scholarly journals A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jiorgos Kourelis ◽  
Farnusch Kaschani ◽  
Friederike M. Grosse-Holz ◽  
Felix Homma ◽  
Markus Kaiser ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Draft Genome ◽  
Model Organism ◽  
Functional Annotations ◽  
Draft Genome Assembly ◽  
Extracellular Proteome ◽  
Protein Encoding ◽  
Gene Models ◽  
Genome Assemblies ◽  
Encoding Genes

Abstract Background Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft assemblies appear incorrect. Results Here we present an improved proteome based on the Niben1.0.1 draft genome assembly guided by gene models from other Nicotiana species. Due to the fragmented nature of the Niben1.0.1 draft genome, many protein-encoding genes are missing or partial. We complement these missing proteins by similarly annotating other draft genome assemblies. This approach overcomes problems caused by mis-annotated exon-intron boundaries and mis-assigned short read transcripts to homeologs in polyploid genomes. With an estimated 98.1% completeness; only 53,411 protein-encoding genes; and improved protein lengths and functional annotations, this new predicted proteome is better in assigning spectra than the preceding proteome annotations. This dataset is more sensitive and accurate in proteomics applications, clarifying the detection by activity-based proteomics of proteins that were previously predicted to be inactive. Phylogenetic analysis of the subtilase family of hydrolases reveal inactivation of likely homeologs, associated with a contraction of the functional genome in this alloploid plant species. Finally, we use this new proteome annotation to characterize the extracellular proteome as compared to a total leaf proteome, which highlights the enrichment of hydrolases in the apoplast. Conclusions This proteome annotation provides the community working with Nicotiana benthamiana with an important new resource for functional proteomics.

scholarly journals Homology-guided re-annotation improves the gene models of the alloploid Nicotiana benthamiana

2018 ◽  
Author(s):  
Jiorgos Kourelis ◽  
Farnusch Kaschani ◽  
Friederike M. Grosse-Holz ◽  
Felix Homma ◽  
Markus Kaiser ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Gene Annotation ◽  
Draft Genome ◽  
Model Organism ◽  
Extracellular Proteins ◽  
Functional Annotations ◽  
Draft Genome Assembly ◽  
Protein Encoding ◽  
Gene Models ◽  
Encoding Genes

Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft assemblies appear incorrect. Here we present an improved re-annotation of the Niben1.0.1 draft genome assembly guided by gene models from other Nicotiana species. This approach overcomes problems caused by mis-annotated exon-intron boundaries and mis-assigned short read transcripts to homeologs in polyploid genomes. With an estimated 98.1% completeness; only 53,411 protein-encoding genes; and improved protein lengths and functional annotations, this new predicted proteome is better than the preceding proteome annotations. This dataset is more sensitive and accurate in proteomics applications, clarifying the detection by activity-based proteomics of proteins that were previously mis-annotated to be inactive. Phylogenetic analysis of the subtilase family of hydrolases reveal a pseudogenisation of likely homeologs, associated with a contraction of the functional genome in this alloploid plant species. We use this gene annotation to assign extracellular proteins in comparison to a total leaf proteome, to display the enrichment of hydrolases in the apoplast.

scholarly journals The Draft Genome of the Non-Host-AssociatedMethanobrevibacter arboriphilusStrain DH1 Encodes a Large Repertoire of Adhesin-Like Proteins

Archaea ◽  
2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Anja Poehlein ◽  
Rolf Daniel ◽  
Henning Seedorf
Keyword(s):  
Draft Genome ◽  
Gc Content ◽  
Model Organism ◽  
Potential Interaction ◽  
Phylogenetic Groups ◽  
Protein Encoding ◽  
Interaction Partners ◽  
Interesting Candidate ◽  
Encoding Genes ◽  
Large Repertoire

