DOCSLIB.ORG

Polyploidy Underlies Co-Option and Diversification of Biosynthetic Triterpene Pathways in the Apple Tribe

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Polyploidy Underlies Co-Option and Diversification of Biosynthetic Triterpene Pathways in the Apple Tribe Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe Wenbing Sua,1,2, Yi Jingb,1, Shoukai Linc,1, Zhen Yueb,1, Xianghui Yanga,1, Jiabao Xub, Jincheng Wuc, Zhike Zhanga, Rui Xiaa, Jiaojiao Zhud, Ning And, Haixin Chenb, Yanping Honga, Yuan Yuana, Ting Longa, Ling Zhanga, Yuanyuan Jianga, Zongli Liua, Hailan Zhanga, Yongshun Gaoa, Yuexue Liua, Hailan Linc, Huicong Wanga, Levi Yante, Shunquan Lina,3, and Zhenhua Liud,3 aState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; bResearch Cooperation Department, Beijing Genomics Institute Genomics, Shenzhen 518083, China; cKey laboratory of Loquat Germplasm Innovation and Utilization (Fujian Province), Putian University, Putian 351100, China; dJoint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; and eFuture Food Beacon and School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom Edited by Richard A. Dixon, University of North Texas, Denton, TX, and approved April 5, 2021 (received for review January 28, 2021) Whole-genome duplication (WGD) plays important roles in plant loquat, that is, ursolic acid (UA) and corosolic acid (CA), are evolution and function, yet little is known about how WGD un- a major class of bioactive compounds with anti-inflammatory, derlies metabolic diversification of natural products that bear sig- antidiabetic, and anticancer activities (15–17). However, gene nificant medicinal properties, especially in nonmodel trees. Here, pathways encoding the biosynthesis of these bioactive triterpenes we reveal how WGD laid the foundation for co-option and differ- have not been identified and characterized in loquat. It has been entiation of medicinally important ursane triterpene pathway du- proposed that members in the apple tribe such as loquat, apple, plicates, generating distinct chemotypes between species and and pear have been derived from an ancient Rosaceae species between developmental stages in the apple tribe. After generat- via WGD (autopolyploidization), although others have suggested ing chromosome-level assemblies of a widely cultivated loquat allopolyploidizations between sister species (18, 19). High-quality variety and Gillenia trifoliata, we define differentially evolved, du- genome assemblies for species within (apple and pear) (20–22) plicated gene pathways and date the WGD in the apple tribe at and outside (strawberry and peach) (23, 24) the apple tribe have PLANT BIOLOGY 13.5 to 27.1 Mya, much more recent than previously thought. We been generated, yet genome sequences from the tribe’sclosest then functionally characterize contrasting metabolic pathways re- outgroup Gillenieae are still not available. sponsible for major triterpene biosynthesis in G. trifoliata and lo- Here, we merge comparative genomics, transcriptomics, metab- quat, which pre- and postdate the Maleae WGD, respectively. Our olomics, and functional assays to understand how WGD under- work mechanistically details the metabolic diversity that arose pinned the diversification of biosynthetic pathways encoding major post-WGD and provides insights into the genomic basis of medic- inal properties of loquat, which has been used in both traditional Significance and modern medicines. Plants are a primary source of both traditional and modern drugs polyploidy | comparative genomics | evolution | triterpene biosynthesis | due to their astounding capability to synthesize diverse molecules. apple tribe The fruit tree loquat in the apple tribe has been long used in medicine to treat cough, chronic bronchitis, and asthma, yet why lants generate a vast array of specialized metabolites, which loquat—but not its relatives—evolved these medicinal properties Pdiffer by species and tissue. This astounding diversity has is unknown. Here, we generate high-quality genomes of loquat long been thought to arise largely by gene duplications, followed and a relative, which are separated by a recent whole-genome by differentiation of gene expression and function between du- duplication (WGD) around 13.5 to 27.1 Mya. We revealed the post- plicates (1–3). Whole-genome duplication (WGD) contributes to WGD diversification of triterpene biosynthesis and the