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Deciphering the major trends of molecular and morphological evolution in the Amoebozoa

Abstract

The present project seeks to characterize amoebozoan diversity in Brazil, integrating aspects of traditional protistology with cutting-edge molecular techniques. Amoebae will be isolated from freshwater and marine environments in order to capture diversity in a comprehensive manner. Collected organisms will be subjected to two main study strategies: 1) unculturable organisms will be photo-documented and single-cell genome amplified, while; 2) culturable organisms will be grown monoxenically in order to generate large quantities of DNA as well as cDNA for transcriptome piro-sequencing using the 454 Titanium platform. Many of the isolated organisms will likely be new or little known species. These will be individually described along with detailed morphological studies using electronic microscopy, and their phylogenetic position will be assessed based on multigene reconstructions, on at least 4 genes (SSU-rDNA, actin, alpha and beta tubulin). Other organisms will have 8-10 genetic markers characterized and used in comprehensive phylogenetic reconstructions with emphasis on the basal relationships of Amoebozoa. The 10-12 organisms which will have the transcriptome comprehensively sequenced will be used in studies illuminating the patterns of evolution by gene duplication in Amoebozoa, with special emphasis on the actin gene family. Finally, photographic, videographic and molecular data generated during the project will be disseminated by publication in highly recognized international journals, and made available to the lay public by the creation and deposition of curated data in publicly available websites. (AU)

