scholarly journals Prometheus: omics portals for interkingdom comparative genomic analyses

2017 ◽  
Author(s):  
Gunhwan Ko ◽  
Insu Jang ◽  
Namjin Koo ◽  
Seong-Jin Park ◽  
Sangho Oh ◽  
...  
Keyword(s):  
Domain Architecture ◽  
Industrial Applications ◽  
Model Organisms ◽  
Comparative Genomic ◽  
Identification System ◽  
New Paradigm ◽  
Comparative Analyses ◽  
Functional Studies ◽  
Gene Search ◽  
Functional Analyses

AbstractFunctional analyses of genes are crucial for unveiling biological responses, for genetic engineering, and for developing new medicines. However, functional analyses have largely been restricted to model organisms, representing a major hurdle for functional studies and industrial applications. To resolve this, comparative genome analyses can be used to provide clues to gene functions as well as their evolutionary history. To this end, we present Prometheus (http://prometheus.kobic.re.kr),web-based omics portal that contains more than 17,215 sequences from prokaryotic and eukaryotic genomes. This portal supports interkingdom comparative analyses via a domain architecture-based gene identification system, Gene Search, and users can easily and rapidly identify single or entire gene sets in specific pathways. Bioinformatics tools for further analyses are provided in Prometheus or through BioExpress, a cloud-based bioinformatics analysis platform. Prometheus suggests a new paradigm for comparative analyses with large amounts of genomic information.

scholarly journals Genome Sequence of the Euryhaline Javafish Medaka, Oryzias javanicus: A Small Aquarium Fish Model for Studies on Adaptation to Salinity

2020 ◽  
Vol 10 (3) ◽  
pp. 907-915 ◽  
Author(s):  
Yusuke Takehana ◽  
Margot Zahm ◽  
Cédric Cabau ◽  
Christophe Klopp ◽  
Céline Roques ◽  
...  
Keyword(s):  
Draft Genome ◽  
Mangrove Ecosystem ◽  
Model Organisms ◽  
Comparative Genomic ◽  
Draft Genome Assembly ◽  
Functional Studies ◽  
Fish Model ◽  
Oryzias Javanicus ◽  
Wide Range ◽  
Adaptation To Salinity

The genus Oryzias consists of 35 medaka-fish species each exhibiting various ecological, morphological and physiological peculiarities and adaptations. Beyond of being a comprehensive phylogenetic group for studying intra-genus evolution of several traits like sex determination, behavior, morphology or adaptation through comparative genomic approaches, all medaka species share many advantages of experimental model organisms including small size and short generation time, transparent embryos and genome editing tools for reverse and forward genetic studies. The Java medaka, Oryzias javanicus, is one of the two species of medaka perfectly adapted for living in brackish/sea-waters. Being an important component of the mangrove ecosystem, O. javanicus is also used as a valuable marine test-fish for ecotoxicology studies. Here, we sequenced and assembled the whole genome of O. javanicus, and anticipate this resource will be catalytic for a wide range of comparative genomic, phylogenetic and functional studies. Complementary sequencing approaches including long-read technology and data integration with a genetic map allowed the final assembly of 908 Mbp of the O. javanicus genome. Further analyses estimate that the O. javanicus genome contains 33% of repeat sequences and has a heterozygosity of 0.96%. The achieved draft assembly contains 525 scaffolds with a total length of 809.7 Mbp, a N50 of 6,3 Mbp and a L50 of 37 scaffolds. We identified 21454 predicted transcripts for a total transcriptome size of 57, 146, 583 bps. We provide here a high-quality chromosome scale draft genome assembly of the euryhaline Javafish medaka (321 scaffolds anchored on 24 chromosomes (representing 97.7% of the total bases)), and give emphasis on the evolutionary adaptation to salinity.

scholarly journals Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity

2021 ◽  
Vol 12 ◽  
Author(s):  
Mehmet Birikmen ◽  
Katherine E. Bohnsack ◽  
Vinh Tran ◽  
Sharvari Somayaji ◽  
Markus T. Bohnsack ◽  
...  
Keyword(s):  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Domain Architecture ◽  
Ribosomal Subunit ◽  
Protein Domain ◽  
Model Organisms ◽  
Eukaryotic Ribosome ◽  
Functional Studies ◽  
Fundamental Information ◽  
Assembly Procedure

