Next Generation Sequencing to Investigate Genomic Diversity in Caryophyllales
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Next Generation Sequencing to Investigate Genomic Diversity in Caryophyllales
bioRxiv preprint doi: https://doi.org/10.1101/646133; this version posted February 11, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Next generation sequencing to investigate genomic diversity in Caryophyllales 2 Boas Pucker1,2*, Tao Feng1,3, Samuel F. Brockington1,2 3 1 Evolution and Diversity, Plant Sciences, University of Cambridge, Cambridge, United Kingdom 4 2 Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, Bielefeld, 5 Germany 6 3 Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China 7 * corresponding author: Boas Pucker, [email protected] 8 9 BP: [email protected], ORCID: 0000-0002-3321-7471 10 TF: [email protected], ORCID: 0000-0002-0489-2021 11 SFB: [email protected], ORCID: 0000-0003-1216-219X 12 13 Key words: whole genome sequencing, genome assembly, anthocyanin, betalain, Kewa caespitosa, 14 Macarthuria australis, Pharnaceum exiguum, Caryophyllales 15 16 Abstract 17 Caryophyllales are a highly diverse and large order of plants with a global distribution. While some 18 species are important crops like Beta vulgaris, many others can survive under extreme conditions. 19 This order is well known for the complex pigment evolution, because the pigments anthocyanins and 20 betalains occur with mutual exclusion in species of the Caryophyllales. Here we report about genome 21 assemblies of Kewa caespitosa (Kewaceae), Macarthuria australis (Macarthuriaceae), and 22 Pharnaceum exiguum (Molluginaceae) which are representing different taxonomic groups in the 23 Caryophyllales. -
Species List
Biodiversity Summary for NRM Regions Species List What is the summary for and where does it come from? This list has been produced by the Department of Sustainability, Environment, Water, Population and Communities (SEWPC) for the Natural Resource Management Spatial Information System. The list was produced using the AustralianAustralian Natural Natural Heritage Heritage Assessment Assessment Tool Tool (ANHAT), which analyses data from a range of plant and animal surveys and collections from across Australia to automatically generate a report for each NRM region. Data sources (Appendix 2) include national and state herbaria, museums, state governments, CSIRO, Birds Australia and a range of surveys conducted by or for DEWHA. For each family of plant and animal covered by ANHAT (Appendix 1), this document gives the number of species in the country and how many of them are found in the region. It also identifies species listed as Vulnerable, Critically Endangered, Endangered or Conservation Dependent under the EPBC Act. A biodiversity summary for this region is also available. For more information please see: www.environment.gov.au/heritage/anhat/index.html Limitations • ANHAT currently contains information on the distribution of over 30,000 Australian taxa. This includes all mammals, birds, reptiles, frogs and fish, 137 families of vascular plants (over 15,000 species) and a range of invertebrate groups. Groups notnot yet yet covered covered in inANHAT ANHAT are notnot included included in in the the list. list. • The data used come from authoritative sources, but they are not perfect. All species names have been confirmed as valid species names, but it is not possible to confirm all species locations. -
Next Generation Sequencing to Investigate Genomic Diversity in Caryophyllales
bioRxiv preprint doi: https://doi.org/10.1101/646133; this version posted May 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Next generation sequencing to investigate genomic diversity in Caryophyllales 2 Boas Pucker1,2*, Tao Feng1,3, Samuel F. Brockington1,2 3 1 Evolution and Diversity, Plant Sciences, University of Cambridge, Cambridge, United Kingdom 4 2 Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, Bielefeld, 5 Germany 6 3 Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China 7 * corresponding author: Boas Pucker, [email protected] 8 9 BP: [email protected], ORCID: 0000-0002-3321-7471 10 TF: [email protected], ORCID: 0000-0002-0489-2021 11 SFB: [email protected], ORCID: 0000-0003-1216-219X 12 13 Key words: whole genome sequencing, genome assembly, anthocyanin, betalain, Kewa caespitosa, 14 Macarthuria australis, Pharnaceum exiguum, Caryophyllales 15 16 Abstract 17 Caryophyllales are a highly diverse and large order of plants with a global distribution. While some 18 species are important crops like Beta vulgaris, many others can survive under extreme conditions. 19 This order is well known for the complex pigment evolution, because the red pigments anthocyanin 20 and betalain occur with mutual exclusion in species of the Caryophyllales. Here we report about 21 genome assemblies of Kewa caespitosa (Kewaceae), Macarthuria australis (Macarthuriaceae), and 22 Pharnaceum exiguum (Molluginaceae) which are representing different taxonomic groups in the 23 Caryophyllales. -
