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1. Positive Selection in Rapidly Evolving Plastid-Nuclear Enzyme Complexes

Author

Rockenbach, Kate, Havird, Justin C, Monroe, J Grey, Triant, Deborah A, Taylor, Douglas R, and Sloan, Daniel B

Subjects
Evolution, Human Genome, Molecular, Endopeptidase Clp, McDonald Kreitman test, plastome, McDonald–Kreitman test, cytonuclear interactions, Chloroplast Proteins, Genetic, chloroplast, Genetics, Polymorphism, Silene, Selection, Phylogeny, Acetyl-CoA Carboxylase, Plant Proteins, Developmental Biology
Abstract

Rates of sequence evolution in plastid genomes are generally low, but numerous angiosperm lineages exhibit accelerated evolutionary rates in similar subsets of plastid genes. These genes include clpP1 and accD, which encode components of the caseinolytic protease (CLP) and acetyl-coA carboxylase (ACCase) complexes, respectively. Whether these extreme and repeated accelerations in rates of plastid genome evolution result from adaptive change in proteins (i.e., positive selection) or simply a loss of functional constraint (i.e., relaxed purifying selection) is a source of ongoing controversy. To address this, we have taken advantage of the multiple independent accelerations that have occurred within the genus Silene (Caryophyllaceae) by examining phylogenetic and population genetic variation in the nuclear genes that encode subunits of the CLP and ACCase complexes. We found that, in species with accelerated plastid genome evolution, the nuclear-encoded subunits in the CLP and ACCase complexes are also evolving rapidly, especially those involved in direct physical interactions with plastid-encoded proteins. A massive excess of nonsynonymous substitutions between species relative to levels of intraspecific polymorphism indicated a history of strong positive selection (particularly in CLP genes). Interestingly, however, some species are likely undergoing loss of the native (heteromeric) plastid ACCase and putative functional replacement by a duplicated cytosolic (homomeric) ACCase. Overall, the patterns of molecular evolution in these plastid-nuclear complexes are unusual for anciently conserved enzymes. They instead resemble cases of antagonistic coevolution between pathogens and host immune genes. We discuss a possible role of plastid-nuclear conflict as a novel cause of accelerated evolution.

