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Supplementary Tables and Figures Table S19 | Selected genus representatives. Subsampling the r89 dataset set by reducing the number of taxa to one representative per genus resulting in 440 genus representatives. Abbreviations: Completeness (Com), contamination (Cont). #GENOME ID GENUS COM CONT QUALITY DESCRIPTION RS_GCF_000745485.1 g__Methanobacterium_D 99.2 0.8 95.2 NCBI representative genome RS_GCF_000023945.1 g__Halorhabdus 98.25 0.87 93.9 Complete NCBI representative genome RS_GCF_000013445.1 g__Methanospirillum 99.02 0.33 97.37 Complete NCBI representative genome RS_GCF_000012285.1 g__Sulfolobus 99.4 0 99.4 Complete NCBI representative genome RS_GCF_900095295.1 g__Methanobacterium_C 99.73 0 99.73 Complete NCBI representative genome RS_GCF_000191585.1 g__Methanobacterium_B 99.2 0 99.2 Complete NCBI representative genome GB_GCA_000802205.2 g__Nitrosocosmicus 98.06 0.97 93.21 GTDB representative genome RS_GCF_000217995.1 g__Methanosalsum 99.35 0 99.35 Complete NCBI representative genome GB_GCA_000375685.1 g__AAA261-N23 73.65 2.21 62.6 GTDB representative genome RS_GCF_000016525.1 g__Methanobrevibacter_A 100 0 100 Complete NCBI representative genome RS_GCF_000621965.1 g__Methanobrevibacter_B 100 0 100 NCBI representative genome RS_GCF_000513315.1 g__Methanobrevibacter_C 99.2 0 99.2 NCBI representative genome RS_GCF_001639295.1 g__Methanobrevibacter_D 97.6 0 97.6 NCBI representative genome GB_GCA_002497075.1 g__UBA472 98.39 0.97 93.54 GTDB representative genome GB_GCA_001775955.1 g__RBG-13-38-9 81.31 2.8 67.31 GTDB representative genome RS_GCF_000337215.1 g__Natronolimnobius 98.92 0.46 96.62 NCBI representative genome RS_GCF_000455365.1 g__Halopiger_B 99.24 0 99.24 NCBI representative genome RS_GCF_000455345.1 g__Halopiger_A 99.62 0.24 98.42 NCBI representative genome GB_GCA_002839705.1 g__UBA349 100 1.6 92 GTDB representative genome GB_GCA_002503395.1 g__UBA60 68.84 0.8 64.84 GTDB representative genome RS_GCF_000226975.2 g__Halobiforma 99.43 0 99.43 Complete NCBI representative genome GB_GCA_002720095.1 g__UBA68 86 5.6 58 GTDB representative genome RS_GCF_000023965.1 g__Halomicrobium 99.93 0 99.93 Complete NCBI representative genome RS_GCF_000337515.1 g__Halovivax 98.65 0 98.65 NCBI representative genome GB_GCA_900177045.1 g__Nitrosotalea 99.51 0 99.51 GTDB representative genome RS_GCF_000223905.1 g__Haloarcula 99.93 0.4 97.93 Complete NCBI representative genome GB_GCA_002503015.1 g__UBA618 83.42 0 83.42 GTDB representative genome GB_GCA_000965745.1 g__GCA-965745 97.94 0 97.94 GTDB representative genome GB_GCA_001587575.1 g__Methanofastidiosum 90.98 2.72 77.38 GTDB representative genome RS_GCF_000196895.1 g__Halalkalicoccus 99.84 0 99.84 Complete NCBI representative genome GB_GCA_002792685.1 g__CG1-02-32-21 66.2 0.93 61.55 GTDB representative genome RS_GCF_000337895.1 g__Halobiforma_A 86.94 0 86.94 NCBI representative genome GB_GCA_002686295.1 g__GCA-2686295 77.57 0 77.57 GTDB representative genome RS_GCF_000022205.1 g__Halorubrum 99.76 0 99.76 Complete NCBI representative genome RS_GCF_000020905.1 g__Desulfurococcus 100 0 100 Complete NCBI representative genome U_76166 g__UBA11855 71.35 2.8 57.35 GTDB representative genome RS_GCF_000283335.1 g__Halogranum 98.61 0.76 94.81 NCBI representative genome U_70249 g__UBA11716 81.07 0.93 76.42 GTDB representative genome GB_GCA_002785105.1 g__CG03 71.12 0 71.12 GTDB representative genome RS_GCF_000495475.1 g__Halobonum 97.54 1.52 89.94 GTDB representative genome GB_GCA_002254545.1 g__ex4484-224 68.22 0.47 65.87 GTDB representative genome GB_GCA_002505585.1 g__UBA489 79.44 0 79.44 GTDB representative genome U_71212 g__UBA9989 85.28 0 85.28 GTDB representative genome GB_GCA_002687825.1 g__GCA-2687825 65.42 0 65.42 GTDB