Ribosome assembly is an essential and carefully choreographed cellular process. In eukaryotes, several 100 proteins, distributed across the nucleolus, nucleus, and cytoplasm, co-ordinate the step-wise assembly of four ribosomal RNAs (rRNAs) and approximately 80 ribosomal proteins (RPs) into the mature ribosomal subunits. Due to the inherent complexity of the assembly process, functional studies identifying ribosome biogenesis factors and, more importantly, their precise functions and interplay are confined to a few and very well-established model organisms. Although best characterized in yeast (Saccharomyces cerevisiae), emerging links to disease and the discovery of additional layers of regulation have recently encouraged deeper analysis of the pathway in human cells. In archaea, ribosome biogenesis is less well-understood. However, their simpler sub-cellular structure should allow a less elaborated assembly procedure, potentially providing insights into the functional essentials of ribosome biogenesis that evolved long before the diversification of archaea and eukaryotes. Here, we use a comprehensive phylogenetic profiling setup, integrating targeted ortholog searches with automated scoring of protein domain architecture similarities and an assessment of when search sensitivity becomes limiting, to trace 301 curated eukaryotic ribosome biogenesis factors across 982 taxa spanning the tree of life and including 727 archaea. We show that both factor loss and lineage-specific modifications of factor function modulate ribosome biogenesis, and we highlight that limited sensitivity of the ortholog search can confound evolutionary conclusions. Projecting into the archaeal domain, we find that only few factors are consistently present across the analyzed taxa, and lineage-specific loss is common. While members of the Asgard group are not special with respect to their inventory of ribosome biogenesis factors (RBFs), they unite the highest number of orthologs to eukaryotic RBFs in one taxon. Using large ribosomal subunit maturation as an example, we demonstrate that archaea pursue a simplified version of the corresponding steps in eukaryotes. Much of the complexity of this process evolved on the eukaryotic lineage by the duplication of ribosomal proteins and their subsequent functional diversification into ribosome biogenesis factors. This highlights that studying ribosome biogenesis in archaea provides fundamental information also for understanding the process in eukaryotes.

scholarly journals Genome sequence of the euryhaline Javafish medaka, Oryzias javanicus: a small aquarium fish model for studies on adaptation to salinity

2019 ◽  
Author(s):  
Yusuke Takehana ◽  
Margot Zahm ◽  
Cédric Cabau ◽  
Christophe Klopp ◽  
Céline Roques ◽  
...  
Keyword(s):  
Draft Genome ◽  
Mangrove Ecosystem ◽  
Model Organisms ◽  
Comparative Genomic ◽  
Draft Genome Assembly ◽  
Functional Studies ◽  
Fish Model ◽  
Oryzias Javanicus ◽  
Wide Range ◽  
Adaptation To Salinity

ABSTRACTBackgroundThe genus Oryzias is constituted of 35 medaka-fish species each exhibiting various ecological, morphological and physiological peculiarities and adaptations. Beyond of being a comprehensive phylogenetic group for studying intra-genus evolution of several traits like sex determination, behaviour, morphology or adaptation through comparative genomic approaches, all medaka species share many advantages of experimental model organisms including small size and short generation time, transparent embryos and genome editing tools for reverse and forward genetic studies. The Java medaka, Oryzias javanicus, is one of the two species of medaka perfectly adapted for living in brackish/sea-waters. Being an important component of the mangrove ecosystem, O. javanicus is also used as a valuable marine test-fish for ecotoxicology studies. Here, we sequenced and assembled the whole genome of O. javanicus, and anticipate this resource will be catalytic for a wide range of comparative genomic, phylogenetic and functional studies.FindingsComplementary sequencing approaches including long-read technology and data integration with a genetic map allowed the final assembly of 908 Mbp of the O. javanicus genome. Further analyses estimate that the O. javanicus genome contains 33% of repeat sequences and has a heterozygosity of 0.96%. The achieved draft assembly contains 525 scaffolds with a total length of 809.7 Mbp, a N50 of 6.3 Mbp and a L50 of 37 scaffolds. We identified 21454 expressed transcripts for a total transcriptome size of 57, 146, 583 bps.ConclusionsWe provide here a high-quality draft genome assembly of the euryhaline Javafish medaka, and give emphasis on the evolutionary adaptation to salinity.

scholarly journals Draft Genome Sequence of Dermatophagoides pteronyssinus, the European House Dust Mite

2017 ◽  
Vol 5 (32) ◽  
Author(s):  
Rose Waldron ◽  
Jamie McGowan ◽  
Natasha Gordon ◽  
Charley McCarthy ◽  
E. Bruce Mitchell ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gene Prediction ◽  
Draft Genome ◽  
Dermatophagoides Pteronyssinus ◽  
Mite Species ◽  
Draft Genome Sequence ◽  
Comparative Genomic ◽  
Genomic Analyses ◽  
Dust Mite ◽  
Functional Analyses

ABSTRACT Dermatophagoides pteronyssinus is the European dust mite and a major source of human allergens. Here, we present the first draft genome sequence of the mite, as well as the ab initio gene prediction and functional analyses that will facilitate comparative genomic analyses with other mite species.

