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  • 1
    Publication Date: 2012-12-04
    Description: Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote-eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have 〉21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Curtis, Bruce A -- Tanifuji, Goro -- Burki, Fabien -- Gruber, Ansgar -- Irimia, Manuel -- Maruyama, Shinichiro -- Arias, Maria C -- Ball, Steven G -- Gile, Gillian H -- Hirakawa, Yoshihisa -- Hopkins, Julia F -- Kuo, Alan -- Rensing, Stefan A -- Schmutz, Jeremy -- Symeonidi, Aikaterini -- Elias, Marek -- Eveleigh, Robert J M -- Herman, Emily K -- Klute, Mary J -- Nakayama, Takuro -- Obornik, Miroslav -- Reyes-Prieto, Adrian -- Armbrust, E Virginia -- Aves, Stephen J -- Beiko, Robert G -- Coutinho, Pedro -- Dacks, Joel B -- Durnford, Dion G -- Fast, Naomi M -- Green, Beverley R -- Grisdale, Cameron J -- Hempel, Franziska -- Henrissat, Bernard -- Hoppner, Marc P -- Ishida, Ken-Ichiro -- Kim, Eunsoo -- Koreny, Ludek -- Kroth, Peter G -- Liu, Yuan -- Malik, Shehre-Banoo -- Maier, Uwe G -- McRose, Darcy -- Mock, Thomas -- Neilson, Jonathan A D -- Onodera, Naoko T -- Poole, Anthony M -- Pritham, Ellen J -- Richards, Thomas A -- Rocap, Gabrielle -- Roy, Scott W -- Sarai, Chihiro -- Schaack, Sarah -- Shirato, Shu -- Slamovits, Claudio H -- Spencer, David F -- Suzuki, Shigekatsu -- Worden, Alexandra Z -- Zauner, Stefan -- Barry, Kerrie -- Bell, Callum -- Bharti, Arvind K -- Crow, John A -- Grimwood, Jane -- Kramer, Robin -- Lindquist, Erika -- Lucas, Susan -- Salamov, Asaf -- McFadden, Geoffrey I -- Lane, Christopher E -- Keeling, Patrick J -- Gray, Michael W -- Grigoriev, Igor V -- Archibald, John M -- BB/G00885X/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Dec 6;492(7427):59-65. doi: 10.1038/nature11681. Epub 2012 Nov 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23201678" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/genetics/metabolism ; Alternative Splicing/genetics ; Cell Nucleus/*genetics ; Cercozoa/cytology/*genetics/metabolism ; Cryptophyta/cytology/*genetics/metabolism ; Cytosol/metabolism ; *Evolution, Molecular ; Gene Duplication/genetics ; Gene Transfer, Horizontal/genetics ; Genes, Essential/genetics ; Genome/*genetics ; Genome, Mitochondrial/genetics ; Genome, Plant/genetics ; Genome, Plastid/genetics ; Molecular Sequence Data ; *Mosaicism ; Phylogeny ; Protein Transport ; Proteome/genetics/metabolism ; Symbiosis/*genetics ; Transcriptome/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2012-12-21
    Description: Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology. Here we describe the draft genomes of the owl limpet (Lottia gigantea), a marine polychaete (Capitella teleta) and a freshwater leech (Helobdella robusta), and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective. We find that the genome organization, gene structure and functional content of these species are more similar to those of some invertebrate deuterostome genomes (for example, amphioxus and sea urchin) than those of other protostomes that have been sequenced to date (flies, nematodes and flatworms). The conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor, establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long- and short-range genetic linkages across metazoans. Superimposed on this broadly conserved pan-bilaterian background we find examples of lineage-specific genome evolution, including varying rates of rearrangement, intron gain and loss, expansions and