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Cheong Xin Chan,
Nicolas A Blouin,
Yunyun Zhuang,
Simone Zäuner, Simon E Prochnik,
Erika Lindquist,
Senjie Lin,
Christoph Benning,
Martin Lohr,
Charles Yarish,
Elisabeth Gantt,
Arthur R Grossman,
Shan Lu,
Kirsten Müller,
John Stiller,
Susan H Brawley,
Debashish Bhattacharya
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ABSTRACT: The red seaweed Porphyra (Bangiophyceae) and related Bangiales have global economic importance. Here we report analysis of a comprehensive transcriptome comprising ca. 4.7 million expressed sequence tag (EST) reads from Porphyra umbilicalis (L.) J. Agardh and Porphyra purpurea (Roth) C. Agardh (ca. 980 Mbp of data generated using 454 FLX pyrosequencing). These ESTs were isolated from the haploid gametophyte (blades from both species) and diploid conchocelis stage (from P. purpurea). In a bioinformatic analysis, only 20% of the contigs were found to encode proteins of known biological function. Comparative analysis of predicted protein functions in mesophilic (including Porphyra) and extremophilic red algae suggest the former has more putative functions related to signaling, membrane transport processes, and establishment of protein complexes. These enhanced functions may reflect general mesophilic adaptations. A near-complete repertoire of genes encoding histones and ribosomal proteins was identified, with some differentially regulated between the blade and conchocelis stage in P. purpurea. This finding may reflect specific regulatory processes associated with these distinct phases of the life history. Fatty acid desaturation patterns, in combination with gene expression profiles, demonstrate differences from seed plants with respect to the transport of fatty acid/lipid among subcellular compartments and the molecular machinery of lipid assembly. We also recovered a near-complete gene repertoire for enzymes involved in the formation of sterols and carotenoids, including candidate genes for the biosynthesis of lutein. Our findings provide key insights into the evolution, development, and biology of Porphyra, an important lineage of red algae.
Journal of Phycology 08/2012; · 2.07 Impact Factor
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ABSTRACT: The plastid is a defining structure of photosynthetic eukaryotes and houses many plant-specific processes, including the light reactions, carbon fixation, pigment synthesis, and other primary metabolic processes. Identifying proteins associated with catalytic, structural, and regulatory functions that are unique to plastid-containing organisms is necessary to fully define the scope of plant biochemistry. Here, we performed phylogenomics on 20 genomes to compile a new inventory of 597 nucleus-encoded proteins conserved in plants and green algae but not in non-photosynthetic organisms. 286 of these proteins are of known function, whereas 311 are not characterized. This inventory was validated as applicable and relevant to diverse photosynthetic eukaryotes using an additional eight genomes from distantly related plants (including Micromonas, Selaginella, and soybean). Manual curation of the known proteins in the inventory established its importance to plastid biochemistry. To predict functions for the 52% of proteins of unknown function, we used sequence motifs, subcellular localization, co-expression analysis, and RNA abundance data. We demonstrate that 18% of the proteins in the inventory have functions outside the plastid and/or beyond green tissues. Although 32% of proteins in the inventory have homologs in all cyanobacteria, unexpectedly, 30% are eukaryote-specific. Finally, 8% of the proteins of unknown function share no similarity to any characterized protein and are plant lineage-specific. We present this annotated inventory of 597 proteins as a resource for functional analyses of plant-specific biochemistry.
Journal of Biological Chemistry 06/2011; 286(24):21427-39. · 4.77 Impact Factor
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Simon E Prochnik,
James Umen,
Aurora M Nedelcu,
Armin Hallmann,
Stephen M Miller,
Ichiro Nishii,
Patrick Ferris,
Alan Kuo,
Therese Mitros,
Lillian K Fritz-Laylin, [......],
Asaf Salamov,
Harris Shapiro,
Jeremy Schmutz,
Jane Grimwood,
Erika Lindquist,
Susan Lucas,
Igor V Grigoriev,
Rüdiger Schmitt,
David Kirk,
Daniel S Rokhsar
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ABSTRACT: The multicellular green alga Volvox carteri and its morphologically diverse close relatives (the volvocine algae) are well suited for the investigation of the evolution of multicellularity and development. We sequenced the 138-mega-base pair genome of V. carteri and compared its approximately 14,500 predicted proteins to those of its unicellular relative Chlamydomonas reinhardtii. Despite fundamental differences in organismal complexity and life history, the two species have similar protein-coding potentials and few species-specific protein-coding gene predictions. Volvox is enriched in volvocine-algal-specific proteins, including those associated with an expanded and highly compartmentalized extracellular matrix. Our analysis shows that increases in organismal complexity can be associated with modifications of lineage-specific proteins rather than large-scale invention of protein-coding capacity.