scholarly journals Colocality to Cofunctionality: Eukaryotic Gene Neighborhoods as a Resource for Function Discovery

2020 ◽  
Author(s):  
Fatima Foflonker ◽  
Crysten E Blaby-Haas
Keyword(s):  
Green Algae ◽  
Sequence Similarity ◽  
Phosphoglycerate Kinase ◽  
Orthologous Gene ◽  
Model Organisms ◽  
Comparative Genomic ◽  
Evolutionary Origins ◽  
Eukaryotic Gene ◽  
Arsenic Detoxification ◽  
Function Discovery

Abstract Diverging from the classic paradigm of random gene order in eukaryotes, gene proximity can be leveraged to systematically identify functionally related gene neighborhoods in eukaryotes, utilizing techniques pioneered in bacteria. Current methods of identifying gene neighborhoods typically rely on sequence similarity to characterized gene products. However, this approach is not robust for nonmodel organisms like algae, which are evolutionarily distant from well-characterized model organisms. Here, we utilize a comparative genomic approach to identify evolutionarily conserved proximal orthologous gene pairs conserved across at least two taxonomic classes of green algae. A total of 317 gene neighborhoods were identified. In some cases, gene proximity appears to have been conserved since before the streptophyte–chlorophyte split, 1,000 Ma. Using functional inferences derived from reconstructed evolutionary relationships, we identified several novel functional clusters. A putative mycosporine-like amino acid, “sunscreen,” neighborhood contains genes similar to either vertebrate or cyanobacterial pathways, suggesting a novel mosaic biosynthetic pathway in green algae. One of two putative arsenic-detoxification neighborhoods includes an organoarsenical transporter (ArsJ), a glyceraldehyde 3-phosphate dehydrogenase-like gene, homologs of which are involved in arsenic detoxification in bacteria, and a novel algal-specific phosphoglycerate kinase-like gene. Mutants of the ArsJ-like transporter and phosphoglycerate kinase-like genes in Chlamydomonas reinhardtii were found to be sensitive to arsenate, providing experimental support for the role of these identified neighbors in resistance to arsenate. Potential evolutionary origins of neighborhoods are discussed, and updated annotations for formerly poorly annotated genes are presented, highlighting the potential of this strategy for functional annotation.

scholarly journals Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Marina Athanasouli ◽  
Hanh Witte ◽  
Christian Weiler ◽  
Tobias Loschko ◽  
Gabi Eberhardt ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Model Organisms ◽  
Parasitic Nematodes ◽  
Comparative Genomic ◽  
Orphan Genes ◽  
Community Based ◽  
Pristionchus Pacificus ◽  
Gene Annotations ◽  
Gene Models

Abstract Background Nematode model organisms such as Caenorhabditis elegans and Pristionchus pacificus are powerful systems for studying the evolution of gene function at a mechanistic level. However, the identification of P. pacificus orthologs of candidate genes known from C. elegans is complicated by the discrepancy in the quality of gene annotations, a common problem in nematode and invertebrate genomics. Results Here, we combine comparative genomic screens for suspicious gene models with community-based curation to further improve the quality of gene annotations in P. pacificus. We extend previous curations of one-to-one orthologs to larger gene families and also orphan genes. Cross-species comparisons of protein lengths, screens for atypical domain combinations and species-specific orphan genes resulted in 4311 candidate genes that were subject to community-based curation. Corrections for 2946 gene models were implemented in a new version of the P. pacificus gene annotations. The new set of gene annotations contains 28,896 genes and has a single copy ortholog completeness level of 97.6%. Conclusions Our work demonstrates the effectiveness of comparative genomic screens to identify suspicious gene models and the scalability of community-based approaches to improve the quality of thousands of gene models. Similar community-based approaches can help to improve the quality of gene annotations in other invertebrate species, including parasitic nematodes.

scholarly journals Genome-Wide Analysis of Biosynthetic Gene Cluster Reveals Correlated Gene Loss with Absence of Usnic Acid in Lichen-Forming Fungi

2020 ◽  
Vol 12 (10) ◽  
pp. 1858-1868
Author(s):  
David Pizarro ◽  
Pradeep K Divakar ◽  
Felix Grewe ◽  
Ana Crespo ◽  
Francesco Dal Grande ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Domain Architecture ◽  
Usnic Acid ◽  
Biosynthetic Gene Cluster ◽  
Fungal Species ◽  
Gene Content ◽  
Gene Arrangement ◽  
Evolutionary Significance ◽  
Comparative Genomic ◽  
Biosynthetic Gene

