Publications by authors named "Simon Prochnik"

25 Publications

  • Page 1 of 1

Draft Nuclear Genome Sequence of the Halophilic and Beta-Carotene-Accumulating Green Alga Strain CCAP19/18.

Genome Announc 2017 Oct 26;5(43). Epub 2017 Oct 26.

Pacific Northwest National Laboratory, Richland, Washington, USA.

The halotolerant alga is a model for stress tolerance and is used commercially for production of beta-carotene (=pro-vitamin A). The presented draft genome of the genuine strain CCAP19/18 will allow investigations into metabolic processes involved in regulation of stress responses, including carotenogenesis and adaptations to life in high-salinity environments.
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http://dx.doi.org/10.1128/genomeA.01105-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5658486PMC
October 2017

Insights into the red algae and eukaryotic evolution from the genome of (Bangiophyceae, Rhodophyta).

Proc Natl Acad Sci U S A 2017 08 17;114(31):E6361-E6370. Epub 2017 Jul 17.

Department of Ecology, Evolution & Natural Resources, Rutgers University, New Brunswick, NJ 08901.

(laver) belongs to an ancient group of red algae (Bangiophyceae), is harvested for human food, and thrives in the harsh conditions of the upper intertidal zone. Here we present the 87.7-Mbp haploid genome (65.8% G + C content, 13,125 gene loci) and elucidate traits that inform our understanding of the biology of red algae as one of the few multicellular eukaryotic lineages. Novel features of the genome shared by other red algae relate to the cytoskeleton, calcium signaling, the cell cycle, and stress-tolerance mechanisms including photoprotection. Cytoskeletal motor proteins in are restricted to a small set of kinesins that appear to be the only universal cytoskeletal motors within the red algae. Dynein motors are absent, and most red algae, including , lack myosin. This surprisingly minimal cytoskeleton offers a potential explanation for why red algal cells and multicellular structures are more limited in size than in most multicellular lineages. Additional discoveries further relating to the stress tolerance of bangiophytes include ancestral enzymes for sulfation of the hydrophilic galactan-rich cell wall, evidence for mannan synthesis that originated before the divergence of green and red algae, and a high capacity for nutrient uptake. Our analyses provide a comprehensive understanding of the red algae, which are both commercially important and have played a major role in the evolution of other algal groups through secondary endosymbioses.
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http://dx.doi.org/10.1073/pnas.1703088114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5547612PMC
August 2017

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity.

Nat Biotechnol 2016 05 18;34(5):562-70. Epub 2016 Apr 18.

Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.

Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop.
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http://dx.doi.org/10.1038/nbt.3535DOI Listing
May 2016

Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga Porphyra umbilicalis.

PLoS One 2016 25;11(3):e0151883. Epub 2016 Mar 25.

Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America.

Porphyra is a macrophytic red alga of the Bangiales that is important ecologically and economically. We describe the genomes of three bacteria in the phylum Planctomycetes (designated P1, P2 and P3) that were isolated from blades of Porphyra umbilicalis (P.um.1). These three Operational Taxonomic Units (OTUs) belong to distinct genera; P2 belongs to the genus Rhodopirellula, while P1 and P3 represent undescribed genera within the Planctomycetes. Comparative analyses of the P1, P2 and P3 genomes show large expansions of distinct gene families, which can be widespread throughout the Planctomycetes (e.g., protein kinases, sensors/response regulators) and may relate to specific habitat (e.g., sulfatase gene expansions in marine Planctomycetes) or phylogenetic position. Notably, there are major differences among the Planctomycetes in the numbers and sub-functional diversity of enzymes (e.g., sulfatases, glycoside hydrolases, polysaccharide lyases) that allow these bacteria to access a range of sulfated polysaccharides in macroalgal cell walls. These differences suggest that the microbes have varied capacities for feeding on fixed carbon in the cell walls of P.um.1 and other macrophytic algae, although the activities among the various bacteria might be functionally complementary in situ. Additionally, phylogenetic analyses indicate augmentation of gene functions through expansions arising from gene duplications and horizontal gene transfers; examples include genes involved in cell wall degradation (e.g., κ-carrageenase, alginate lyase, fucosidase) and stress responses (e.g., efflux pump, amino acid transporter). Finally P1 and P2 contain various genes encoding selenoproteins, many of which are enzymes that ameliorate the impact of environmental stresses that occur in the intertidal habitat.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0151883PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4807772PMC
August 2016

Identification and distribution of the NBS-LRR gene family in the Cassava genome.