representative genome U_75797 g__UBA12501 73.68 1.87 64.33 GTDB representative genome RS_GCF_000179575.2 g__Methanothermococcus 99.05 0 99.05 Complete NCBI representative genome GB_GCA_001515185.1 g__DG-33 63.87 0.8 59.87 GTDB representative genome U_71538 g__UBA10219 71.31 2.8 57.31 GTDB representative genome RS_GCF_000264495.1 g__Thermogladius 100 0 100 Complete NCBI representative genome U_71529 g__UBA10210 83.02 2.8 69.02 GTDB representative genome U_71533 g__UBA10214 79.63 0 79.63 GTDB representative genome U_71535 g__UBA10216 66.28 0 66.28 GTDB representative genome GB_GCA_001563305.1 g__ISO4-G1 96.37 0.81 92.32 GTDB representative genome RS_GCF_001971705.1 g__Natronorubrum 99.11 0.19 98.16 Complete NCBI representative genome GB_GCA_002505525.1 g__UBA431 73.36 0 73.36 GTDB representative genome U_67580 g__UBA8695 70.76 0 70.76 GTDB representative genome 1 GB_GCA_002727675.1 g__UBA8690 68.69 0 68.69 GTDB representative genome GB_GCA_001775965.1 g__RBG-16-57-9 76.13 0 76.13 GTDB representative genome GB_GCA_001595885.1 g__SG8-5 72.24 0.8 68.24 GTDB representative genome GB_GCA_002699425.1 g__UBA12002 78.93 0.93 74.28 GTDB representative genome GB_GCA_002495885.1 g__UBA148 96.24 2.29 84.79 GTDB representative genome GB_GCA_002496385.1 g__UBA147 89.6 3.2 73.6 GTDB representative genome GB_GCA_001761425.1 g__SG9 87.77 0 87.77 GTDB representative genome GB_GCA_001775995.1 g__RBG-16-48-13 84.11 1.44 76.91 GTDB representative genome GB_GCA_002495315.1 g__UBA141 91.91 0 91.91 GTDB representative genome RS_GCF_900110215.1 g__Halorientalis 99.93 1.7 91.43 NCBI representative genome RS_GCF_000220175.1 g__Nitrosoarchaeum 100 0 100 GTDB representative genome RS_GCF_000517625.1 g__Halostagnicola 100 0 100 Complete NCBI representative genome RS_GCF_000152265.2 g__Ferroplasma 98.74 0.81 94.69 Complete NCBI representative genome GB_GCA_002505935.1 g__UBA226 71.07 0 71.07 GTDB representative genome RS_GCF_000195935.2 g__Pyrococcus 100 0 100 Complete NCBI representative genome GB_GCA_002495525.1 g__UBA9562 78.9 0.8 74.9 GTDB representative genome GB_GCA_002457195.1 g__UBA501 57.26 0 57.26 GTDB representative genome RS_GCF_000015205.1 g__Pyrobaculum 100 0 100 GTDB representative genome GB_GCA_000008085.1 g__Nanoarchaeum 73.13 0 73.13 GTDB representative genome GB_GCA_002763025.1 g__1-14-0-10-32-24 64.49 0.93 59.84 GTDB representative genome RS_GCF_001748385.1 g__Vulcanisaeta_A 100 2.21 88.95 NCBI representative genome RS_GCF_000017945.1 g__Ignicoccus_A 99.37 0.84 95.17 Complete NCBI representative genome GB_GCA_002718195.1 g__UBA15 68.8 1.52 61.2 GTDB representative genome GB_GCA_001786415.1 g__RBG-13-33-26 65.65 0 65.65 GTDB representative genome GB_GCA_002762795.1 g__1-14-0-10-37-12 78.5 0 78.5 GTDB representative genome RS_GCF_000008265.1 g__Picrophilus 99.59 0 99.59 Complete NCBI representative genome RS_GCF_000196655.1 g__Methanohalobium 100 1.96 90.2 Complete NCBI representative genome GB_GCA_002687795.1 g__GCA-2687795 72.04 0.93 67.39 GTDB representative genome RS_GCF_000304355.2 g__Methanoculleus 98.37 0.65 95.12 Complete NCBI representative genome GB_GCA_002010075.1 g__JdFR-19 96.73 0 96.73 GTDB representative genome GB_GCA_002011125.1 g__JdFR-18 98.13 1.87 88.78 GTDB representative genome RS_GCF_002177135.1 g__Natronolimnobius_A 98.92 0.38 97.02 NCBI representative genome GB_GCA_001723845.1 g__WOR-SM1-SCG-A 79.06 5.14 53.36 GTDB representative genome GB_GCA_002011035.1 g__JdFR-11 100 0.93 95.35 GTDB representative genome GB_GCA_002011075.1 g__JdFR-13 93.2 0.97 88.35 GTDB representative genome GB_GCA_000389735.1 g__Acd1 99.4 0 99.4 GTDB representative genome GB_GCA_001800745.1 g__COMBO-69-17 77.47 0.4 75.47 GTDB representative genome GB_GCA_002779595.1 g__CG07-land 76.25 0 76.25 GTDB representative genome GB_GCA_000402775.1 