contractions of gene families, and the evolution of clade-specific genes that produce the unique content of each genome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4085046/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4085046/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Simakov, Oleg -- Marletaz, Ferdinand -- Cho, Sung-Jin -- Edsinger-Gonzales, Eric -- Havlak, Paul -- Hellsten, Uffe -- Kuo, Dian-Han -- Larsson, Tomas -- Lv, Jie -- Arendt, Detlev -- Savage, Robert -- Osoegawa, Kazutoyo -- de Jong, Pieter -- Grimwood, Jane -- Chapman, Jarrod A -- Shapiro, Harris -- Aerts, Andrea -- Otillar, Robert P -- Terry, Astrid Y -- Boore, Jeffrey L -- Grigoriev, Igor V -- Lindberg, David R -- Seaver, Elaine C -- Weisblat, David A -- Putnam, Nicholas H -- Rokhsar, Daniel S -- R01 GM 074619/GM/NIGMS NIH HHS/ -- R01 GM074619/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 Jan 24;493(7433):526-31. doi: 10.1038/nature11696. Epub 2012 Dec 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23254933" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Body Patterning/*genetics ; Conserved Sequence/genetics ; *Evolution, Molecular ; Genes, Homeobox/genetics ; Genetic Linkage ; Genetic Speciation ; Genome/*genetics ; Humans ; INDEL Mutation/genetics ; Introns/genetics ; Leeches/anatomy & histology/*genetics ; Mollusca/anatomy & histology/*genetics ; Multigene Family/genetics ; *Phylogeny ; Polychaeta/anatomy & histology/*genetics ; Synteny/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2012-06-30
    Description: Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Floudas, Dimitrios -- Binder, Manfred -- Riley, Robert -- Barry, Kerrie -- Blanchette, Robert A -- Henrissat, Bernard -- Martinez, Angel T -- Otillar, Robert -- Spatafora, Joseph W -- Yadav, Jagjit S -- Aerts, Andrea -- Benoit, Isabelle -- Boyd, Alex -- Carlson, Alexis -- Copeland, Alex -- Coutinho, Pedro M -- de Vries, Ronald P -- Ferreira, Patricia -- Findley, Keisha -- Foster, Brian -- Gaskell, Jill -- Glotzer, Dylan -- Gorecki, Pawel -- Heitman, Joseph -- Hesse, Cedar -- Hori, Chiaki -- Igarashi, Kiyohiko -- Jurgens, Joel A -- Kallen, Nathan -- Kersten, Phil -- Kohler, Annegret -- Kues, Ursula -- Kumar, T K Arun -- Kuo, Alan -- LaButti, Kurt -- Larrondo, Luis F -- Lindquist, Erika -- Ling, Albee -- Lombard, Vincent -- Lucas, Susan -- Lundell, Taina -- Martin, Rachael -- McLaughlin, David J -- Morgenstern, Ingo -- Morin, Emanuelle -- Murat, Claude -- Nagy, Laszlo G -- Nolan, Matt -- Ohm, Robin A -- Patyshakuliyeva, Aleksandrina -- Rokas, Antonis -- Ruiz-Duenas, Francisco J -- Sabat, Grzegorz -- Salamov, Asaf -- Samejima, Masahiro -- Schmutz, Jeremy -- Slot, Jason C -- St John, Franz -- Stenlid, Jan -- Sun, Hui -- Sun, Sheng -- Syed, Khajamohiddin -- Tsang, Adrian -- Wiebenga, Ad -- Young, Darcy -- Pisabarro, Antonio -- Eastwood, Daniel C -- Martin, Francis -- Cullen, Dan -- Grigoriev, Igor V -- Hibbett, David S -- New York, N.Y. -- Science. 2012 Jun 29;336(6089):1715-9. doi: 10.1126/science.1221748.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biology Department, Clark University, Worcester, MA 01610, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22745431" target="_blank"〉PubMed〈/a〉
    Keywords: Basidiomycota/classification/*enzymology/*genetics ; Bayes Theorem ; *Evolution, Molecular ; *Genome, Fungal ; Indoles ; Lignin/*metabolism ; Peroxidases/*genetics/metabolism ; Wood/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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