Published
2016

2. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2009-30 September 2009

Author

Abdoullaye, Doukary, Acevedo, I., Adebayo, Abisola A., Behrmann-Godel, Asminca, Benjamin, R.C., Bock, Dan G., Born, Céline, Brouat, Carine, Caccone, Adalgisa, Cao, Ling-Zhen, Casado-Amezua, P., Catanéo, J., Correa-Ramirez, M.M., Cristescu, Melania E., Dobigny, Gauthier, Egbosimba, Emmanuelle E., Etchberger, Lianna K., Fan, Bin, Fields, Peter D., Forcioli, D., Furla, P., Garcia de Leon, F.J., García-Jiménez, R., Gauthier, Philippe, Cergz, René, Conzalez, Clementina, Granjon, Laurent, Guttiérrez-Rodriguez, Carla, Havill, Nathan P., Helsen, P., Hether, Tylier D., Hoffman, Eric A., Hu, Xiangyang, Ingvarsson, Pär K., Ishizaki, S., Ji, Heyi, Ji, X.S., Jimenez, M.L., Kapil, R., Karban, R., Keller, Stephen R., Kubota, S., Li, Shuzhen, Li, Wansha, Lim, Douglas D., Lin, Haoran, Liu, Xiaochun, Luo, Yayan, Machor-Dom, A., Martin, Andrew P., Matthysen, E., Mazzella, Maxwell N., McGeoch, Mélodie A., Meng, Zining, Nishizawa, M., O'Brien, Patricia, Ohara, M., Ornelas, Juan Francisco, Ortu, M.F., Pedersen, Amy B., Preston, L., Ren, Qin, Rothhaupt, Karl-Otto, Sackett, Loren C., Sang, Qing, Sawyer, G.M., Shiojiri, K., Taylor, Douglas R., van Dongen, S., Jansen van Vuuren, Bettine, Vandewoestijne, S., Wang, H., Wang, J.T., Lewang,, Xu, Xiang-Li, Yang, Guang, Yang, Yongping, Zeng, Y.Q., Zhang, Qing-Wen, Zhang, Yongping, Zhao, Y., Zhou, Yan, Molecular Ecology Resources Primer Office Development Consortium, ., Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Great Lakes Institute for Environmental Research, University of Windsor [Ca], Limnological Institute, University of Konstanz, Department of Biological Sciences, The Open University [Milton Keynes] (OU), Stellenbosch University, Department of Ecology and Evolutionary Biology [New Haven], Yale University [New Haven], College of Agronomy and Biotechnology, Southwest University, Université de Nice Sophia-Antipolis (UNSA), Laboratorio de Genetica de la Conservacion, Instituto de Investigaciones Biológicas Clemente Estable [Montevideo] (IIBCE), Centro de Investigaciones Biológicas del Noroeste,S.C., Partenaires INRAE, Institut de Recherche pour le Développement, Department of Biology, Utah State University (USU), Sun Yat-Sen University [Guangzhou] (SYSU), Northern Arizona University [Flagstaff], Universidad Nacional Autónoma de México (UNAM), Institut de Recherche pour le Développement (IRD), Forest Service, Northern Research Station, United States Department of Agriculture, Evolutionary Ecology Group, University of Antwerp (UA), Départment of biology, University of Central Florida [Orlando] (UCF), Chinese Academy of Sciences (CAS), Umeå University, Graduate School of Environmental Science, Hokkaido University [Sapporo, Japan], Nanjing Normal University (NNU), Shandong Agricultural University (SDAU), Department of Entomology, University of California [Davis] (UC Davis), University of California-University of California, Department of Ecology and Evolutionary Biology (Faculty of Biology), University of Science-Vietnam National Universities, South African National Parks, University of Cambridge [UK] (CAM), University of Edinburgh, Center of Ecological Research, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Biodiversity Research Centre, Université Catholique de Louvain = Catholic University of Louvain (UCL), and Molecular Ecology Resources Primer Office Development Consortium

Subjects
0106 biological sciences, Cnidaria, Mediterranean climate, ved/biology.organism_classification_rank.species, Zoology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Symbiodinium, Eunicella singularis, REFERENCEMENT, Anthozoa, ddc:570, GENBANK, Genetics, Temperate climate, Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, biology, ved/biology, biology.organism_classification, INSECTE, Gorgonian, CATALOGUE, Microsatellite, GENETIQUE DES POPULATIONS, ECOLOGIE, Biotechnology
Abstract

Correspondance: Molecular Ecology Resources Primer Development Consortium, E-mail: editorial.office@molecolres.com; International audience; This article documents the addition of 238 microsatellite marker loci and 72 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Adelges tsugae, Artemisia tridentata, Astroides calycularis, Azorella selago, Botryllus schlosseri, Botrylloides violaceus, Cardiocrinum cordatum var. glehnii, Campylopterus curvipennis, Colocasia esculenta, Cynomys ludovicianus, Cynomys leucurus, Cynomys gunnisoni, Epinephelus coioides, Eunicella singularis, Gammarus pulex, Homoeosoma nebulella, Hyla squirella, Lateolabrax japonicus, Mastomys erythroleucus, Pararge aegeria, Pardosa sierra, Phoenicopterus ruber ruber and Silene latifolia. These loci were cross-tested on the following species: Adelges abietis, Adelges cooleyi, Adelges piceae, Pineus pini, Pineus strobi, Tubastrea micrantha, three other Tubastrea species, Botrylloides fuscus, Botrylloides simodensis, Campylopterus hemileucurus, Campylopterus rufus, Campylopterus largipennis, Campylopterus villaviscensio, Phaethornis longuemareus, Florisuga mellivora, Lampornis amethystinus, Amazilia cyanocephala, Archilochus colubris, Epinephelus lanceolatus, Epinephelus fuscoguttatus, Symbiodinium temperate-A clade, Gammarus fossarum, Gammarus roeselii, Dikerogammarus villosus and Limnomysis benedeni. This article also documents the addition of 72 sequencing primer pairs and 52 allele specific primers for Neophocaena phocaenoides

Published
2010

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