excep- the generation of single gene duplicates and has played impor- tionally high levels of bioactive ursane-type triterpenes specifically tant roles in plant genome function and evolution (4–6). Ex- in loquat. Our work underscores the importance of WGD- amples for WGD-associated metabolic diversity are known for associated metabolic diversification underlying the bioactivity of the innovation of glucosinolates in the Brassicales and for oil some medicinal plants. biosynthesis in wild olive trees (7–9). In addition to underlying change in enzyme functions, WGD also plays a role in the evolution Author contributions: W.S., Y. Jing, Shoukai Lin, Z.Y., X.Y., Shunquan Lin, and Zhenhua of metabolic gene expression, which further impacts the biosynthesis Liu designed research; W.S., Y. Jing, Shoukai Lin, Z.Y., and X.Y. performed research; Y.Y., of specialized metabolites (3, 10, 11). However, tracing the evo- T.L., L.Z., Y. Jiang, Zongli Liu, H.Z., Y.G., Y.L., H.L., H.W., and Zhenhua Liu contributed new reagents/analytic tools; W.S., Y. Jing, Shoukai Lin, Z.Y., X.Y., J.X., J.W., Z.Z., R.X., J.Z., N.A., lution of a particular metabolic pathway and characterizing func- H.C., Y.H., Shunquan Lin, and Zhenhua Liu analyzed data; and W.S., Y. Jing, L.Y., Shun- tional impacts of WGDs are still challenging, mainly due to the quan Lin, and Zhenhua Liu wrote the paper. ancient status of relevant WGDs and the formidable complexity of The authors declare no competing interest. metabolic pathways. This article is a PNAS Direct Submission. Within the apple tribe there exist medicinally important but This open access article is distributed under Creative Commons Attribution-NonCommercial- understudied species harboring metabolic innovations that we NoDerivatives License 4.0 (CC BY-NC-ND). hypothesized were based on the foundation laid by the tribe- 1W.S., Y. Jing, Shoukai Lin, Z.Y., and X.Y. contributed equally to this work. Eriobotrya specific WGD. A native species from China, loquat ( 2Present address: Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou japonica Lindl), has been cultivated as a fruit tree worldwide and 350013, China. used in both traditional and modern medicines (12, 13). Uses in- 3To whom correspondence may be addressed. Email: [email protected] or loquat@ clude treatment of coughing, documented as early as 1590 CE in the scau.edu.cn. Chinese Encyclopedia of Botany and Medicines [Li Shi-Zhen, Ben This article contains supporting information online at https://www.pnas.org/lookup/suppl/ Cao Gang Mu (14)] and recent commercial herbal syrups treating doi:10.1073/pnas.2101767118/-/DCSupplemental. throat pain. Recent work showed that ursane-type triterpenes in Published May 13, 2021. PNAS 2021 Vol. 118 No. 20 e2101767118 https://doi.org/10.1073/pnas.2101767118 | 1of11 Downloaded by guest on September 25, 2021 triterpenes within and outside of theappletribe.Wefirstgenerate To determine species groupings in relation to the Maleae WGD, chromosome-level assemblies of a widely cultivated loquat cul- we used 661 single-copy orthologs from 10 related species for tivar E. japonica cultivar (cv.) Jiefangzhong (which produces high phylogenetic analysis. This revealed loquat grouping with pear and levels of ursane-type triterpene) and Gillenia trifoliata.This apple and separated from G. trifoliata, peach (Prunus persica), and allowed us to first identify a single WGD marking the origin of the other Rosaceae species (Fig. 1A). Molecular clock analysis indi- apple tribe at 13.5 to 27.1 Mya, much more recent than previously cated that the apple tribe (Maleae) diverged from Gillenieae be- thought (18, 22). We then identified a well-conserved group of tween 13.5 and 27.1 Mya (Fig. 1A), suggesting that the emergence enzymatic genes, which we functionally confirm to be responsible of the apple tribe was much more recent than previously thought for the biosynthesis of bioactive ursane-type triterpenes differen- (18, 22). Using intra- and intergenomic syntenic analysis, we ob- tially in species within (apple, pear, and loquat) and outside (G. served a 2:1 syntenic depth ratio when comparing loquat with the trifoliata and peach) the apple tribe. Our analysis shows how WGD species (G. trifoliata and P. Persica) that diverged before the split underlaid the diversification of metabolic pathways responsible for with Maleae but showed a 1:1 syntenic depth ratio within Maleae major triterpene biosynthesis. In addition, WGD provided a basis (apple versus loquat) (Fig. 1B). Furthermore, the spectrum of for the evolution of functionally critical gene expression differenti- synonymous substitutions per synonymous site (Ks) of these syn- ation and co-option for biosynthesis of triterpenes. Taken together, tenic blocks confirmed a single WGD peak (Ks around 0.16) for our results provide a clear example of the post-WGD diversification the two Maleae species (loquat and apple) but not for G. trifoliata of an important metabolic pathway and identify the genomic basis and the outgroup