BMC Genomics 2015 May 7;16:360. Epub 2015 May 7.

Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA.

Background: Plant resistance genes (R genes) exist in large families and usually contain both a nucleotide-binding site domain and a leucine-rich repeat domain, denoted NBS-LRR. The genome sequence of cassava (Manihot esculenta) is a valuable resource for analysing the genomic organization of resistance genes in this crop.

Results: With searches for Pfam domains and manual curation of the cassava gene annotations, we identified 228 NBS-LRR type genes and 99 partial NBS genes. These represent almost 1% of the total predicted genes and show high sequence similarity to proteins from other plant species. Furthermore, 34 contained an N-terminal toll/interleukin (TIR)-like domain, and 128 contained an N-terminal coiled-coil (CC) domain. 63% of the 327 R genes occurred in 39 clusters on the chromosomes. These clusters are mostly homogeneous, containing NBS-LRRs derived from a recent common ancestor.

Conclusions: This study provides insight into the evolution of NBS-LRR genes in the cassava genome; the phylogenetic and mapping information may aid efforts to further characterize the function of these predicted R genes.
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http://dx.doi.org/10.1186/s12864-015-1554-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4422547PMC
May 2015

The Chlamydomonas genome project: a decade on.

Trends Plant Sci 2014 Oct 17;19(10):672-80. Epub 2014 Jun 17.

US Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA. Electronic address:

The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis, and micronutrient homeostasis. Ten years since its genome project was initiated an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the omics era. Housed at Phytozome, the plant genomics portal of the Joint Genome Institute (JGI), the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of whole transcriptome sequencing (RNA-Seq) data. We present here the past, present, and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions, and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes.
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http://dx.doi.org/10.1016/j.tplants.2014.05.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4185214PMC
October 2014

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication.

Nat Biotechnol 2014 Jul 8;32(7):656-62. Epub 2014 Jun 8.

1] Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France. [2] INRA, US 1279 Etude du Polymorphisme des Génomes Végétaux (EPGV), Evry, France.

Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes--a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes--and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement.
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http://dx.doi.org/10.1038/nbt.2906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4113729PMC
July 2014

The Capsella rubella genome and the genomic consequences of rapid mating system evolution.

Nat Genet 2013 Jul 9;45(7):831-5. Epub 2013 Jun 9.

Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.

The shift from outcrossing to selfing is common in flowering plants, but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self compatible <200,000 years ago. We report a C. rubella reference genome sequence and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor Capsella grandiflora. We found a clear shift in the expression of genes associated with flowering phenotypes, similar to that seen in Arabidopsis, in which self fertilization evolved about 1 million years ago. Comparisons of the two Capsella species showed evidence of rapid genome-wide relaxation of purifying selection in C. rubella without a concomitant change in transposable element abundance. Overall we document that the transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection.
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http://dx.doi.org/10.1038/ng.2669DOI Listing
July 2013

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution.

Nat Genet 2013 May 24;45(5):487-94. Epub 2013 Mar 24.

Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA)-Centro di Ricerca per la Frutticoltura, Rome, Italy.

Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.
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http://dx.doi.org/10.1038/ng.2586DOI Listing
May 2013

The Reference Genome of the Halophytic Plant Eutrema salsugineum.

Front Plant Sci 2013 21;4:46. Epub 2013 Mar 21.

School of Plant Sciences, University of Arizona Tucson, AZ, USA.

