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Morphological and Molecular Taxonomic Identification and Phylogenetics of Criconematoidea Marco Cordero University of Arkansas, Fayetteville

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Morphological and Molecular Taxonomic Identification and Phylogenetics of Criconematoidea Marco Cordero University of Arkansas, Fayetteville University of Arkansas, Fayetteville ScholarWorks@UARK Theses and Dissertations 5-2013 Morphological and Molecular Taxonomic Identification and Phylogenetics of Criconematoidea Marco Cordero University of Arkansas, Fayetteville Follow this and additional works at: http://scholarworks.uark.edu/etd Part of the Plant Breeding and Genetics Commons, and the Plant Pathology Commons Recommended Citation Cordero, Marco, "Morphological and Molecular Taxonomic Identification and Phylogenetics of Criconematoidea" (2013). Theses and Dissertations. 774. http://scholarworks.uark.edu/etd/774 This Dissertation is brought to you for free and open access by ScholarWorks@UARK. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of ScholarWorks@UARK. For more information, please contact [email protected], [email protected]. MORPHOLOGICAL AND MOLECULAR TAXONOMIC IDENTIFICATION AND PHYLOGENETICS OF CRICONEMATOIDEA MORPHOLOGICAL AND MOLECULAR TAXONOMIC IDENTIFICATION AND PHYLOGENETICS OF CRICONEMATOIDEA A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Plant Science By Marco Antonio Cordero López Universidad Nacional Experimental del Táchira Agronomic Engineering, 1986 Universidad Nacional Experimental del Táchira Master in Agronomy, 1996 May 2013 University of Arkansas ABSTRACT The superfamily Criconematoidea has been studied since 1886. It is composed of two families: Criconematidae (subfam. Criconematinae, Hemicycliophorinae) and Tylenchulidae (subfam. Tylenchulinae, Paratylenchinae and Tylenchocriconematinae). Multiple species in genera have been identified and differences and similarities have been found. Species belonging to genera Mesocriconema and Criconemoides show very few differences making their identification difficult. Seventy two populations were studied. They were collected in Arkansas and/or received from the following states: California, Florida, Kansas, Missouri, North Carolina and Tennessee. Populations of the following species were identified: Mesocriconema curvatum, M. kirjanovae, M. onoense, M. ornatum, M. sphaerocephala, M. surinamense, M. vadense, M. xenoplax, Criconemoides informis, Bakernema inaequale, C. petasum, C. sphagni, C. mutabile, Ogma octangulare, Xenocriconemella macrodora, Hemicriconemoides chitwoodi, Hemicycliophora epicharoides, H. gigas, H. labiata, H. typica, H. pruni, H. shepherdi, H. vidua, H. zuckermani, Gracilacus straeleni and Paratylenchus labiosus. The new species reported are Mesocriconema ozarkiense n. sp., Criconema arkaense n. sp., Criconema warrenense n. sp., Hemicaloosia uarki n. sp and Hemicycliophora wyei n. sp. In addition, species were characterized morphologically and molecularly using the conserved region 18S for some species and the Internal transcriber spacer 1, ITS1, from ribosomal DNA for all. Phylogenetic studies were performed using both rDNA amplicons to study the relationship among genera and species rejecting the hypothesis of a common ancestor. This dissertation is approved for recommendation To the Graduate Council. Dissertation Director ________________________________________________ Dr. Robert T. Robbins Dissertation Committee: ________________________________________________ Dr. Terrence L. Kirkpatrick ________________________________________________ Dr. Allen Szalanski _________________________________________________ Dr. Craig Rothrock _________________________________________________ Dr. John Clark DISSERTATION DUPLICATION RELEASE I hereby authorize the University of Arkansas Libraries to duplicate this dissertation when needed for research and/or scholarship Agreed ____________________________________________ Marco Antonio Cordero López Refuse ____________________________________________ Marco Antonio Cordero López ACKNOWLEDGMENTS Its have been four years of intense and rewarding work at Cralley – Warren Laboratory at Arkansas Agricultural Research and Extension Center in Fayetteville. I would like to express my sincere gratitude to my mayor advisor Dr. Robert T. Robbins for his direction, assistance, guidance and friendship. My deepest gratitude to Dr. Allen Szalanski for help me with the molecular techniques and software used in this research. Equally, I want to thank to the rest of my committee members: Dr. Terrence L. Kirkpatrick, Dr. Craig Rothrock and Dr. John Clark for their advice and guidance. Special thanks to the Department head of the Plant Pathology Department Dr Rick Bennett and the staff at campus: Cindy Morley, Debby Huey and Kim Keeney and my appreciation to Pat Nelson for her friendship and help at the beginning of my studies. Thank you very much to the personnel at Cralley-Warren Laboratory: Larry Jackson, Devine Crippen, Mary Thomas and Virgil Piazza The author would like to thanks also to all the graduate students at the Department of Plant Pathology for your friendship and support. Special thanks to Robin Roggio at Interlibrary loan at Mullins Library for her help finding valuable papers that help me to reach my objectives. To conclude, I would to thanks my father, my mother, my sister and brother for their invaluable support. DEDICATORY To my grandparents Candelaria, Nacha, Juan Antonio, and Enrique. TABLE OF CONTENTS I. INTRODUCTION 1 II. TAXONOMIC AND MOLECULAR IDENTIFICATION OF MESOCRICONEMA AND CRICONEMOIDES SPECIES (NEMATODA: CRICONEMATIDAE). 