Load more

Recommended publications
  • Stomata Size in Relation to Ploidy Level in North American Hawthorns (Crataegus, Rosaceae) Author(S): Brechann V
    Stomata Size in Relation to Ploidy Level in North American Hawthorns (Crataegus, Rosaceae) Author(s): Brechann V. McGoey Kelvin Chau Timothy A. Dickinson Source: Madroño, 61(2):177-193. 2014. Published By: California Botanical Society DOI: http://dx.doi.org/10.3120/0024-9637-61.2.177 URL: http://www.bioone.org/doi/full/10.3120/0024-9637-61.2.177 BioOne (www.bioone.org) is a nonprofit, online aggregation of core research in the biological, ecological, and environmental sciences. BioOne provides a sustainable online platform for over 170 journals and books published by nonprofit societies, associations, museums, institutions, and presses. Your use of this PDF, the BioOne Web site, and all posted and associated content indicates your acceptance of BioOne’s Terms of Use, available at www.bioone.org/page/ terms_of_use. Usage of BioOne content is strictly limited to personal, educational, and non-commercial use. Commercial inquiries or rights and permissions requests should be directed to the individual publisher as copyright holder. BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research. MADRON˜ O, Vol. 61, No. 2, pp. 177–193, 2014 STOMATA SIZE IN RELATION TO PLOIDY LEVEL IN NORTH AMERICAN HAWTHORNS (CRATAEGUS,ROSACEAE) BRECHANN V. MCGOEY Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2 [email protected] KELVIN CHAU Canadian Food Inspection Agency, 1124 Finch Ave. W, Unit 2, Toronto, ON, Canada M3J 2E2 TIMOTHY A. DICKINSON Green Plant Herbarium (TRT), Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, ON, Canada M5S 2C6, and Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2 ABSTRACT The impacts of ploidy level changes on plant physiology and ecology present interesting avenues of research, and many questions remain unanswered.
    [Show full text]
  • Natural Communities of Michigan: Classification and Description
    Natural Communities of Michigan: Classification and Description Prepared by: Michael A. Kost, Dennis A. Albert, Joshua G. Cohen, Bradford S. Slaughter, Rebecca K. Schillo, Christopher R. Weber, and Kim A. Chapman Michigan Natural Features Inventory P.O. Box 13036 Lansing, MI 48901-3036 For: Michigan Department of Natural Resources Wildlife Division and Forest, Mineral and Fire Management Division September 30, 2007 Report Number 2007-21 Version 1.2 Last Updated: July 9, 2010 Suggested Citation: Kost, M.A., D.A. Albert, J.G. Cohen, B.S. Slaughter, R.K. Schillo, C.R. Weber, and K.A. Chapman. 2007. Natural Communities of Michigan: Classification and Description. Michigan Natural Features Inventory, Report Number 2007-21, Lansing, MI. 314 pp. Copyright 2007 Michigan State University Board of Trustees. Michigan State University Extension programs and materials are open to all without regard to race, color, national origin, gender, religion, age, disability, political beliefs, sexual orientation, marital status or family status. Cover photos: Top left, Dry Sand Prairie at Indian Lake, Newaygo County (M. Kost); top right, Limestone Bedrock Lakeshore, Summer Island, Delta County (J. Cohen); lower left, Muskeg, Luce County (J. Cohen); and lower right, Mesic Northern Forest as a matrix natural community, Porcupine Mountains Wilderness State Park, Ontonagon County (M. Kost). Acknowledgements We thank the Michigan Department of Natural Resources Wildlife Division and Forest, Mineral, and Fire Management Division for funding this effort to classify and describe the natural communities of Michigan. This work relied heavily on data collected by many present and former Michigan Natural Features Inventory (MNFI) field scientists and collaborators, including members of the Michigan Natural Areas Council.