Halophytes are plants that can naturally tolerate high concentrations of salt in the soil, and their tolerance to salt stress may occur through various evolutionary and molecular mechanisms. Eutrema salsugineum is a halophytic species in the Brassicaceae that can naturally tolerate multiple types of abiotic stresses that typically limit crop productivity, including extreme salinity and cold. It has been widely used as a laboratorial model for stress biology research in plants. Here, we present the reference genome sequence (241 Mb) of E. salsugineum at 8× coverage sequenced using the traditional Sanger sequencing-based approach with comparison to its close relative Arabidopsis thaliana. The E. salsugineum genome contains 26,531 protein-coding genes and 51.4% of its genome is composed of repetitive sequences that mostly reside in pericentromeric regions. Comparative analyses of the genome structures, protein-coding genes, microRNAs, stress-related pathways, and estimated translation efficiency of proteins between E. salsugineum and A. thaliana suggest that halophyte adaptation to environmental stresses may occur via a global network adjustment of multiple regulatory mechanisms. The E. salsugineum genome provides a resource to identify naturally occurring genetic alterations contributing to the adaptation of halophytic plants to salinity and that might be bioengineered in related crop species.
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http://dx.doi.org/10.3389/fpls.2013.00046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3604812PMC
March 2013

Porphyra (Bangiophyceae) Transcriptomes Provide Insights Into Red Algal Development And Metabolism.

J Phycol 2012 Dec 3;48(6):1328-42. Epub 2012 Oct 3.

Department of Ecology, Evolution and Natural Resources, Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, 08901, USA.

The red seaweed Porphyra (Bangiophyceae) and related Bangiales have global economic importance. Here, we report the analysis of a comprehensive transcriptome comprising ca. 4.7 million expressed sequence tag (EST) reads from P. umbilicalis (L.) J. Agardh and P. 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 that 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.
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http://dx.doi.org/10.1111/j.1529-8817.2012.01229.xDOI Listing
December 2012

MAJOR DEVELOPMENTAL REGULATORS AND THEIR EXPRESSION IN TWO CLOSELY RELATED SPECIES OF PORPHYRA (RHODOPHYTA)(1).

J Phycol 2012 Aug 12;48(4):883-96. Epub 2012 Apr 12.

Department of Biology, East Carolina University, Greenville, NC 27848, USADelaware Biotechnology Institute, Delaware Technology Park, Newark DE 19711, USADOE Joint Genomics Institute, Walnut Creek, CA 94598, USADepartment of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USADepartment of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, 06901, USADepartment of Marine Sciences, University of Connecticut, Groton, CT 06340, USASchool of Marine Science, University of Maine, Orono, ME 04469 USA.

Little is known about the genetic and biochemical mechanisms that underlie red algal development, for example, why the group failed to evolve complex parenchyma and tissue differentiation. Here we examined expressed sequence tag (EST) data from two closely related species, Porphyra umbilicalis (L.) J. Agardh and P. purpurea (Roth) C. Agardh, for conserved developmental regulators known from model eukaryotes, and their expression levels in several developmental stages. Genes for most major developmental families were present, including MADS-box and homeodomain (HD) proteins, SNF2 chromatin-remodelers, and proteins involved in sRNA biogenesis. Some of these genes displayed altered expression correlating with different life history stages or cell types. Notably, two ESTs encoding HD proteins showed eightfold higher expression in the P. purpurea sporophyte (conchocelis) than in the gametophyte (blade), whereas two MADS domain-containing paralogs showed significantly different patterns of expression in the conchocelis and blade respectively. These developmental gene families do not appear to have undergone the kinds of dramatic expansions in copy number found in multicellular land plants and animals, which are important for regulating developmental processes in those groups. Analyses of small RNAs did not validate the presence of miRNAs, but homologs of Argonaute were present. In general, it appears that red algae began with a similar molecular toolkit for directing development as did other multicellular eukaryotes, but probably evolved altered roles for many key proteins, as well as novel mechanisms yet to be discovered.
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http://dx.doi.org/10.1111/j.1529-8817.2012.01138.xDOI Listing
August 2012

The Cassava Genome: Current Progress, Future Directions.

Trop Plant Biol 2012 Mar 5;5(1):88-94. Epub 2012 Jan 5.