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Scientific publications (18)
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
GEISEN, STEFAN; MITCHELL, EDWARD A. D.; WILKINSON, DAVID M.; ADL, SINA; BONKOWSKI, MICHAEL; BROWN, MATTHEW W.; FIORE-DONNO, ANNA MARIA; HEGER, THIERRY J.; JASSEY, VINCENT E. J.; KRASHEVSKA, VALENTYNA; et al. Soil protistology rebooted: 30 fundamental questions to start with. SOIL BIOLOGY & BIOCHEMISTRY, v. 111, p. 94-103, . (13/04585-3)
BLANDENIER, QUENTIN; LARA, ENRIQUE; MITCHELL, EDWARD A. D.; ALCANTARA, DANIEL M. C.; SIEMENSMA, FERRY J.; TODOROV, MILCHO; LAHR, DANIEL J. G.. NAD9/NAD7 (mitochondrial nicotinamide adenine dinucleotide dehydrogenase gene)-A new ``Holy Grail{''} phylogenetic and DNA-barcoding marker for Arcellinida (Amoebozoa)?. EUROPEAN JOURNAL OF PROTISTOLOGY, v. 58, p. 175-186, . (13/04585-3)
LAHR, DANIEL J. G.; BOSAK, TANJA; LARA, ENRIQUE; MITCHELL, EDWARD A. D.. The Phanerozoic diversification of silica-cycling testate amoebae and its possible links to changes in terrestrial ecosystems. PeerJ, v. 3, . (13/04585-3)
LAHR, DANIEL J. G.; KOSAKYAN, ANUSH; LAR, ENRIQUE; MITCHELL, EDWARD A. D.; MORAIS, LUANA; PORFIRIO-SOUSA, ALFREDO L.; RIBEIRO, GIULIA M.; TICE, ALEXANDER K.; PANEK, TOMAS; KANG, SEUNGHO; et al. Phylogenomics and Morphological Reconstruction of Arcellinida Testate Amoebae Highlight Diversity of Microbial Eukaryotes in the Neoproterozoic. Current Biology, v. 29, n. 6, p. 991+, . (13/25729-3, 15/02689-1, 13/04585-3, 13/12852-1)
DUMACK, KENNETH; GOERZEN, DIANA; GONZALEZ-MIGUENS, RUBEN; SIEMENSMA, FERRY; LAHR, DANIEL J. G.; LARA, ENRIQUE; BONKOWSKI, MICHAEL. Molecular investigation of Phryganella acropodia Hertwig et Lesser, 1874 (Arcellinida, Amoebozoa). EUROPEAN JOURNAL OF PROTISTOLOGY, v. 75, . (13/04585-3)
KOSAKYAN, ANUSH; LAHR, DANIEL J. G.; MULOT, MATTHIEU; MEISTERFELD, RALF; MITCHELL, EDWARD A. D.; LARA, ENRIQUE. Phylogenetic reconstruction based on COI reshuffles the taxonomy of hyalosphenid shelled (testate) amoebae and reveals the convoluted evolution of shell plate shapes. CLADISTICS, v. 32, n. 6, p. 606-623, . (13/04585-3)
GOMAA, FATMA; LAHR, DANIEL J. G.; TODOROV, MILCHO; LI, JINGCHUN; LARA, ENRIQUE. A contribution to the phylogeny of agglutinating Arcellinida (Amoebozoa) based on SSU rRNA gene sequences. EUROPEAN JOURNAL OF PROTISTOLOGY, v. 59, p. 99-107, . (13/04585-3)
HOFSTATTER, PAULO G.; BROWN, MATTHEWW.; LAHR, DANIEL J. G.. Comparative Genomics Supports Sex and Meiosis in Diverse Amoebozoa. GENOME BIOLOGY AND EVOLUTION, v. 10, n. 11, p. 3118-3128, . (15/06306-0, 13/04585-3)
MORAIS, LUANA; FAIRCHILD, THOMAS RICH; LAHR, DANIEL J. G.; RUDNITZKI, ISAAC D.; SCHOPF, J. WILLIAM; GARCIA, AMANDA K.; KUDRYAVTSEV, ANATOLIY B.; ROMERO, GUILHERME R.. Carbonaceous and siliceous Neoproterozoic vase-shaped microfossils (Urucum Formation, Brazil) and the question of early protistan biomineralization. JOURNAL OF PALEONTOLOGY, v. 91, n. 3, p. 393-406, . (13/04585-3, 13/12852-1)
FUCIKOVA, KAROLINA; LAHR, DANIEL J. G.. Uncovering Cryptic Diversity in Two Amoebozoan Species Using Complete Mitochondrial Genome Sequences. Journal of Eukaryotic Microbiology, v. 63, n. 1, p. 112-122, . (13/04585-3)
LAHR, DANIEL J. G.; LAUGHINGHOUSE, HAYWOOD DAIL; OLIVERIO, ANGELA M.; GAO, FENG; KATZ, LAURA A.. How discordant morphological and molecular evolution among microorganisms can revise our notions of biodiversity on Earth. BIOESSAYS, v. 36, n. 10, p. 950-959, . (13/04585-3)
DUMACK, KENNETH; KAHLICH, CHRISTOPHER; LAHR, DANIEL J. G.; BONKOWSKI, MICHAEL. Reinvestigation of Phryganella paradoxa (Arcellinida, Amoebozoa) Penard 1902. Journal of Eukaryotic Microbiology, v. 66, n. 2, p. 232-243, . (13/04585-3)
SCHIESARI, LUIS; MATIAS, MIGUEL G.; PRADO, PAULO INACIO; LEIBOLD, MATHEW A.; ALBERT, CECILE H.; HOWETH, JENNIFER G.; LEROUX, SHAWN J.; PARDINI, RENATA; SIQUEIRA, TADEU; BRANCALION, PEDRO H. S.; et al. Towards an applied metaecology. PERSPECTIVES IN ECOLOGY AND CONSERVATION, v. 17, n. 4, p. 172-181, . (15/18790-3, 15/17984-9, 13/04585-3, 14/10470-7, 13/50424-1)
MACHICAO, JEANETH; FILHO, HUMBERTO A.; LAHR, DANIEL J. G.; BUCKERIDGE, MARCOS; BRUNO, ODEMIR M.. Topological assessment of metabolic networks reveals evolutionary information. SCIENTIFIC REPORTS, v. 8, . (14/08026-1, 13/04585-3)
KOSAKYAN, ANUSH; GOMAA, FATMA; LARA, ENRIQUE; LAHR, DANIEL J. G.. Current and future perspectives on the systematics, taxonomy and nomenclature of testate amoebae. EUROPEAN JOURNAL OF PROTISTOLOGY, v. 55, n. B, SI, p. 105-117, . (13/04585-3)
FERES, JORDANA C.; PORFIRIO-SOUSA, ALFREDO L.; RIBEIRO, GIULIA M.; ROCHA, GUSTAVO M.; STERZA, JOSE MAURO; SOUZA, MARIA BEATRIZ G.; SOARES, CARLOS EDUARDO A.; LAHR, DANIEL J. G.. Morphological and Morphometric Description of a Novel Shelled Amoeba Arcellagandalfi sp nov (Amoebozoa: Arcellinida) from Brazilian Continental Waters. ACTA PROTOZOOLOGICA, v. 55, n. 4, p. 221-229, . (13/04585-3)
TREVISAN, BRUNA; ALCANTARA, DANIEL M. C.; MACHADO, DENIS JACOB; MARQUES, FERNANDO P. L.; LAHR, DANIEL J. G.. Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies. PeerJ, v. 7, . (16/20792-7, 13/04585-3, 17/11063-4, 18/03534-0)

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