Biodiversity Summary: Swan, Western Australia
Biodiversity Summary for NRM Regions Species List What is the summary for and where does it come from? This list has been produced by the Department of Sustainability, Environment, Water, Population and Communities (SEWPC) for the Natural Resource Management Spatial Information System. The list was produced using the AustralianAustralian Natural Natural Heritage Heritage Assessment Assessment Tool Tool (ANHAT), which analyses data from a range of plant and animal surveys and collections from across Australia to automatically generate a report for each NRM region. Data sources (Appendix 2) include national and state herbaria, museums, state governments, CSIRO, Birds Australia and a range of surveys conducted by or for DEWHA. For each family of plant and animal covered by ANHAT (Appendix 1), this document gives the number of species in the country and how many of them are found in the region. It also identifies species listed as Vulnerable, Critically Endangered, Endangered or Conservation Dependent under the EPBC Act. A biodiversity summary for this region is also available. For more information please see: www.environment.gov.au/heritage/anhat/index.html Limitations • ANHAT currently contains information on the distribution of over 30,000 Australian taxa. This includes all mammals, birds, reptiles, frogs and fish, 137 families of vascular plants (over 15,000 species) and a range of invertebrate groups. Groups notnot yet yet covered covered in inANHAT ANHAT are notnot included included in in the the list. list. • The data used come from authoritative sources, but they are not perfect. All species names have been confirmed as valid species names, but it is not possible to confirm all species locations. -
One-Seeded Fruits in the Core Caryophyllales: Their Origin and Structural Diversity
RESEARCH ARTICLE One-Seeded Fruits in the Core Caryophyllales: Their Origin and Structural Diversity Alexander P. Sukhorukov1*, Evgeny V. Mavrodiev2, Madeleen Struwig3, Maya V. Nilova1, Khalima Kh. Dzhalilova1, Sergey A. Balandin4, Andrey Erst5¤a, Anastasiya A. Krinitsyna1 1 Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 2 Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America, 3 Department of Botany, University of Zululand, KwaDlangezwa 3880, KwaZulu-Natal, South Africa, 4 Department of Geobotany, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 5 Herbarium, Central Siberian Botanical Garden, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia ¤a Current address: Tomsk State University, Tomsk, Russia * [email protected] Abstract OPEN ACCESS The core Caryophyllales consist of approximately 30 families (12 000 species) distributed Citation: Sukhorukov AP, Mavrodiev EV, Struwig M, worldwide. Many members evolved one-seeded or conjoined fruits, but their origin and Nilova MV, Dzhalilova KK, Balandin SA, et al. (2015) structural diversity have not been investigated. A comparative anatomical investigation of One-Seeded Fruits in the Core Caryophyllales: Their the one-seeded fruits within the core Caryophyllales was conducted. The origin of the one- Origin and Structural Diversity. PLoS ONE 10(2): e0117974. doi:10.1371/journal.pone.0117974 seeded fruits and the evolutionary reconstructions of some carpological characters were traced using a tree based on rbcl and matK data in order to understand the ancestral char- Academic Editor: Wei Wang, Henan Agricultural Univerisity, CHINA acters and their changes. The one-seeded fruit type is inferred to be an ancestral character state in core Caryophyllales, with a subsequent increase in the seed number seen in all Received: October 28, 2014 major clades. -
Northern Agricultural, Western Australia
Biodiversity Summary for NRM Regions Guide to Users Background What is the summary for and where does it come from? This summary has been produced by the Department of Sustainability, Environment, Water, Population and Communities (SEWPC) for the Natural Resource Management Spatial Information System. It highlights important elements of the biodiversity of the region in two ways: • Listing species which may be significant for management because they are found only in the region, mainly in the region, or they have a conservation status such as endangered or vulnerable. • Comparing the region to other parts of Australia in terms of the composition and distribution of its species, to suggest components of its biodiversity which may be nationally significant. The summary was produced using the Australian Natural Natural Heritage Heritage Assessment Assessment Tool Tool (ANHAT), which analyses