The starchy swollen roots of cassava provide an essential food source for nearly a billion people, as well as possibilities for bioenergy, yet improvements to nutritional content and resistance to threatening diseases are currently impeded. A 454-based whole genome shotgun sequence has been assembled, which covers 69% of the predicted genome size and 96% of protein-coding gene space, with genome finishing underway. The predicted 30,666 genes and 3,485 alternate splice forms are supported by 1.4 M expressed sequence tags (ESTs). Maps based on simple sequence repeat (SSR)-, and EST-derived single nucleotide polymorphisms (SNPs) already exist. Thanks to the genome sequence, a high-density linkage map is currently being developed from a cross between two diverse cassava cultivars: one susceptible to cassava brown streak disease; the other resistant. An efficient genotyping-by-sequencing (GBS) approach is being developed to catalog SNPs both within the mapping population and among diverse African farmer-preferred varieties of cassava. These resources will accelerate marker-assisted breeding programs, allowing improvements in disease-resistance and nutrition, and will help us understand the genetic basis for disease resistance.
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http://dx.doi.org/10.1007/s12042-011-9088-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322327PMC
March 2012

Analysis of Porphyra membrane transporters demonstrates gene transfer among photosynthetic eukaryotes and numerous sodium-coupled transport systems.

Plant Physiol 2012 Apr 14;158(4):2001-12. Epub 2012 Feb 14.

Department of Ecology, Evolution and Natural Resources, and Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey 08901, USA.

Membrane transporters play a central role in many cellular processes that rely on the movement of ions and organic molecules between the environment and the cell, and between cellular compartments. Transporters have been well characterized in plants and green algae, but little is known about transporters or their evolutionary histories in the red algae. Here we examined 482 expressed sequence tag contigs that encode putative membrane transporters in the economically important red seaweed Porphyra (Bangiophyceae, Rhodophyta). These contigs are part of a comprehensive transcriptome dataset from Porphyra umbilicalis and Porphyra purpurea. Using phylogenomics, we identified 30 trees that support the expected monophyly of red and green algae/plants (i.e. the Plantae hypothesis) and 19 expressed sequence tag contigs that show evidence of endosymbiotic/horizontal gene transfer involving stramenopiles. The majority (77%) of analyzed contigs encode transporters with unresolved phylogenies, demonstrating the difficulty in resolving the evolutionary history of genes. We observed molecular features of many sodium-coupled transport systems in marine algae, and the potential for coregulation of Porphyra transporter genes that are associated with fatty acid biosynthesis and intracellular lipid trafficking. Although both the tissue-specific and subcellular locations of the encoded proteins require further investigation, our study provides red algal gene candidates associated with transport functions and novel insights into the biology and evolution of these transporters.
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http://dx.doi.org/10.1104/pp.112.193896DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3320202PMC
April 2012

The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage.

J Biol Chem 2011 Jun 22;286(24):21427-39. Epub 2011 Apr 22.

Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA.

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.
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http://dx.doi.org/10.1074/jbc.M111.233734DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3122202PMC
June 2011

Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri.

Science 2010 Jul;329(5988):223-6

U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.

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.
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http://dx.doi.org/10.1126/science.1188800DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2993248PMC
July 2010

Evolution of an expanded sex-determining locus in Volvox.

Science 2010 Apr;328(5976):351-4

The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.

Although dimorphic sexes have evolved repeatedly in multicellular eukaryotes, their origins are unknown. The mating locus (MT) of the sexually dimorphic multicellular green alga Volvox carteri specifies the production of eggs and sperm and has undergone a remarkable expansion and divergence relative to MT from Chlamydomonas reinhardtii, which is a closely related unicellular species that has equal-sized gametes. Transcriptome analysis revealed a rewired gametic expression program for Volvox MT genes relative to Chlamydomonas and identified multiple gender-specific and sex-regulated transcripts. The retinoblastoma tumor suppressor homolog MAT3 is a Volvox MT gene that displays sexually regulated alternative splicing and evidence of gender-specific selection, both of which are indicative of cooption into the sexual cycle. Thus, sex-determining loci affect the evolution of both sex-related and non-sex-related genes.
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http://dx.doi.org/10.1126/science.1186222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880461PMC
April 2010

The dynamic genome of Hydra.

Nature 2010 Mar 14;464(7288):592-6. Epub 2010 Mar 14.

US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.

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.
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http://dx.doi.org/10.1038/nature08830DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4479502PMC
March 2010

The genome of Naegleria gruberi illuminates early eukaryotic versatility.

Cell 2010 Mar;140(5):631-42

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.

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.
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http://dx.doi.org/10.1016/j.cell.2010.01.032DOI Listing
March 2010

The Chlamydomonas genome reveals the evolution of key animal and plant functions.