Science 07/2010; 329(5988):223-6. · 31.20 Impact Factor
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Jarrod A Chapman,
Ewen F Kirkness,
Oleg Simakov,
Steven E Hampson,
Therese Mitros,
Thomas Weinmaier,
Thomas Rattei,
Prakash G Balasubramanian,
Jon Borman,
Dana Busam, [......],
J Craig Venter,
Ulrich Technau,
Bert Hobmayer,
Thomas C G Bosch,
Thomas W Holstein,
Toshitaka Fujisawa,
Hans R Bode,
Charles N David,
Daniel S Rokhsar,
Robert E Steele
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ABSTRACT: The freshwater cnidarian Hydra was first described in 1702 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals. Today, Hydra is an important model for studies of axial patterning, stem cell biology and regeneration. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann-Mangold organizer, pluripotency genes and the neuromuscular junction.
Nature 03/2010; 464(7288):592-6. · 36.28 Impact Factor
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Lillian K Fritz-Laylin, Simon E Prochnik,
Michael L Ginger,
Joel B Dacks,
Meredith L Carpenter,
Mark C Field,
Alan Kuo,
Alex Paredez,
Jarrod Chapman,
Jonathan Pham, [......],
Hank Tu,
Asaf Salamov,
Erika Lindquist,
Harris Shapiro,
Susan Lucas,
Igor V Grigoriev,
W Zacheus Cande,
Chandler Fulton,
Daniel S Rokhsar,
Scott C Dawson
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ABSTRACT: Genome sequences of diverse free-living protists are essential for understanding eukaryotic evolution and molecular and cell biology. The free-living amoeboflagellate Naegleria gruberi belongs to a varied and ubiquitous protist clade (Heterolobosea) that diverged from other eukaryotic lineages over a billion years ago. Analysis of the 15,727 protein-coding genes encoded by Naegleria's 41 Mb nuclear genome indicates a capacity for both aerobic respiration and anaerobic metabolism with concomitant hydrogen production, with fundamental implications for the evolution of organelle metabolism. The Naegleria genome facilitates substantially broader phylogenomic comparisons of free-living eukaryotes than previously possible, allowing us to identify thousands of genes likely present in the pan-eukaryotic ancestor, with 40% likely eukaryotic inventions. Moreover, we construct a comprehensive catalog of amoeboid-motility genes. The Naegleria genome, analyzed in the context of other protists, reveals a remarkably complex ancestral eukaryote with a rich repertoire of cytoskeletal, sexual, signaling, and metabolic modules.
Cell 03/2010; 140(5):631-42. · 32.40 Impact Factor
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Sabeeha S Merchant, Simon E Prochnik,
Olivier Vallon,
Elizabeth H Harris,
Steven J Karpowicz,
George B Witman,
Astrid Terry,
Asaf Salamov,
Lillian K Fritz-Laylin,
Laurence Maréchal-Drouard, [......],
Wing Chi Abby Ngau,
Bobby Otillar,
Alexander Poliakov,
Aaron Porter,
Lukasz Szajkowski,
Gregory Werner,
Kemin Zhou,
Igor V Grigoriev,
Daniel S Rokhsar,
Arthur R Grossman
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ABSTRACT: Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.
Science 11/2007; 318(5848):245-50. · 31.20 Impact Factor
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Sabeeha S. Merchant, Simon E. Prochnik,
Olivier Vallon,
Elizabeth H. Harris,
Steven J. Karpowicz,
George B. Witman,
Astrid Terry,
Asaf Salamov,
Lillian K. Fritz-Laylin,
Laurence Maréchal-Drouard, [......],
Wing Chi Abby Ngau,
Bobby Otillar,
Alexander Poliakov,
Aaron Porter,
Lukasz Szajkowski,
Gregory Werner,
Kemin Zhou,
Igor V. Grigoriev,
Daniel S. Rokhsar,
Arthur R. Grossman
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ABSTRACT: Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying
chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were
inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ∼120-megabase nuclear
genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated
with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic
and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.