data from a range of plant and animal surveys and collections from across Australia to automatically generate a report for each NRM region. Data sources (Appendix 2) include national and state herbaria, museums, state governments, CSIRO, Birds Australia and a range of surveys conducted by or for DEWHA. Limitations • ANHAT currently contains information on the distribution of over 30,000 Australian taxa. This includes all mammals, birds, reptiles, frogs and fish, 137 families of vascular plants (over 15,000 species) and a range of invertebrate groups. The list of families covered in ANHAT is shown in Appendix 1. Groups notnot yet yet covered covered in inANHAT ANHAT are are not not included included in the in the summary. • The data used for this summary come from authoritative sources, but they are not perfect. -
Floristic Survey of Northern Sandplains Between Perth and Geraldton
Research Library Resource management technical reports Natural resources research 8-1994 Floristic survey of Northern sandplains between Perth and Geraldton Edward Arnold Griffin Follow this and additional works at: https://researchlibrary.agric.wa.gov.au/rmtr Part of the Natural Resources and Conservation Commons, and the Plant Sciences Commons Recommended Citation Griffin, E A. (1994), Floristic survey of Northern sandplains between Perth and Geraldton. Department of Agriculture and Food, Western Australia, Perth. Report 144. This report is brought to you for free and open access by the Natural resources research at Research Library. It has been accepted for inclusion in Resource management technical reports by an authorized administrator of Research Library. For more information, please contact [email protected], [email protected], [email protected]. ISSN 1039-7205 DEPARTMENT OF AGRICULTURE WESTERN AUSTRALIA FLORISTIC SURVEY OF NORTHERN SANDPLAINS BETWEEN PERTH AND GERALDTON Compiled by: E.A. Griffin In association with the Spatial Resource Information Group Department of Agriculture Western Australia South Perth, Western Australia 6151 August 1994 2,CDU_Iq' Vin,H L_ __) ICK MU 144 RESOURCE MANAGEMENT TECHNICAL REPORT series Information for contributors Scientists who wish to publish the results of their investigations have access to a large number of journals. However, for a variety of reasons the editors of most of these journals are unwilling to accept articles that are lengthy or contain information that is preliminary in nature. Nevertheless, much material of this type is often of interest and value to other scientists and to administrators, and should be published. -
Evolution of L‐
Research Evolution of L-DOPA 4,5-dioxygenase activity allows for recurrent specialisation to betalain pigmentation in Caryophyllales Hester Sheehan1* , Tao Feng1,2* , Nathanael Walker-Hale1* , Samuel Lopez-Nieves1 , Boas Pucker1,3 , Rui Guo1,2,4 , Won C. Yim5 , Roshani Badgami1 , Alfonso Timoneda1 , Lijun Zhao6 , Helene Tiley7 , Dario Copetti8,9,10 , Michael J. Sanderson11 , John C. Cushman5 , Michael J. Moore7 , Stephen A. Smith6 and Samuel F. Brockington1 1Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge, CB2 3EA, UK; 2CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; 3CeBiTec & Faculty of Biology, Bielefeld University, Universitaetsstrasse, Bielefeld 33615, Germany; 4College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; 5Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89577, USA; 6Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA; 7Department of Biology, Oberlin College, Science Center K111, Oberlin, OH 44074, USA; 8Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; 9Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland; 10Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland; 11Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St, Tucson, AZ 85721, USA Summary Author for correspondence: The evolution of L-DOPA 4,5-dioxygenase activity, encoded by the gene DODA, was a key Samuel F. Brockington step in the origin of betalain biosynthesis in Caryophyllales. We previously proposed that L- Tel: +44 (0)1223 336268 DOPA 4,5-dioxygenase activity evolved via a single Caryophyllales-specific neofunctionalisa- Email: [email protected] tion event within the DODA gene lineage. -
Floristic Survey of Northern Sandplains Between Perth and Geraldton
