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1B-O Lichen: from genome to ecosystem in a changing world (1B-O3) Submission ID: IAL0262-00001 PARTIAL GENOME OF THE PHYCOBIONT TREBOUXIA TR-9 ISOLATED FROM RAMALINA FARINACEA (L.) ACH. SEQUENCED BY 454 PYROSEQUENCING Martínez- Alberola F. 1 , Barreno E. 1 , Marín I. 2 , Del Campo E. M. 3 , Casano L. M. 3 , Guéra A. 3 , Aldecoa R. 2 , Del Hoyo A. 3 1 Botany, University of Valencia, Inst. Cavanilles of Biodiversity and Evolutionary Biology, Fac. of Biology , Valencia, Burjassot, Spain 2 Instituto De Biomedicina, CSIC, Valencia, Valencia, Spain 3 Plant Biology, University of Alcalá, Madrid / Alcalá De Henares, Spain The chloroplast, mitochondrial and nuclear genomes of Trebouxia sp. TR-9 phycobionts, isolated from Ramalina farinacea (L.) Ach., have being partially sequenced by 454 pyrosequencing to analyze genome structure, repeats characterization and finding of new gene sequences compared to green algae genome databases. We show that these sequencing technologies are highly productive and generate a lot of information on phycobiont genomes. Our research group has isolated two different Trebouxia phycobionts (TR-1 and TR-9) that always coexist on R. farinacea, even in geographically distant localities. Total Trebouxia sp. TR-9 DNA was extracted and loaded on a ¼ GS FLX Titanium 454 pyrosequencing run. Reads were assembled with MIRA3 software; the obtained contigs were analyzed with the BLAST algorithm against Chlamydomonas reinhardtii P.A. Dangeard, Chlorella variabilis NC64A, Arabidopsis thaliana (L.) Heynh. and NCBI databases. We have generated 240256 reads and their average length was 579.87 bp, 75% were assembled in 20787 contigs with a total consensus of 9211887 bp and a total average coverage of 41.76. C.reinhardtii and C.variabilis NC64A proteins were used for comparative analyses against TR-9 sequences by the tBLASTn algorithm. On this way, a total of 2.799 possible homologies with both species were found (Max. Evalue: 10-3). A big number of Trebouxia sp. TR-9 sequences were obtained; and we have identified mitochondrial and partial chloroplast genomes. We also found C. reinhardtii flagella proteome orthologs as well as oxidative stress, glucid metabolism or CO 2 concentrating mechanisms among others. It has been determined the presence of similar repetitive sequences in 612 contigs containing mobile elements and 653 showing another type of repeated sequences. [MCINN (CGL2009-13429- C02-01/02) and Generalitat Valenciana (PROMETEO 174/2008 GVA)] (1B-O4) Submission ID: IAL0018-00001 TREBOUXIA DECOLORANS - ARE THERE FUNGAL GENES IN LICHEN ALGAE? Beck A. 1 , Divakar P. K. 2 , Zhang N. 3 , Molina M. C. 2 , Price D. 4 , Bhattacharya D. 4 , Struwe L. 3,4 1 Lichenology Dept., Botanische staatssammlung muenchen, Muenchen, Bavaria, Germany 2 Departamento de Biología Vegetal II, Universidad Complutense, Madrid, Spain 3 Department of Plant Biology and Pathology, Rutgers University, New Brunswick, United States 4 Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, United States Horizontal gene transfer (HGT) is widespread in prokaryotes and viruses and HGT from bacteria has contributed to yeast evolution. HGT between eukaryotes has also been recently reported. Nevertheless, very little is known about potential gene transfer between the partners in the lichen symbiosis, even though close physical proximity and symbiosis are thought to facilitate HGT. Here we used novel genome data from Trebouxia decolorans to investigate the possible existence of fungal derived genes in lichen algae. Phylogenomic analysis using predicted proteins from the T. decolorans genome returned 10,165 alignments that included other Gen- Bank entries. These were used to infer PhyML trees of which 459 trees showed T. decolorans to form a monophyletic group with fungal sequences, supported at a bootstrap level ≥ 70%. Detailed analysis of these likely HGT candidates will be presented. The Trebouxia source culture was axenic and algal-fungal associations in the phylogenomic output are low (2.5%), suggesting the results are not explained by fungal contamination. 20