    [Show full text]
  • Human OMG Blocking Peptide (CDBP2120) This Product Is for Research Use Only and Is Not Intended for Diagnostic Use
    Human OMG blocking peptide (CDBP2120) This product is for research use only and is not intended for diagnostic use. PRODUCT INFORMATION Product Overview Blocking/Immunizing peptide for anti-OMG antibody Antigen Description OMG (oligodendrocyte myelin glycoprotein) is a protein-coding gene. Diseases associated with OMG include patulous eustachian tube, and internuclear ophthalmoplegia, and among its related super-pathways are p75NTR regulates axonogenesis and Development MAG-dependent inhibition of neurite outgrowth. GO annotations related to this gene include identical protein binding. Nature Synthetic Expression System N/A Species Human Species Reactivity Human Conjugate Unconjugated Applications Apuri, BL, ELISA Procedure None Format Lyophilized powder Size 100 μg Preservative None Storage Shipped at ambient temperature, store at -20°C. ANTIGEN GENE INFORMATION Gene Name OMG oligodendrocyte myelin glycoprotein [ Homo sapiens ] Official Symbol OMG Synonyms OMG; oligodendrocyte myelin glycoprotein; oligodendrocyte-myelin glycoprotein; OMGP; Entrez Gene ID 4974 mRNA Refseq NM_002544 45-1 Ramsey Road, Shirley, NY 11967, USA Email: [email protected] Tel: 1-631-624-4882 Fax: 1-631-938-8221 1 © Creative Diagnostics All Rights Reserved Protein Refseq NP_002535 UniProt ID P23515 Chromosome Location 17q11-q12 Pathway Axonal growth inhibition (RHOA activation), organism-specific biosystem; Signal Transduction, organism-specific biosystem; Signalling by NGF, organism-specific biosystem; p75 NTR receptor-mediated signalling, organism-specific biosystem; p75(NTR)-mediated signaling, organism-specific biosystem; p75NTR regulates axonogenesis, organism-specific biosystem; Function identical protein binding; 45-1 Ramsey Road, Shirley, NY 11967, USA Email: [email protected] Tel: 1-631-624-4882 Fax: 1-631-938-8221 2 © Creative Diagnostics All Rights Reserved.
    [Show full text]
  • Phylogeny of Maleae (Rosaceae) Based on Multiple Chloroplast Regions: Implications to Genera Circumscription
    Hindawi BioMed Research International Volume 2018, Article ID 7627191, 10 pages https://doi.org/10.1155/2018/7627191 Research Article Phylogeny of Maleae (Rosaceae) Based on Multiple Chloroplast Regions: Implications to Genera Circumscription Jiahui Sun ,1,2 Shuo Shi ,1,2,3 Jinlu Li,1,4 Jing Yu,1 Ling Wang,4 Xueying Yang,5 Ling Guo ,6 and Shiliang Zhou 1,2 1 State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China 2University of the Chinese Academy of Sciences, Beijing 100043, China 3College of Life Science, Hebei Normal University, Shijiazhuang 050024, China 4Te Department of Landscape Architecture, Northeast Forestry University, Harbin 150040, China 5Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China 6Beijing Botanical Garden, Beijing 100093, China Correspondence should be addressed to Ling Guo; [email protected] and Shiliang Zhou; [email protected] Received 21 September 2017; Revised 11 December 2017; Accepted 2 January 2018; Published 19 March 2018 Academic Editor: Fengjie Sun Copyright © 2018 Jiahui Sun et al. Tis is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Maleae consists of economically and ecologically important plants. However, there are considerable disputes on generic circumscription due to the lack of a reliable phylogeny at generic level. In this study, molecular phylogeny of 35 generally accepted genera in Maleae is established using 15 chloroplast regions. Gillenia isthemostbasalcladeofMaleae,followedbyKageneckia + Lindleya, Vauquelinia, and a typical radiation clade, the core Maleae, suggesting that the proposal of four subtribes is reasonable.