Science 10/2007; 318(5848):245-250. · 31.20 Impact Factor
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ABSTRACT: Understanding how animal complexity has arisen and identifying the key genetic components of this process is a central goal of evolutionary developmental biology. The discovery of microRNAs (miRNAs) as key regulators of development has identified a new set of candidates for this role. microRNAs are small noncoding RNAs that regulate tissue-specific or temporal gene expression through base pairing with target mRNAs. The full extent of the evolutionary distribution of miRNAs is being revealed as more genomes are scrutinized. To explore the evolutionary origins of metazoan miRNAs, we searched the genomes of diverse animals occupying key phylogenetic positions for homologs of experimentally verified human, fly, and worm miRNAs. We identify 30 miRNAs conserved across bilaterians, almost double the previous estimate. We hypothesize that this larger than previously realized core set of miRNAs was already present in the ancestor of all Bilateria and likely had key roles in allowing the evolution of diverse specialist cell types, tissues, and complex morphology. In agreement with this hypothesis, we found only three, conserved miRNA families in the genome of the sea anemone Nematostella vectensis and no convincing family members in the genome of the demosponge Reniera sp. The dramatic expansion of the miRNA repertoire in bilaterians relative to sponges and cnidarians suggests that increased miRNA-mediated gene regulation accompanied the emergence of triploblastic organ-containing body plans.
Archiv für Entwickelungsmechanik der Organismen 02/2007; 217(1):73-7. · 1.77 Impact Factor
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Sima Misra,
Madeline A Crosby,
Christopher J Mungall,
Beverley B Matthews,
Kathryn S Campbell,
Pavel Hradecky,
Yanmei Huang,
Joshua S Kaminker,
Gillian H Millburn, Simon E Prochnik, [......],
John Richter,
Susan Russo,
Andrew J Schroeder,
Sheng Qiang Shu,
Mark Stapleton,
Chihiro Yamada,
Michael Ashburner,
William M Gelbart,
Gerald M Rubin,
Suzanna E Lewis
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ABSTRACT: The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing each predicted peptide to SWISS-PROT and TrEMBL sequences.
Although the number of predicted protein-coding genes in Drosophila remains essentially unchanged, the revised annotation significantly improves gene models, resulting in structural changes to 85% of the transcripts and 45% of the predicted proteins. We annotated transposable elements and non-protein-coding RNAs as new features, and extended the annotation of untranslated (UTR) sequences and alternative transcripts to include more than 70% and 20% of genes, respectively. Finally, cDNA sequence provided evidence for dicistronic transcripts, neighboring genes with overlapping UTRs on the same DNA sequence strand, alternatively spliced genes that encode distinct, non-overlapping peptides, and numerous nested genes.
Identification of so many unusual gene models not only suggests that some mechanisms for gene regulation are more prevalent than previously believed, but also underscores the complex challenges of eukaryotic gene prediction. At present, experimental data and human curation remain essential to generate high-quality genome annotations.
Genome biology 02/2002; 3(12):RESEARCH0083. · 6.63 Impact Factor
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Sima Misra,
Christopher J Mungall,
Kathryn S Campbell,
Pavel Hradecky,
Yanmei Huang,
Joshua S Kaminker,
Gillian H Millburn, Simon E Prochnik,
Jonathan L Tupy,
Eleanor J Whitfield, [......],
Michael Ashburner,
Gerald M Rubin,
Suzanna E Lewis,
Madeline Crosby,
Beverley Matthews,
Christopher D Smith,
Benjamin P Berman,
Susan Russo,
Andrew Schroeder,
William Martin Gelbart
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ABSTRACT: Molecular and Cellular Biology The recent completion of the Drosophila melanogaster genomic sequence to high quality, and the availability of a greatly expanded set of Drosophila cDNA sequences, afforded FlyBase the opportunity to significantly improve genomic annotations.
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Sabeeha S Merchant, Simon E Prochnik,
Olivier Vallon,
Elizabeth H Harris,
Steven J Karpowicz,
George B Witman,
Astrid Terry,
Asaf Salamov,
Lillian K Fritz-Laylin,
Laurence Maréchal-Drouard, [......],
Erika Lindquist,
Harris Shapiro,
Susan M Lucas,
Jane Grimwood,
Jeremy Schmutz,
Chlamydomonas Annotation,
Jgi Annotation Team,
Igor V Grigoriev,
Daniel S Rokhsar,
Arthur R Grossman
[show abstract]
[hide abstract]
ABSTRACT: Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ~120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.
