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  • 1
    Publication Date: 2011-02-05
    Description: We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529199/" 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/PMC3529199/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Colbourne, John K -- Pfrender, Michael E -- Gilbert, Donald -- Thomas, W Kelley -- Tucker, Abraham -- Oakley, Todd H -- Tokishita, Shinichi -- Aerts, Andrea -- Arnold, Georg J -- Basu, Malay Kumar -- Bauer, Darren J -- Caceres, Carla E -- Carmel, Liran -- Casola, Claudio -- Choi, Jeong-Hyeon -- Detter, John C -- Dong, Qunfeng -- Dusheyko, Serge -- Eads, Brian D -- Frohlich, Thomas -- Geiler-Samerotte, Kerry A -- Gerlach, Daniel -- Hatcher, Phil -- Jogdeo, Sanjuro -- Krijgsveld, Jeroen -- Kriventseva, Evgenia V -- Kultz, Dietmar -- Laforsch, Christian -- Lindquist, Erika -- Lopez, Jacqueline -- Manak, J Robert -- Muller, Jean -- Pangilinan, Jasmyn -- Patwardhan, Rupali P -- Pitluck, Samuel -- Pritham, Ellen J -- Rechtsteiner, Andreas -- Rho, Mina -- Rogozin, Igor B -- Sakarya, Onur -- Salamov, Asaf -- Schaack, Sarah -- Shapiro, Harris -- Shiga, Yasuhiro -- Skalitzky, Courtney -- Smith, Zachary -- Souvorov, Alexander -- Sung, Way -- Tang, Zuojian -- Tsuchiya, Dai -- Tu, Hank -- Vos, Harmjan -- Wang, Mei -- Wolf, Yuri I -- Yamagata, Hideo -- Yamada, Takuji -- Ye, Yuzhen -- Shaw, Joseph R -- Andrews, Justen -- Crease, Teresa J -- Tang, Haixu -- Lucas, Susan M -- Robertson, Hugh M -- Bork, Peer -- Koonin, Eugene V -- Zdobnov, Evgeny M -- Grigoriev, Igor V -- Lynch, Michael -- Boore, Jeffrey L -- P42 ES004699/ES/NIEHS NIH HHS/ -- P42 ES004699-25/ES/NIEHS NIH HHS/ -- P42ES004699/ES/NIEHS NIH HHS/ -- R01 ES019324/ES/NIEHS NIH HHS/ -- R24 GM078274/GM/NIGMS NIH HHS/ -- R24 GM078274-01A1/GM/NIGMS NIH HHS/ -- R24GM07827401/GM/NIGMS NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2011 Feb 4;331(6017):555-61. doi: 10.1126/science.1197761.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA. jcolbour@indiana.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21292972" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Amino Acid Sequence ; Animals ; Base Sequence ; Chromosome Mapping ; Daphnia/*genetics/physiology ; *Ecosystem ; Environment ; Evolution, Molecular ; Gene Conversion ; Gene Duplication ; Gene Expression ; Gene Expression Profiling ; Gene Expression Regulation ; Genes ; Genes, Duplicate ; *Genome ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Sequence Analysis, DNA
    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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  • 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: 2016-02-26
    Description: The fungal kingdom is the source of almost all industrial enzymes in use for lignocellulose bioprocessing. We developed a systems-level approach that integrates transcriptomic sequencing, proteomics, phenotype, and biochemical studies of relatively unexplored basal fungi. Anaerobic gut fungi isolated from herbivores produce a large array of biomass-degrading enzymes that synergistically degrade crude, untreated plant biomass and are competitive with optimized commercial preparations from Aspergillus and Trichoderma. Compared to these model platforms, gut fungal enzymes are unbiased in substrate preference due to a wealth of xylan-degrading enzymes. These enzymes are universally catabolite-repressed and are further regulated by a rich landscape of noncoding regulatory RNAs. Additionally, we identified several promising sequence-divergent enzyme candidates for lignocellulosic bioprocessing.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Solomon, Kevin V -- Haitjema, Charles H -- Henske, John K -- Gilmore, Sean P -- Borges-Rivera, Diego -- Lipzen, Anna -- Brewer, Heather M -- Purvine, Samuel O -- Wright, Aaron T -- Theodorou, Michael K -- Grigoriev, Igor V -- Regev, Aviv -- Thompson, Dawn A -- O'Malley, Michelle A -- New York, N.Y. -- Science. 2016 Mar 11;351(6278):1192-5. doi: 10.1126/science.aad1431. Epub 2016 Feb 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical Engineering, University of California, Santa Barbara (UCSB), Santa Barbara, CA 93106, USA. ; Broad Institute of MIT and Harvard, Cambridge, MA 02143, USA. ; U.S. Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA. ; Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA. ; Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA. ; Animal Production, Welfare and Veterinary Sciences, Harper Adams University, Newport, Shropshire TF10 8NB, UK. ; Department of Chemical Engineering, University of California, Santa Barbara (UCSB), Santa Barbara, CA 93106, USA. momalley@engineering.ucsb.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26912365" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Aspergillus/*enzymology/genetics/isolation & purification ; Biotechnology/*methods ; Cellulases/genetics/isolation & purification/*metabolism ; Cellulose/metabolism ; Gastrointestinal Tract/*microbiology ; Herbivory ; RNA, Untranslated/genetics ; Substrate Specificity ; Trichoderma/*enzymology/genetics/isolation & purification ; Xylans/*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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