3 A. Abstract 4 B. Introduction 5 C. Materials and Methods 7 D. Results and Conclusions 9 E. Literature cited 35 F. Tables 41 G. Figures 60 H. Appendix 78 III. TAXONOMIC AND MOLECULAR IDENTIFICATION OF BAKERNEMA, CRICONEMA, HEMICRICONEMOIDES, OGMA AND XENOCRICONEMELLA SPECIES (NEMATODA: CRICONEMATIDAE) 80 A. Abstract 81 B. Introduction 82 C. Materials and Methods 83 D. Results and Conclusions 86 E. Literature cited 104 F. Tables 110 G. Figures 118 H. Appendix 132 IV. TAXONOMIC AND MOLECULAR IDENTIFICATION OF HEMICALOOSIA, HEMICYCLIOPHORA, GRACILACUS AND PARATYLENCHUS SPECIES (NEMATODA: CRICONEMATIDAE) 134 A. Abstract 135 B. Introduction 136 C. Materials and Methods 137 D. Results and Conclusions 140 E. Literature cited 166 F. Tables 171 G. Figures 181 H. Appendix 195 V. MOLECULAR BASED-PHYLOGENETIC RELATIONSHIPS IN THE SUPERFAMILY CRICONEMATOIDEA 197 A. Abstract 198 B. Introduction 199 C. Materials and Methods 201 D. Results and Conclusions 203 E. Literature cited 208 F. Table 212 G. Figures 213 VI. GENERAL CONCLUSION 218 INTRODUCTION The history of the superfamily Criconematoidea began in 1882-1883 at the international expedition to Hoste Island, Chile from which Criconema giardi (Certes, 1889) Micoletsky, 1925 was described. Two schemes of classification for Criconematoidea have been proposed: A) the superfamily Criconematoidea was raised one level to the suborder Criconematina by Siddiqi with three families Criconematoidea, Hemiciclyophoroidea and Tylenchuloidea and B) the scheme by Raski and Luc which proposed the superfamily Criconematoidea consisting of two families Criconematidae and Tylenchulidae. The morphological character that clusters the superfamiliy Criconematoidea is the typical criconematoid esophagus. However, the group shows diverse degrees of variation on morpho-anatomical characters among the species which frequently makes their identification complex. Molecular phylogenetics is an excellent method to determine relationships among taxa based on the information resulting from different molecular markers and morphological identification. The nuclear ribosomal genes, 18S, 5.8S and 28S, which have low variability (i.e. low rate of evolution), are important genetic markers currently used in phylogenetic studies on different organisms in the same taxa that diverged a long time ago. Conversely, the ITS1-rDNA and ITS2 -rDNA regions have a high rate of evolution because of mutations. These markers show greater similarities within species and less among species. Therefore the combination of morphological and taxonomic identification along with the use of nuclear ribosomal 18S and internal transcribed spacer 1 (ITS1) are promising tools to recognize and understand true relationships between the species belonging to the superfamily Criconematoidea. 1 The major objectives of this study were: i) to integrate the morphological and morphometrical characterization of populations of known and unknown Criconematoidea species in the United States; ii) to characterize molecularly Criconematoidea species using ITS1 rRNA gene; and iii) reconstruct the phylogenetic position of these species in the Criconematinae using the analysis of this gene. 2 TAXONOMIC AND MOLECULAR IDENTIFICATION OF Mesocriconema and Criconemoides SPECIES (NEMATODA: CRICONEMATIDAE) Marco A. Cordero1, Robert T. Robbins1 and Allen L. Szalanski2 ______________________________ 1 Graduate assistant and University Professor, Department of Plant Pathology, Cralley/Warren Research Lab., 2601 N. Young Ave., University of Arkansas, Fayetteville, AR 72704. 2 Professor, Department of Entomology, 319 Agriculture Bldg. University of Arkansas, Fayetteville, AR 72701. The authors thank Keith Striegler, University of Missouri; Weimen Ye, North Carolina Department of Agriculture; Tim Todd, Kansas State University; Ernest Bernard, University of Tennessee and Howard Ferris, University of California-Davis for providing specimens for this study and Mourad Benamara, Institute for Nanoscience and Engineering, University of Arkansas, Fayetteville for his support with the scanning electron microscope. This paper was edited by Running head: TAXONOMIC AND MOLECULAR
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