The 7 th International Association for Lichenology Symposium 2012 (1B-O5) Submission ID: IAL0145-00001 PELTIGERA LICHEN SYMBIOMES: METAGENOMICS OF A COMPLEX NATURAL COMMUNITY Andresson O. 1 , Jónsson Z. O. 1 , Xavier B. B. 1 , Manoharan S. S. 1 , Miao V. 2 , Snaebjarnarson V. 1 , Jonsson H. 1 1 Department of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland 2 Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada Genomic analyses of lichens can be carried out in two fundamentally different ways. First, by the classical approach starting with pure, usually clonal, cultures of the individual symbiotic organisms, an approach which is essentially the same as generally used in genomics. This works fine if both (or all) symbionts can be cultured. The second approach starts with field material and the symbiont genomes are analyzed simultaneously. At first sight this approach appears only slightly more complicated than with the cultured material. In the best case, there is a fairly even proportion of two genomes, and after assembly of the basic sequence reads, it is simply a matter of sorting into two bins. In practice, there are several levels of complications. First, there may be more than two major symbionts, as in the case of tripartite lichens, and they may contribute very different numbers of genomes, including variable numbers of organelle genomes. Second, as the contributing organisms are not purely clonal, there may be considerable polymorphism. This complicates genome assembly and annotation, but can also contribute information on community structure. Third, a variety of microbes are present in natural lichen communities, both on surfaces and internal. This microbiome can account for a large part of the total metagenomic DNA, and can be very disperse in terms of taxonomy and clonality. Results and methodology from the genomic sequencing and analysis of the major components of the Peltigera membranacea and P. malacea symbiotic genomes, the mycobiont, the Nostoc photobiont, and the microbiome, will be presented as well as major features of transcriptomic analyses from thallus, rhizines and apothecia. Use of alternative homologs and differential gene expression in the different tissues yields molecular information on the nature of this widespread symbiosis, and the genome sequence base provides a platform for a wide range of investigations, e.g. using an array of molecular markers and transcriptome sequencing of multiple samples. (1B-O6) Submission ID: IAL0229-00002 DECODING SYMBIOSIS: THE TWO GENOMES OF THE LICHEN CLADONIA GRAYI Armaleo D. 1 , Mueller O. 1 , Lutzoni F. 1 , Martin F. 2 , Blanc G. 3 , Merchant S. 4 , Collart F. 5 1 Department of Biology, Duke University, Durham, United States 2 Tree-microbe Interactions, Institut National de la Recherche Scientifique, Nancy, France 3 Institut de Microbiologie De La Mediterranee, Aix-Marseille Université, Marseille, France 4 Chemistry and Biochemistry, University of California, L.A., Los Angeles, United States 5 Biosciences, Argonne National Laboratory, Argonne, United States We analyzed the genomes of the lichen fungus Cladonia grayi (34 Mb) and its alga, Asterochloris sp. (56 Mb), sequenced using DNA from the isolated symbionts grown in culture. We used several approaches to distinguish genes relevant to the lichen symbiosis from those not specifically constrained by it. One method involved searching for genes with a phylogenetic signature characterized by an early burst of positive selection followed by stabilizing selection. Another was an analysis of gene family expansion and contraction in the symbionts compared to their phylogenetic relatives. Both fungus and alga contain expanded families of novel proteins as well as of known proteins. We will focus on specific transcription factors and transporters. Finally, analyses of global transcriptional changes during early interactions between fungus and alga were combined with gene family data to further define genes relevant to symbiosis. Specific features will be discussed in detail. 21 1B-O
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The 7 th IAL Symposium 2012 Lichens
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The 7 th International Association
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Welcome Message The 7 th Internatio
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Report The 7 th International Assoc
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