    [Show full text]
  • CALIFORNIA STATE UNIVERSITY, NORTHRIDGE Bioinformatic
    CALIFORNIA STATE UNIVERSITY, NORTHRIDGE Bioinformatic Comparison of the EVI2A Promoter and Coding Regions A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Biology By Max Weinstein May 2020 The thesis of Max Weinstein is approved: Professor Rheem D. Medh Date Professor Virginia Oberholzer Vandergon Date Professor Cindy Malone, Chair Date California State University Northridge ii Table of Contents Signature Page ii List of Figures v Abstract vi Introduction 1 Ecotropic Viral Integration Site 2A, a Gene within a Gene 7 Materials and Methods 11 PCR and Cloning of Recombinant Plasmid 11 Transformation and Cell Culture 13 Generation of Deletion Constructs 15 Transfection and Luciferase Assay 16 Identification of Transcription Factor Binding Sites 17 Determination of Region for Analysis 17 Multiple Sequence Alignment (MSA) 17 Model Testing 18 Tree Construction 18 Promoter and CDS Conserved Motif Search 19 Results and Discussion 20 Choice of Species for Analysis 20 Mapping of Potential Transcription Factor Binding Sites 20 Confirmation of Plasmid Generation through Gel Electrophoresis 21 Analysis of Deletion Constructs by Transient Transfection 22 EVI2A Coding DNA Sequence Phylogenetics 23 EVI2A Promoter Phylogenetics 23 EVI2A Conserved Leucine Zipper 25 iii EVI2A Conserved Casein kinase II phosphorylation site 26 EVI2A Conserved Sox-5 Binding Site 26 EVI2A Conserved HLF Binding Site 27 EVI2A Conserved cREL Binding Site 28 EVI2A Conserved CREB Binding Site 28 Summary 29 Appendix: Figures 30 Literature Cited 44 iv List of Figures Figure 1. EVI2A is nested within the gene NF1 30 Figure 2 Putative Transcriptions Start Site 31 Figure 3. Gel Electrophoresis of pGC Blue cloned, Restriction Digested Plasmid 32 Figure 4.
    [Show full text]
  • (Rosaceae), I. Differentiation of Mespilus and Crataegus
    Phytotaxa 257 (3): 201–229 ISSN 1179-3155 (print edition) http://www.mapress.com/j/pt/ PHYTOTAXA Copyright © 2016 Magnolia Press Article ISSN 1179-3163 (online edition) http://dx.doi.org/10.11646/phytotaxa.257.3.1 STUDIES IN MESPILUS, CRATAEGUS, AND ×CRATAEMESPILUS (ROSACEAE), I. DIFFERENTIATION OF MESPILUS AND CRATAEGUS, EXPANSION OF ×CRATAEMESPILUS, WITH SUPPLEMENTARY OBSERVATIONS ON DIFFERENCES BETWEEN THE CRATAEGUS AND AMELANCHIER CLADES JAMES B. PHIPPS Department of Biology, The University of Western Ontario, London, Ontario N6A 5B7, Canada; email: [email protected] Abstract The paper argues the position for retaining a monotypic Mespilus, i.e., in the sense of M. germanica, the medlar. Recent cladistic papers lend support for Mespilus being sister to Crataegus, and there is a clear morphological distinction from Cra- taegus, emphasized by adaptation to carnivore frugivory. Mespilus secured, the paper then treats each of the known hybrids between Mespilus and Crataegus, making the new combination Crataemespilus ×canescens (J.B. Phipps) J.B. Phipps. Keywords: Crataemespilus ×canescens (J.B. Phipps) J.B. Phipps comb. nov.; inflorescence position; medlar; Mespilus a folk-genus; Mespilus distinct from Crataegus; Rosaceae; taxonomic history of Mespilus Introduction The author has a long-standing interest in generic delimitation in the Maloid genera of the Rosaceae (Maleae Small, formerly Maloideae C. Weber, Pyrinae Dumort.), as shown particularly in a series of papers with K. Robertson, J. Rohrer, and P.G. Smith (Phipps et al. 1990, 1991; Robertson at al. 1991, 1992; Rohrer at al. 1991, 1994) which treated all 28 genera of Maleae as recognised by us. There is also a revisionary treatment of New World Heteromeles M.J.
