scholarly journals Delineation of metabolic gene clusters in plant genomes by chromatin signatures

2016 ◽  
Vol 44 (5) ◽  
pp. 2255-2265 ◽  
Author(s):  
Nan Yu ◽  
Hans-Wilhelm Nützmann ◽  
James T. MacDonald ◽  
Ben Moore ◽  
Ben Field ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Plant Genomes ◽  
Metabolic Gene

scholarly journals The PhytoClust tool for metabolic gene clusters discovery in plant genomes

2017 ◽  
Vol 45 (12) ◽  
pp. 7049-7063 ◽  
Author(s):  
Nadine Töpfer ◽  
Lisa-Maria Fuchs ◽  
Asaph Aharoni
Keyword(s):  
Gene Clusters ◽  
Plant Genomes ◽  
Metabolic Gene

scholarly journals The PhytoClust Tool for Metabolic Gene Clusters Discovery in Plant Genomes

2016 ◽  
Author(s):  
Nadine Töpfer ◽  
Lisa-Maria Fuchs ◽  
Asaph Aharoni
Keyword(s):  
Markov Models ◽  
Enrichment Analysis ◽  
Gene Clusters ◽  
Putative Gene ◽  
Specialized Metabolism ◽  
Plant Genomes ◽  
Metabolic Gene ◽  
A Genome ◽  
Enzyme Families ◽  
Species Specific

AbstractThe existence of Metabolic Gene Clusters (MGCs) in plant genomes has recently raised increased interest. Thus far, MGCs were commonly identified for pathways of specialized metabolism, mostly those associated with terpene type products. For efficient identification of novel MGCs computational approaches are essential. Here we present PhytoClust; a tool for the detection of candidate MGCs in plant genomes. The algorithm employs a collection of enzyme families related to plant specialized metabolism, translated into hidden Markov models, to mine given genome sequences for physically co-localized metabolic enzymes. Our tool accurately identifies previously characterized plant MBCs. An exhaustive search of 31 plant genomes detected 1232 and 5531 putative gene cluster types and candidates, respectively. Clustering analysis of putative MGCs types by species reflected plant taxonomy. Furthermore, enrichment analysis revealed taxa- and species-specific enrichment of certain enzyme families in MGCs. When operating through our web-interface, PhytoClust users can mine a genome either based on a list of known cluster types or by defining new cluster rules. Moreover, for selected plant species, the output can be complemented by co-expression analysis. Altogether, we envisage PhytoClust to enhance novel MGCs discovery which will in turn impact the exploration of plant metabolism.

scholarly journals Multigenome analysis implicates miniature inverted-repeat transposable elements (MITEs) in metabolic diversification in eudicots

2018 ◽  
Vol 115 (28) ◽  
pp. E6650-E6658 ◽  
Author(s):  
Alexander M. Boutanaev ◽  
Anne E. Osbourn
Keyword(s):  
Transposable Elements ◽  
Inverted Repeat ◽  
Cluster Formation ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Terpene Synthase ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Systematic Analysis ◽  
Plant Genomes

Plants produce a plethora of natural products, including many drugs. It has recently emerged that the genes encoding different natural product pathways may be organized as biosynthetic gene clusters in plant genomes, with >30 examples reported so far. Despite superficial similarities with microbes, these clusters have not arisen by horizontal gene transfer, but rather by gene duplication, neofunctionalization, and relocation via unknown mechanisms. Previously we reported that two Arabidopsis thaliana biosynthetic gene clusters are located in regions of the genome that are significantly enriched in transposable elements (TEs). Other plant biosynthetic gene clusters also harbor abundant TEs. TEs can mediate genomic rearrangement by providing homologous sequences that enable illegitimate recombination and gene relocation. Thus, TE-mediated recombination may contribute to plant biosynthetic gene cluster formation. TEs may also facilitate establishment of regulons. However, a systematic analysis of the TEs associated with plant biosynthetic gene clusters has not been carried out. Here we investigate the TEs associated with clustered terpene biosynthetic genes in multiple plant genomes and find evidence to suggest a role for miniature inverted-repeat transposable elements in cluster formation in eudicots. Through investigation of the newly sequenced Amborella trichopoda, Aquilegia coerulea, and Kalanchoe fedtschenkoi genomes, we further show that the “block” mechanism of founding of biosynthetic gene clusters through duplication and diversification of pairs of terpene synthase and cytochrome P450 genes that is prevalent in the eudicots arose around 90–130 million years ago, after the appearance of the basal eudicots and before the emergence of the superrosid clade.

