes in Fagales with MuSSE model. Fig. S9. Evolution of dispersal modes in Fagales with Mk1 model. Fig. S10. Reconstruction of pollination syndromes in Fagales with BiSSE model. Fig. S11. Reconstruction of pollination syndromes in Fagales with Mk1 model. Fig. S12. Reconstruction of habitat shifts in Fagales with MuSSE model. Fig. S13. Reconstruction of habitat shifts in Fagales with Mk1 model. Fig. S14. Stratigraphy of fossil fagalean genera. Table S1 Genera of Fagales indicating the number of recognized and sampled species, nut sizes, habits, pollination modes, and geographic distributions. Table S2 List of taxa included in this study, sources of plant material, and GenBank accession numbers. Table S3 Primers used for amplification and sequencing in this study. Table S4 Fossil age constraints utilized in this study of Fagales diversification. Table S5 Fossil fruits reviewed in this study. Xiang et al., Page S2 Table S6 Statistics from the analyses of the various data sets. Table S7 Estimated ages for all families and genera of Fagales using BEAST. -
Global Biogeographic Synthesis and Priority Conservation Regions of the Relict Tree Family Juglandaceae
Appendix S1 An update on the classification of subfamilies, genera and species of the relict tree family Juglandaceae Yi-Gang Song1,2,3, Yann Fragnière1, Hong-Hu Meng4, Ying Li2,3, Sébastien Bétrisey1, Adriana Corrales5, Steven Manchester6, Min Deng2,3, Anna K. Jasińska7, Hoàng Văn Sâm8, Gregor Kozlowski1,9 1 Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland 2 Shanghai Chenshan Plant Science Research Centre, Chinese Academy of Sciences / Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China 3 Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China 4 Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Xuefu Rd. 88, Wuhua District, Kunming 650223, China 5 Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Carrera 24No. 63C-69, Bogota 111221, Colombia 6 Florida Museum of Natural History, University of Florida, 1659 Museum Rd, Gainesville, FL 32611, USA 7 Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland 8 Vietnam National University of Forestry, Xuan Mai, Ha Noi, Vietnam 9 Natural History Museum Fribourg, Chemin du Musée 6, CH-1700 Fribourg, Switzerland Correspondence Gregor Kozlowski, Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland. E-mail: [email protected] -
Genomic Variation Among and Within Six Juglans Species
G3: Genes|Genomes|Genetics Early Online, published on May 23, 2018 as doi:10.1534/g3.118.200030 Genomic variation among and within six Juglans species. Kristian A. Stevens1,*, Keith Woeste4, Sandeep Chakraborty2, Marc W. Crepeau1, Charles A. Leslie2, Pedro J. Martínez-García2, Daniela Puiu3, Jeanne Romero-Severson6, Mark Coggeshall4, Abhaya M. Dandekar2, Daniel Kluepfel5, David B. Neale2, Steven L. Salzberg3,7, and Charles H. Langley1 1Department of Evolution and Ecology, University of California, Davis, Davis, CA 2Department of Plant Sciences University of California, Davis, CA 3Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 4 USDA Forest Service Hardwood Tree Improvement and Regeneration Center, Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 5USDA Agricultural Research Station, Davis, CA 6Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 7Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University. * Department of Evolution and Ecology, University of California, Davis, California 95616 Corresponding author: E-mail: [email protected] ABSTRACT Genomic analysis in Juglans (walnuts) is expected to transform the breeding and agricultural production of both nuts and lumber. To that end, we report here the determination of reference sequences for six additional relatives of Juglans regia: Juglans sigillata (also from section Dioscaryon), Juglans nigra, Juglans microcarpa, Juglans hindsii (from section Rhysocaryon), Juglans cathayensis (from section Cardiocaryon), and the closely related Pterocarya stenoptera. While these are ‘draft’ genomes, ranging in size between 640Mbp and 990Mbp, their contiguities and accuracies can support powerful annotations of genomic variation that are often the foundation of new avenues of research and breeding. -
ABSTRACT GUO, YUELONG. Molecular
ABSTRACT GUO, YUELONG. Molecular Systematics of Philadelphus and Molecular Evolution of LFY in the Core Eudicots. (Under the direction of Qiuyun (Jenny) Xiang). Phylogenetic analysis is a powerful tool for elucidating evolutionary relationships of organisms and genes and for testing taxonomic and evolutionary hypotheses. I conducted phylogenetic analyses of DNA sequences from five gene regions to evaluate the classification scheme of Philadelphus and used phylogenetic analyses to provide a framework for examining molecular evolution of the LFY gene in plants. Results from my study suggested that Philadelphus is a paraphyletic group with the monotypic genus Carpenteria nested within. Three evolutionary distinct clades were identified in this large Carpenteria-Philadelphus complex, the subgenus Deutzoides clade, the genus Carpenteria clade, and the remaining Core- Philadelphus clade with each supported by a long branch and merited the recognition of a distinct genus. Our results indicated that Subg. Philadelphus and Subg. Deutzioides are not monophyletic. Subgenera Gemmatus and Macrothyrsus were nested within Subg. Philadelphus, for which the monophyly could not be evaluated due to sampling of only one species from each subgenus. Philadelphus hirsutus from Subg. Duetzioides is also nested within the large subg. Philadelphus, agreeing with evidence from leaf anatomy. Sectional and series classifications within Subg. Philadelphus were not supported by the results from phylogenetic analyses. Results from biogeographic analysis using the Statistical Bayes-DIVA method implemented in the S-DIVA and divergence time analysis accounting for phylogenetic uncertainty and molecular rate variation using BEAST suggested an origin of Philadelphus s. l. in southwestern North America in the Oligocene and subsequently dispersals into other areas.