    [Show full text]
  • PROGRAM and ABSTRACTS for 2020 ANNUAL MEETING of the SOCIETY for GLYCOBIOLOGY November 9–12, 2020 Phoenix, AZ, USA 1017 2020 Sfg Virtual Meeting Preliminary Schedule
    Downloaded from https://academic.oup.com/glycob/article/30/12/1016/5948902 by guest on 25 January 2021 PROGRAM AND ABSTRACTS FOR 2020 ANNUAL MEETING OF THE SOCIETY FOR GLYCOBIOLOGY November 9–12, 2020 Phoenix, AZ, USA 1017 2020 SfG Virtual Meeting Preliminary Schedule Mon. Nov 9 (Day 1) TOKYO ROME PACIFIC EASTERN EASTERN SESSION TIME TIME TIME START END TIME TIME 23:30 15:30 6:30 9:30 9:50 Welcome and Introduction - Michael Tiemeyer, CCRC UGA Downloaded from https://academic.oup.com/glycob/article/30/12/1016/5948902 by guest on 25 January 2021 23:30 15:30 6:30 9:50 – 12:36 Session 1: Glycobiology of Normal and Disordered Development | Chair: Kelly Ten-Hagen, NIH/NIDCR 23:50 15:50 6:50 9:50 10:10 KEYNOTE: “POGLUT1 mutations cause myopathy with reduced Notch signaling and α-dystroglycan hypoglycosylation” - Carmen Paradas Lopez, Biomedical Institute Sevilla 0:12 16:12 7:12 10:12 10:24 Poster Talk: “Regulation of Notch signaling by O-glycans in the intestine” – Mohd Nauman, Albert Einstein 0:26 16:26 7:26 10:26 10:38 Poster Talk: “Generation of an unbiased interactome for the tetratricopeptide repeat domain of the O-GlcNAc transferase indicates a role for the enzyme in intellectual disability” – Hannah Stephen, University of Georgia 0:40 16:30 7:30 10:40 10:50 Q&A 10:52 11:12 7:52 10:52 11:12 KEYNOTE: “Aberrations in N-cadherin Processing Drive PMM2-CDG Pathogenesis” - Heather Flanagan-Steet, Greenwood Genetics Center 1:14 11:26 8:14 11:14 11:26 Poster Talk: “Functional analyses of TMTC-type protein O-mannosyltransferases in Drosophila model
    [Show full text]
  • Mysterious Chokeberries: New Data on the Diversity and Phylogeny of Aronia Medik. (Rosaceae)
    European Journal of Taxonomy 570: 1–14 ISSN 2118-9773 https://doi.org/10.5852/ejt.2019.570 www.europeanjournaloftaxonomy.eu 2019 · Shipunov A. et al. This work is licensed under a Creative Commons Attribution License (CC BY 4.0). Research article Mysterious chokeberries: new data on the diversity and phylogeny of Aronia Medik. (Rosaceae) Alexey SHIPUNOV 1,*, Sofia GLADKOVA 2, Polina TIMOSHINA 3, Hye Ji LEE 4, Jinhee CHOI 5, Sarah DESPIEGELAERE 5 & Bryan CONNOLLY 5 1,4,5,6 Minot State University, Biology, 500 University Ave, Minot, ND, USA. 2,3 Department of Biology, Moscow State University, Russia. 7 Framingham State University, Biology, 100 State St, Framingham, MA, USA. * Corresponding author: [email protected] 2 Email: [email protected] 3 Email: [email protected] 4 Email: [email protected] 5 Email: [email protected] 6 Email: [email protected] 7 Email: [email protected] Abstract. Aronia Medik. (chokeberry, Rosaceae) is a genus of woody shrubs with two or three North American species. Species boundaries and relationships between species of Aronia are frequently under question. The only European species in the genus, A. mitschurinii A.K.Skvortsov & Maitul., is suggested to be an inter-generic hybrid. In order to clarify the relationships between species of Aronia, we performed several morphometric and molecular analyses and found that the molecular and morphological diversity within data on American Aronia is low, and species boundaries are mostly not clearly expressed. Whereas morphology is able to separate American species from A. mitschurinii, there is no support for such discrimination from the molecular data; our analyses did not reveal evidence of A.