Research Library Resource management technical reports Natural resources research 8-1994 Floristic survey of Northern sandplains between Perth and Geraldton Edward Arnold Griffin Follow this and additional works at: https://researchlibrary.agric.wa.gov.au/rmtr Part of the Natural Resources and Conservation Commons, and the Plant Sciences Commons Recommended Citation Griffin, E A. (1994), Floristic survey of Northern sandplains between Perth and Geraldton. Department of Primary Industries and Regional Development, Western Australia, Perth. Report 144. This report is brought to you for free and open access by the Natural resources research at Research Library. It has been accepted for inclusion in Resource management technical reports by an authorized administrator of Research Library. For more information, please contact [email protected]. ISSN 1039-7205 DEPARTMENT OF AGRICULTURE WESTERN AUSTRALIA FLORISTIC SURVEY OF NORTHERN SANDPLAINS BETWEEN PERTH AND GERALDTON Compiled by: E.A. Griffin In association with the Spatial Resource Information Group Department of Agriculture Western Australia South Perth, Western Australia 6151 August 1994 2,CDU_Iq' Vin,H L_ __) ICK MU 144 RESOURCE MANAGEMENT TECHNICAL REPORT series Information for contributors Scientists who wish to publish the results of their investigations have access to a large number of journals. However, for a variety of reasons the editors of most of these journals are unwilling to accept articles that are lengthy or contain information that is preliminary in nature. Nevertheless, much material of this type is often of interest and value to other scientists and to administrators, and should be published. The RESOURCE MANAGEMENT TECHNICAL REPORT series provides an avenue for dissemination of such material. -
Blurring the Boundaries Between a Branch and a Flower: Potential Developmental Venues in CACTACEAE
plants Review Blurring the Boundaries between a Branch and a Flower: Potential Developmental Venues in CACTACEAE Isaura Rosas-Reinhold 1,2 , Alma Piñeyro-Nelson 3,4 , Ulises Rosas 1 and Salvador Arias 1,* 1 Instituto de Biología, Jardín Botánico, Universidad Nacional Autónoma de México, Ciudad de México C.P.04510, Mexico; [email protected] (I.R.-R.); [email protected] (U.R.) 2 Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, A. P. 70-153, Ciudad de México C.P.04510, Mexico 3 Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México C.P.04510, Mexico; [email protected] 4 Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México C.P.04960, Mexico * Correspondence: [email protected] Abstract: Flowers are defined as short shoots that carry reproductive organs. In Cactaceae, this term acquires another meaning, since the flower is interpreted as a branch with a perianth at the tip, with all reproductive organs embedded within the branch, thus giving way to a structure that has been called a “flower shoot”. These organs have long attracted the attention of botanists and cactologists; however, the understanding of the morphogenetic processes during the development of these structures is far from clear. In this review, we present and discuss some classic flower concepts used to define floral structures in Cactaceae in the context of current advances in flower developmental genetics and evolution. Finally, we propose several hypotheses to explain the origin Citation: Rosas-Reinhold, I.; of these floral shoot structures in cacti, and we suggest future research approaches and methods that Piñeyro-Nelson, A.; Rosas, U.; could be used to fill the gaps in our knowledge regarding the ontogenetic origin of the “flower” in Arias, S. -
Phylogeny and Generic Delimitation in Molluginaceae, New Pigment Data in Caryophyllales, and the New Family Corbichoniaceae Mats Thulin,1 Abigail J
TAXON 65 (4) • August 2016: 775–793 Thulin & al. • Phylogeny of Molluginaceae Phylogeny and generic delimitation in Molluginaceae, new pigment data in Caryophyllales, and the new family Corbichoniaceae Mats Thulin,1 Abigail J. Moore,2 Hesham El-Seedi,3,4 Anders Larsson,1 Pascal-Antoine Christin5 & Erika J. Edwards2 1 Systematic Biology, EBC, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden 2 Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St, Box G-W, Providence, Rhode Island 02912, U.S.A. 3 Division of Pharmacognosy, BMC, Uppsala University, Box 574, 751 23 Uppsala, Sweden 4 Department of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia 5 Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, U.K. Author for correspondence: Mats Thulin, [email protected] ORCID PAC, http://orcid.org/0000-0001-6292-8734 DOI http://dx.doi.org/10.12705/654.6 Abstract The circumscription of Molluginaceae has changed radically in recent years, with Corbichonia being moved to Lophiocarpaceae, Limeum to Limeaceae, Macarthuria to Macarthuriaceae and all species of Hypertelis, except the type, to Kewa in Kewaceae. In a broad analysis of core Caryophyllales using plastid trnK-matK and rbcL sequences, the position of Molluginaceae in a strict sense as sister to the Portulacineae clade is corroborated, as are the positions of Corbichonia, Limeum and Kewa outside the family. The phylogeny of Molluginaceae is reconstructed based on trnK-matK and nuclear ITS sequences of about half of the currently recognized species in the family and with representatives from all recognized genera.