Methanobrevibacter arboriphilusstrain DH1 is an autotrophic methanogen that was isolated from the wetwood of methane-emitting trees. This species has been of considerable interest for its unusual oxygen tolerance and has been studied as a model organism for more than four decades. Strain DH1 is closely related to other host-associatedMethanobrevibacterspecies from intestinal tracts of animals and the rumen, making this strain an interesting candidate for comparative analysis to identify factors important for colonizing intestinal environments. Here, the genome sequence ofM. arboriphilusstrain DH1 is reported. The draft genome is composed of 2.445.031 bp with an average GC content of 25.44% and predicted to harbour 1964 protein-encoding genes. Among the predicted genes, there are also more than 50 putative genes for the so-called adhesin-like proteins (ALPs). The presence of ALP-encoding genes in the genome of this non-host-associated methanogen strongly suggests that target surfaces for ALPs other than host tissues also need to be considered as potential interaction partners. The high abundance of ALPs may also indicate that these types of proteins are more characteristic for specific phylogenetic groups of methanogens rather than being indicative for a particular environment the methanogens thrives in.

scholarly journals Draft Genome Sequence of Tubulinosema ratisbonensis, a Microsporidian Species Infecting the Model Organism Drosophila melanogaster

2019 ◽  
Vol 8 (31) ◽  
Author(s):  
Valérie Polonais ◽  
Sebastian Niehus ◽  
Ivan Wawrzyniak ◽  
Adrien Franchet ◽  
Christine Gaspin ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Genome Sequence ◽  
Genetic Model ◽  
Draft Genome ◽  
Model Organism ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Protein Encoding ◽  
Host Parasite ◽  
Encoding Genes

We present the draft genome sequence of Tubulinosema ratisbonensis, a microsporidium species infecting Drosophila melanogaster. A total of 3,013 protein-encoding genes and an array of transposable elements were identified. This work represents a necessary step to develop a novel model of host-parasite relationships using the highly tractable genetic model D. melanogaster.

scholarly journals Draft Genome Sequence of the Axenic Strain Phormidesmispriestleyi ULC007, a Cyanobacterium Isolated from Lake Bruehwiler (Larsemann Hills, Antarctica)

2017 ◽  
Vol 5 (7) ◽  
Author(s):  
Yannick Lara ◽  
Benoit Durieu ◽  
Luc Cornet ◽  
Olivier Verlaine ◽  
Rosmarie Rippka ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Axenic Strain ◽  
Larsemann Hills ◽  
Freshwater Cyanobacterium ◽  
Protein Encoding ◽  
Encoding Genes

ABSTRACT Phormidesmis priestleyi ULC007 is an Antarctic freshwater cyanobacterium. Its draft genome is 5,684,389 bp long. It contains a total of 5,604 protein-encoding genes, of which 22.2% have no clear homologues in known genomes. To date, this draft genome is the first one ever determined for an axenic cyanobacterium from Antarctica.

scholarly journals Draft Genome Sequence of Ezakiella peruensis Strain M6.X2, a Human Gut Gram-Positive Anaerobic Coccus

2018 ◽  
Vol 6 (9) ◽  
pp. e01487-17
Author(s):  
Awa Diop ◽  
Khoudia Diop ◽  
Enora Tomei ◽  
Didier Raoult ◽  
Florence Fenollar ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Antibiotic Resistance Genes ◽  
Draft Genome Sequence ◽  
Human Gut ◽  
Gene Encoding ◽  
Content Type ◽  
Protein Encoding ◽  
Short Palindromic Repeat ◽  
Encoding Genes

ABSTRACT We report here the draft genome sequence of Ezakiella peruensis strain M6.X2T. The draft genome is 1,672,788 bp long and harbors 1,589 predicted protein-encoding genes, including 26 antibiotic resistance genes with 1 gene encoding vancomycin resistance. The genome also exhibits 1 clustered regularly interspaced short palindromic repeat region and 333 genes acquired by horizontal gene transfer.

scholarly journals Draft Genome Assembly of a Filamentous Euendolithic (True Boring) Cyanobacterium, Mastigocoleus testarum Strain BC008

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Brandon S. Guida ◽  
Ferran Garcia-Pichel
Keyword(s):  
Genome Assembly ◽  
Draft Genome ◽  
Model Organism ◽  
Carbonate Dissolution ◽  
Draft Genome Assembly

Mastigocoleus testarum strain BC008 is a model organism used to study marine photoautotrophic carbonate dissolution. It is a multicellular, filamentous, diazotrophic, euendolithic cyanobacterium ubiquitously found in marine benthic environments. We present an accurate draft genome assembly of 172 contigs spanning 12,700,239 bp with 9,131 annotated genes with an average G+C% of 37.3.

scholarly journals Draft Genome Sequence of the Hydrogenogenic Carboxydotroph Moorella stamsii DSM 26271