    [Show full text]
  • The Transcriptional Landscape and Hub Genes Associated with Physiological Responses to Drought Stress in Pinus Tabuliformis
    International Journal of Molecular Sciences Article The Transcriptional Landscape and Hub Genes Associated with Physiological Responses to Drought Stress in Pinus tabuliformis Tariq Pervaiz 1,† , Shuang-Wei Liu 1,†, Saleem Uddin 1 , Muhammad Waqas Amjid 2 , Shi-Hui Niu 1,* and Harry X. Wu 1,3,4,* 1 Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; [email protected] (T.P.); [email protected] (S.-W.L.); [email protected] (S.U.) 2 State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China; [email protected] 3 Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Linnaeus vag 6, SE-901 83 Umea, Sweden 4 CSIRO National Research Collection Australia, Black Mountain Laboratory, Canberra, ACT 2601, Australia * Correspondence: [email protected] (S.-H.N.); [email protected] (H.X.W.) † These authors contributed equally. Abstract: Drought stress has an extensive impact on regulating various physiological, metabolic, and molecular responses. In the present study, the Pinus tabuliformis transcriptome was studied to Citation: Pervaiz, T.; Liu, S.-W.; evaluate the drought-responsive genes using RNA- Sequencing approache. The results depicted Uddin, S.; Amjid, M.W.; Niu, S.-H.; that photosynthetic rate and H2O conductance started to decline under drought but recovered 24 h Wu, H.X. The Transcriptional after re-watering; however, the intercellular CO2 concentration (Ci) increased with the onset of Landscape and Hub Genes drought.
    [Show full text]
  • Discoveryspace: an Interactive Data Analysis Application
    Open Access Software2007RobertsonetVolume al. 8, Issue 1, Article R6 DiscoverySpace: an interactive data analysis application comment Neil Robertson, Mehrdad Oveisi-Fordorei, Scott D Zuyderduyn, Richard J Varhol, Christopher Fjell, Marco Marra, Steven Jones and Asim Siddiqui Address: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre (BCCRC), British Columbia Cancer Agency (BCCA), Vancouver, BC, Canada. reviews Correspondence: Neil Robertson. Email: [email protected]. Mehrdad Oveisi-Fordorei. Email: [email protected]. Asim Siddiqui. Email: [email protected] Published: 08 January 2007 Received: 24 March 2006 Revised: 4 July 2006 Genome Biology 2007, 8:R6 (doi:10.1186/gb-2007-8-1-r6) Accepted: 8 January 2007 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2007/8/1/R6 reports © 2007 Robertson et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Interactive<p>DiscoverySpace, data analysis a graphical application for bioinformatics data analysis, in particular analysis of SAGE data, is described</p> deposited research Abstract DiscoverySpace is a graphical application for bioinformatics data analysis. Users can seamlessly traverse references between biological databases and draw together annotations in an intuitive tabular interface. Datasets can be compared using a suite of novel tools to aid in the identification of significant patterns. DiscoverySpace is of broad utility and its particular strength is in the analysis of serial analysis of gene expression (SAGE) data.