Science 2007 Oct;318(5848):245-50

Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA.

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.
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http://dx.doi.org/10.1126/science.1143609DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875087PMC
October 2007

Novel sfi1 alleles uncover additional functions for Sfi1p in bipolar spindle assembly and function.

Mol Biol Cell 2007 Jun 28;18(6):2047-56. Epub 2007 Mar 28.

Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom.

A variety of spindle and kinetochore defects have been shown to induce a mitotic delay through activation of the spindle checkpoint. With the aim of identifying novel mitotic defects we carried out a mad1 synthetic lethal screen in budding yeast. In this screen, four novel alleles of sfi1 were isolated. SFI1 is an essential gene, previously identified through its interaction with centrin/CDC31 and shown to be required for spindle pole body (SPB) duplication. The new mutations were all found in the C-terminal domain of Sfi1p, which has no known function, but it is well conserved among budding yeasts. Analysis of the novel sfi1 mutants, through a combination of light and electron microscopy, revealed duplicated SPBs <0.3 microm apart. Importantly, these SPBs have completed duplication, but they are not separated, suggesting a possible defect in splitting of the bridge. We discuss possible roles for Sfi1p in this step in bipolar spindle assembly.
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http://dx.doi.org/10.1091/mbc.e06-10-0918DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1877113PMC
June 2007

Novel metabolism in Chlamydomonas through the lens of genomics.

Curr Opin Plant Biol 2007 Apr 8;10(2):190-8. Epub 2007 Feb 8.

Department of Plant Biology, The Carnegie Institution, 260 Panama Street, Stanford, California 94305, USA.

Chlamydomonas has traditionally been exploited as an organism that is associated with sophisticated physiological, genetic and molecular analyses, all of which have been used to elucidate several biological processes, especially photosynthesis and flagella function and assembly. Recently, the genomics of Chlamydomonas has been combined with other technologies to unveil new aspects of metabolism, including inorganic carbon utilization, anaerobic fermentation, the suite and functions of selenoproteins, and the regulation of vitamin biosynthesis. These initial findings represent the first glimpse through a genomic window onto the highly complex metabolisms that characterize a unicellular, photosynthetic eukaryote that has maintained both plant-like and animal-like characteristics over evolutionary time.
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http://dx.doi.org/10.1016/j.pbi.2007.01.012DOI Listing
April 2007

Evidence for a microRNA expansion in the bilaterian ancestor.

Dev Genes Evol 2007 Jan 14;217(1):73-7. Epub 2006 Nov 14.

DOE Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, CA 94598, USA.

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.
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http://dx.doi.org/10.1007/s00427-006-0116-1DOI Listing
January 2007

Large-scale trends in the evolution of gene structures within 11 animal genomes.

PLoS Comput Biol 2006 Mar 3;2(3):e15. Epub 2006 Mar 3.

Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA.

We have used the annotations of six animal genomes (Homo sapiens, Mus musculus, Ciona intestinalis, Drosophila melanogaster, Anopheles gambiae, and Caenorhabditis elegans) together with the sequences of five unannotated Drosophila genomes to survey changes in protein sequence and gene structure over a variety of timescales--from the less than 5 million years since the divergence of D. simulans and D. melanogaster to the more than 500 million years that have elapsed since the Cambrian explosion. To do so, we have developed a new open-source software library called CGL (for "Comparative Genomics Library"). Our results demonstrate that change in intron-exon structure is gradual, clock-like, and largely independent of coding-sequence evolution. This means that genome annotations can be used in new ways to inform, corroborate, and test conclusions drawn from comparative genomics analyses that are based upon protein and nucleotide sequence similarities.
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http://dx.doi.org/10.1371/journal.pcbi.0020015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1386723PMC
March 2006

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.

Genome Biol 2002 31;3(12):RESEARCH0083. Epub 2002 Dec 31.

Department of Molecular and Cell Biology, University of California, Life Sciences Addition, Berkeley, CA 94720-3200, USA.

Background: 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.

Results: 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.

Conclusions: 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.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC151185PMC
http://dx.doi.org/10.1186/gb-2002-3-12-research0083DOI Listing
June 2003
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