Abstract Lichen-forming fungi are known to produce a large number of secondary metabolites. Some metabolites are deposited in the cortical layer of the lichen thallus where they exert important ecological functions, such as UV filtering. The fact that closely related lineages of lichen-forming fungi can differ in cortical chemistry suggests that natural product biosynthesis in lichens can evolve independent from phylogenetic constraints. Usnic acid is one of the major cortical pigments in lichens. Here we used a comparative genomic approach on 46 lichen-forming fungal species of the Lecanoromycetes to elucidate the biosynthetic gene content and evolution of the gene cluster putatively responsible for the biosynthesis of usnic acid. Whole-genome sequences were gathered from taxa belonging to different orders and families of Lecanoromycetes, where Parmeliaceae is the most well-represented taxon, and analyzed with a variety of genomic tools. The highest number of biosynthetic gene clusters was found in Evernia prunastri, Pannoparmelia angustata, and Parmotrema austrosinense, respectively, and lowest in Canoparmelia nairobiensis, Bulbothrix sensibilis, and Hypotrachyna scytodes. We found that all studied species producing usnic acid contain the putative usnic acid biosynthetic gene cluster, whereas the cluster was absent in all genomes of species lacking usnic acid. The absence of the gene cluster was supported by an additional unsuccessful search for ß-ketoacylsynthase, the most conserved domain of the gene cluster, in the genomes of species lacking usnic acid. The domain architecture of this PKS cluster—homologous to the already known usnic acid PKS cluster (MPAS) and CYT450 (MPAO)—varies within the studied species, whereas the gene arrangement is highly similar in closely related taxa. We hypothesize that the ancestor of these lichen-forming fungi contained the putative usnic acid producing PKS cluster and that the gene cluster was lost repeatedly during the evolution of these groups. Our study provides insight into the genomic adaptations to the evolutionary success of these lichen-forming fungal species and sets a baseline for further exploration of biosynthetic gene content and its evolutionary significance.

scholarly journals An immunologically anomalous but considerably bioactive GH produced by a novel GH1 mutation (p.D116E)

2009 ◽  
Vol 161 (2) ◽  
pp. 301-306 ◽  
Author(s):  
Sumito Dateki ◽  
Kazuko Hizukuri ◽  
Toshiaki Tanaka ◽  
Noriyuki Katsumata ◽  
Paravee Katavetin ◽  
...  
Keyword(s):  
Rare Condition ◽  
Normal Range ◽  
Functional Studies ◽  
Provocation Tests ◽  
Old Japanese ◽  
Igf Binding ◽  
Functional Analyses ◽  
Igf Binding Protein

ContexAlthough GH values measured by an immunoassay usually reflect GH bioactivities, discrepancy exists between immunoactivity and bioactivity in a rare condition known as ‘bioinactive GH’.ObjectiveTo report an immunologically anomalous but considerably bioactive GH.MethodsWe performed mutational and functional analyses of GH1 in a 7-year-old Japanese boy with short stature (−3.0 s.d.) in whom serum GH values measured with a Tosoh immunoassay kit were all undetectable in three provocation tests, whereas urine GH value measured with a Hitachi immunoassay kit was within the normal range. Serum IGF-1 was at a low-normal range, and IGF-binding protein-3 was below the normal range.ResultsMutation analysis showed a missense GH produced by a novel GH1 mutation (p.D116E) of paternal origin and a frameshift mutation (p.Q68fsX106) of maternal origin. Genotype–phenotype correlations in this family and in vitro functional studies indicated that the p.D116E-GH was immeasurable with the Tosoh kit but was measurable, though maybe not precise, with a Daiichi kit, and had a reduced in vivo bioactivity. The p.Q68fsX106 yielded no GH protein.ConclusionsThe results suggest that the p.D116E affects the GH epitope primarily recognized by the Tosoh kit but not by the Hitachi or the Daiichi kits, thereby producing an immunologically anomalous but considerably bioactive GH. The presence of such a hormone discordant for immunoactivity and bioactivity should be kept in mind, to allow for an appropriate assessment of endocrine data.

scholarly journals Heterelogous Expression of Plant Genes

2009 ◽  
Vol 2009 ◽  
pp. 1-16 ◽  
Author(s):  
Filiz Yesilirmak ◽  
Zehra Sayers
Keyword(s):  
Large Scale ◽  
Protein Production ◽  
Insect Cells ◽  
Protein Characterization ◽  
Model Organisms ◽  
Plant Proteins ◽  
Production Methods ◽  
Functional Studies ◽  
Recombinant Plant ◽  
Plant Genes

Heterologous expression allows the production of plant proteins in an organism which is simpler than the natural source. This technology is widely used for large-scale purification of plant proteins from microorganisms for biochemical and biophysical analyses. Additionally expression in well-defined model organisms provides insights into the functions of proteins in complex pathways. The present review gives an overview of recombinant plant protein production methods using bacteria, yeast, insect cells, and Xenopus laevis oocytes and discusses the advantages of each system for functional studies and protein characterization.

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