g__SCGC-AAA252-I15 62.31 0.93 57.66 GTDB representative genome RS_GCF_001469955.1 g__Haloprofundus 99.24 0.1 98.74 NCBI representative genome GB_GCA_001717015.1 g__Methanosuratus 91.59 0 91.59 GTDB representative genome GB_GCA_002688265.1 g__GCA-2688265 74.3 0.93 69.65 GTDB representative genome RS_GCF_000224475.1 g__Halolamina 97.28 1.71 88.73 Complete NCBI representative genome RS_GCF_000213215.1 g__Acidianus 99.4 0 99.4 Complete NCBI representative genome RS_GCF_000006805.1 g__Halobacterium 99.42 0 99.42 Complete NCBI representative genome U_68175 g__UBA10521 79.66 5.23 53.51 GTDB representative genome RS_GCF_900095815.1 g__Methanothermobacter 100 0 100 Complete NCBI representative genome GB_GCA_001563905.1 g__B1-Br10-U2g19 68.61 0 68.61 GTDB representative genome RS_GCF_000215995.1 g__Pyrococcus_A 100 0 100 Complete NCBI representative genome GB_GCA_001412335.1 g__SD8 97.53 2.83 83.38 GTDB representative genome GB_GCA_000405685.1 g__JGI-0000106-J15 56.55 0.49 54.1 GTDB representative genome GB_GCA_002713205.1 g__GCA-2713205 81.07 1.94 71.37 GTDB representative genome GB_GCA_002728275.1 g__GCA-2728275 83.18 1.87 73.83 GTDB representative genome GB_GCA_002855745.1 g__Thermofilum_A 99.26 0.74 95.56 GTDB representative genome RS_GCF_001412615.1 g__Pyrodictium 99.37 3.8 80.37 Complete NCBI representative genome GB_GCA_000496195.1 g__A07HB70 85.2 0.2 84.2 GTDB representative genome RS_GCF_000025325.1 g__Haloterrigena 99.49 0.95 94.74 Complete NCBI representative genome RS_GCF_000015145.1 g__Hyperthermus 98.73 1.42 91.63 Complete NCBI representative genome GB_GCA_002509225.1 g__UBA102 80.76 2.78 66.86 GTDB representative genome GB_GCA_001516585.1 g__Thermocladium 97.43 0.74 93.73 GTDB representative genome GB_GCA_001940705.1 g__AB-25 90.12 3.19 74.17 GTDB representative genome RS_GCF_001950595.1 g__CBA1134 98.8 0.4 96.8 GTDB representative genome GB_GCA_001515205.2 g__YNP-45 89.72 1.87 80.37 GTDB representative genome RS_GCF_001886955.1 g__Halodesulfurarchaeum 96.09 1.06 90.79 Complete NCBI representative genome U_71513 g__GW2011-AR9 75.49 0.93 70.84 GTDB
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    UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE THE ISOLATION AND CHARACTERIZATION OF NOVEL EXTREME HALOPHILIC ARCHAEA FROM A LOW-SALT, SULFIDE- AND SULFUR-RICH SPRING. A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By KRISTEN NICHOLE SAVAGE Norman, Oklahoma 2009 THE ISOLATION AND CHARACTERIZATION OF NOVEL EXTREME HALOPHILIC ARCHAEA FROM A LOW-SALT, SULFIDE- AND SULFUR-RICH SPRING. A DISSERTATION APPROVED FOR THE DEPARTMENT OF BOTANY AND MICROBIOLOGY BY __________________________ Dr. Lee R. Krumholz, Chair __________________________ Dr. Mostafa S. Elshahed __________________________ Dr. Joseph M. Suflita __________________________ Dr. Michael J. McInerney __________________________ Dr. R. Paul Philp © Copyright by KRISTEN NICHOLE SAVAGE 2009 All Rights Reserved. I dedicate this to my parents, Monty and Debbie Savage. You honestly believed from the day that I was born that I could be anything that I wanted to be. Thank you for believing in me, and I hope that I have become a person that you can be proud of. Acknowledgements I would not be here today without the support of many people. I am grateful to so many in this department, for people in my family and my friends but I feel that there are some that deserve special acknowledgement I would like to thank all members of my committee each of you were integral in my development as a scientist. Each of you contributed to my education in one way or another and for that I am very appreciative. I truly believe you have given me the tools to succeed. I know that now it is up to me to make the most of those as I take the next step in my scientific career.