    [Show full text]
  • Supplementary Methods
    Supplementary methods Somatic mutation and gene expression data This section describes the somatic mutation and gene expression data used in our pathway and network analysis. Gene-level mutation data Pathway and network databases record interactions at the gene or protein level. Therefore, we combine somatic mutation data for coding and non-coding elements into gene-level scores using the following procedure. P-values from the PCAWG-2-5-9-14 analysis summarize the statistical significance of somatic mutations on these regions. For each gene, we use Fisher’s method to combine P-values for multiple regions that are associated to the gene to create three gene scores: (1) a coding gene score (GS-C); (2) a non-coding (promoter, 5’ UTR, 3’ UTR, and enhancer) gene score (GS-N); and (3) a combined coding-and-non-coding (coding, promoter, 5’ UTR, 3’ UTR, and enhancer) gene score (GS-CN). Mutation data We obtained and processed two sources of somatic mutation data on various coding and non- coding regions associated with one or more genes: (1) binary mutation data that describe the presence or absence of mutations in a region for each sample in a tumor cohort and (2) integrated driver score P-values that describe the statistical significance of mutations in a region across samples in a cohort. 1. For binary mutation data we used the following procedure: a. We obtained somatic mutations from the PCAWG MAF (syn7364923). b. We retained mutations in a pan-cancer tumor cohort that excludes samples from the lymphoma and melanoma tumor cohorts, i.e., the Lymph-BNHL, Lymph-CLL, Lymph-NOS, and Skin-Melanoma cohorts, as well as 69 hypermutated samples with over 30 mutations/MB, which are listed by donor (syn7894281) or aliquot ID (syn7814911).
    [Show full text]
  • The Draft Genomes of Softshell Turtle and Green Sea Turtle Yield Insights
    LETTERS OPEN The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan Zhuo Wang1,12, Juan Pascual-Anaya2,12, Amonida Zadissa3,12, Wenqi Li4,12, Yoshihito Niimura5, Zhiyong Huang1, Chunyi Li4, Simon White3, Zhiqiang Xiong1, Dongming Fang1, Bo Wang1, Yao Ming1, Yan Chen1, Yuan Zheng1, Shigehiro Kuraku2, Miguel Pignatelli6, Javier Herrero6, Kathryn Beal6, Masafumi Nozawa7, Qiye Li1, Juan Wang1, Hongyan Zhang4, Lili Yu1, Shuji Shigenobu7, Junyi Wang1, Jiannan Liu4, Paul Flicek6, Steve Searle3, Jun Wang1,8,9, Shigeru Kuratani2, Ye Yin4, Bronwen Aken3, Guojie Zhang1,10,11 & Naoki Irie2 The unique anatomical features of turtles have raised Three major hypotheses have been proposed for the evolutionary unanswered questions about the origin of their unique body origin of turtles, including that they (i) constitute early-diverged rep- plan. We generated and analyzed draft genomes of the soft- tiles, called anapsids3, (ii) are a sister group of the lizard-snake-tuatara shell turtle (Pelodiscus sinensis) and the green sea turtle (Lepidosauria) clade4 or (iii) are closely related to a lineage that (Chelonia mydas); our results indicated the close relationship includes crocodilians and birds (Archosauria)5–8. Even using molecular of the turtles to the bird-crocodilian lineage, from which they approaches, inconsistency still remains6–9. To clarify the evolution of split ~267.9–248.3 million years ago (Upper Permian to Triassic). the turtle-specific body plan, we first addressed the question of evolu- We also found extensive expansion of olfactory receptor genes tionary origin of the turtle by performing the first genome-wide phylo- in these turtles.
    [Show full text]