2018 ◽  
Vol 6 (18) ◽  
Author(s):  
Anja Poehlein ◽  
Tim Böer ◽  
Kerrin Steensen ◽  
Rolf Daniel
Keyword(s):  
Carbon Monoxide ◽  
Genome Sequence ◽  
Anaerobic Bacterium ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Obligate Anaerobic ◽  
Protein Encoding ◽  
Encoding Genes

ABSTRACT The spore-forming, thermophilic, and obligate anaerobic bacterium Moorella stamsii was isolated from digester sludge. Apart from its ability to use carbon monoxide for growth, M. stamsii harbors several enzymes for the use of different sugars. The draft genome has a size of 3,329 Mb and contains 3,306 predicted protein-encoding genes.

scholarly journals Genome Sequence of Creatinine-Fermenting Tissierella creatinophila Strain KRE 4T (DSM 6911)

2017 ◽  
Vol 5 (12) ◽  
Author(s):  
Heiko Nacke ◽  
Rolf Daniel ◽  
Anja Poehlein
Keyword(s):  
Sewage Sludge ◽  
Genome Sequence ◽  
Draft Genome ◽  
Strictly Anaerobic ◽  
Circular Chromosome ◽  
Content Type ◽  
Protein Encoding ◽  
Encoding Genes

ABSTRACT Tissierella creatinophila strain KRE 4T (DSM 6911) is a strictly anaerobic, creatinine-fermenting, and creatine-fermenting organism, which has been isolated from sewage sludge. The draft genome consists of one circular chromosome (2.5 Mb) and harbors 2,533 predicted protein-encoding genes.

scholarly journals Genome Sequence of the Poly-3-Hydroxybutyrate Producer Clostridium acetireducens DSM 10703

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Sebastian Flüchter ◽  
Anja Poehlein ◽  
Bettina Schiel-Bengelsdorf ◽  
Rolf Daniel ◽  
Peter Dürre
Keyword(s):  
Genome Sequence ◽  
Anaerobic Bacterium ◽  
Draft Genome ◽  
Strictly Anaerobic ◽  
Circular Chromosome ◽  
Protein Encoding ◽  
Encoding Genes

Here, we report the genome sequence of Clostridium acetireducens (DSM 10703 T ), a strictly anaerobic bacterium capable of fermenting acetate and leucine to butyrate, isovalerate, and poly-3-hydroxybutyrate. The draft genome consists of a circular chromosome with a size of 2.4 Mb and harbors 2,239 predicted protein-encoding genes.

scholarly journals The Draft Reference Genome for Hirudo verbana, the Medicinal Leech

2020 ◽  
Author(s):  
Riley T. Paulsen ◽  
Diing D.M. Agany ◽  
Jason Petersen ◽  
Christel M. Davis ◽  
Erik A. Ehli ◽  
...  
Keyword(s):  
Nervous System ◽  
Genome Assembly ◽  
Draft Genome ◽  
Model Organism ◽  
Medicinal Leech ◽  
Comparative Approach ◽  
Neural Pathways ◽  
Sequencing Platform ◽  
Draft Genome Assembly ◽  
Hirudo Verbana

The medicinal leech, Hirudo verbana, is a powerful model organism for investigating fundamental neurobehavioral processes. The well-documented arrangement and properties of H. verbana’s nervous system allows changes at the level of specific neurons or synapses to be linked to physiological and behavioral phenomena. Juxtaposed to the extensive knowledge of H. verbana’s nervous system is a limited, but recently expanding, portfolio of molecular and multi-omics tools. Together, the advancement of genetic databases for H. verbana will complement existing pharmacological and electrophysiological data by affording targeted manipulation and analysis of gene expression in neural pathways of interest. Here, we present the first draft genome assembly for H. verbana, which is approximately 250 Mbp in size and consists of 61,282 contigs. Whole genome sequencing was conducted using an Illumina sequencing platform followed by genome assembly with CLC-Bio Genomics Workbench and subsequent functional annotation. Ultimately, the diversity of organisms for which we have genomic information should parallel the availability of next generation sequencing technologies to widen the comparative approach to understand the involvement and discovery of genes in evolutionarily conserved processes. Results of this work hope to facilitate comparative studies with H. verbana and provide the foundation for future, more complete, genome assemblies of the leech.

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