  • The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts

    The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts

    biomolecules Review The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts Laura Matarredona ,Mónica Camacho, Basilio Zafrilla , María-José Bonete and Julia Esclapez * Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain; [email protected] (L.M.); [email protected] (M.C.); [email protected] (B.Z.); [email protected] (M.-J.B.) * Correspondence: [email protected]; Tel.: +34-965-903-880 Received: 31 July 2020; Accepted: 24 September 2020; Published: 29 September 2020 Abstract: Over the years, in order to survive in their natural environment, microbial communities have acquired adaptations to nonoptimal growth conditions. These shifts are usually related to stress conditions such as low/high solar radiation, extreme temperatures, oxidative stress, pH variations, changes in salinity, or a high concentration of heavy metals. In addition, climate change is resulting in these stress conditions becoming more significant due to the frequency and intensity of extreme weather events. The most relevant damaging effect of these stressors is protein denaturation. To cope with this effect, organisms have developed different mechanisms, wherein the stress genes play an important role in deciding which of them survive. Each organism has different responses that involve the activation of many genes and molecules as well as downregulation of other genes and pathways. Focused on salinity stress, the archaeal domain encompasses the most significant extremophiles living in high-salinity environments. To have the capacity to withstand this high salinity without losing protein structure and function, the microorganisms have distinct adaptations.
  • Session 2019-20

    Session 2019-20

    S.N. CONTENTS Page 1. Taxonomy 1 2. H Taxonomy 10 3. K M 14 4. K Protista 32 5. K Fungi 37 6. P Kngdom 53 A. A 53 B. B 62 C. Pteridophyta 66 D. Gymnosperms 71 7. Eerci-I (Cceptua Qti) 83 RLD 8. Eer-II (Previou Y Qestio)2019-20100 9. Eer-III (Analytica Q) 118 10. Eer-IV (Asser & R) 128 11. Virus 132 12. Lchen 135 13. MrrhizaSession 137 14. T World 138 E ALLEN NEET SYLLABUS DIVERSITY IN LIVING WORLD : What is living? ; Biodiversity; Need for classification; Three domains of life; Taxonomy & Systematics; Concept of species and taxonomical hierarchy; Binomial nomenclature; Tools for study of Taxonomy – Museums, Zoos, Herbaria, Botanical gardens. Five kingdom classification; salient features and classification of Monera; Protista and Fungi into major groups; Lichens; Viruses and Viroids. Salient features and classification of plants into major groups-Algae, Bryophytes, Pteridophytes, Gymnosperms and Angiosperms (three to five salient and distinguishing features and at least two examples of each category); Angiosperms- classification up to class, characteristic features and examples). Aristotle (384-322 BC) He was a Greek philosopher and scientist born in the city of Stagira, Chalkidice of classical Greece. His father died when Aristotle was a child. At eighteen, he joined Plato's Academy in Athens and remained there until the age of thirty seven (c.347 BC). His writings cover many subjects including physics, biology, zoology, metaphysics, poetry, politics and government. Shortly after Plato died, Aristotle left Athens and, at the request of Philip of Macedon, tutored Alexander the Great. Aristotle was the first genuine scientist in history and every scientist is in his debt.He is regarded as father of biology and zoology.