scholarly journals Metabolic gene clusters encoding the enzymes of two branches of the 3-oxoadipate pathway in the pathogenic yeast Candida albicans

2015 ◽  
Vol 15 (3) ◽  
Author(s):  
Gabriela Gérecová ◽  
Martina Neboháčová ◽  
Igor Zeman ◽  
Leszek P. Pryszcz ◽  
Ľubomír Tomáška ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Gene Clusters ◽  
Pathogenic Yeast ◽  
Metabolic Gene

scholarly journals RNA sequencing of an nsdC mutant reveals global regulation of secondary metabolic gene clusters in Aspergillus flavus

2016 ◽  
Vol 182 ◽  
pp. 150-161 ◽  
Author(s):  
Matthew K. Gilbert ◽  
Brian M. Mack ◽  
Qijian Wei ◽  
John M. Bland ◽  
Deepak Bhatnagar ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Aspergillus Flavus ◽  
Gene Clusters ◽  
Global Regulation ◽  
Metabolic Gene

scholarly journals Comparative Phylogenomic Synteny Network Analysis of Mammalian and Angiosperm Genomes

2018 ◽  
Author(s):  
Tao Zhao ◽  
M. Eric Schranz
Keyword(s):  
Large Scale ◽  
Homeobox Gene ◽  
Gene Families ◽  
Gene Clusters ◽  
Parahox Gene ◽  
Family Networks ◽  
Plant Genomes ◽  
Eukaryotic Gene ◽  
Syntenic Gene ◽  
Phylogenetic Profiling

AbstractBackgroundSynteny analysis is a valuable approach for understanding eukaryotic gene and genome evolution, but still relies largely on pairwise or reference-based comparisons. Network approaches can be utilized to expand large-scale phylogenomic microsynteny studies. There is now a wealth of completed mammalian (animal) and angiosperm (plant) genomes, two very important lineages that have evolved and radiated over the last ~170 million years. Genomic organization and conservation differs greatly between these two groups; however, a systematic and comparative characterization of synteny between the two lineages using the same approaches and metrics has not been undertaken.ResultsWe have built complete microsynteny networks for 87 mammalian and 107 angiosperm genomes, which contain 1,464,753 nodes (genes) and 49,426,268 edges (syntenic connections between genes) for mammals, and 2,234,461 nodes and 46,938,272 edges for angiosperms, respectively. Exploiting network statistics, we present the functional characteristics of extremely conserved and diversified gene families. We summarize the features of all syntenic gene clusters and present lineage-wide phylogenetic profiling, revealing intriguing sub-clade lineage-specific clusters. We depict several representative clusters of important developmental genes in humans, such as CENPJ, p53 and NFE2. Finally, we present the complete homeobox gene family networks for both mammals (including Hox and ParaHox gene clusters) and angiosperms.ConclusionsOur results illustrate and quantify overall synteny conservation and diversification properties of all annotated genes for mammals and angiosperms and show that plant genomes are in general more dynamic.

scholarly journals Investigation of terpene diversification across multiple sequenced plant genomes

2014 ◽  
Vol 112 (1) ◽  
pp. E81-E88 ◽  
Author(s):  
Alexander M. Boutanaev ◽  
Tessa Moses ◽  
Jiachen Zi ◽  
David R. Nelson ◽  
Sam T. Mugford ◽  
...  
Keyword(s):  
Cytochromes P450 ◽  
Gene Clusters ◽  
Metabolic Diversity ◽  
Plant Genomes ◽  
Gene Pairs ◽  
Genetic Components ◽  
Dynamic Genome ◽  
Scaffold Diversity ◽  
Terpenoid Synthase ◽  
Key Events

Plants produce an array of specialized metabolites, including chemicals that are important as medicines, flavors, fragrances, pigments and insecticides. The vast majority of this metabolic diversity is untapped. Here we take a systematic approach toward dissecting genetic components of plant specialized metabolism. Focusing on the terpenes, the largest class of plant natural products, we investigate the basis of terpene diversity through analysis of multiple sequenced plant genomes. The primary drivers of terpene diversification are terpenoid synthase (TS) “signature” enzymes (which generate scaffold diversity), and cytochromes P450 (CYPs), which modify and further diversify these scaffolds, so paving the way for further downstream modifications. Our systematic search of sequenced plant genomes for all TS and CYP genes reveals that distinct TS/CYP gene pairs are found together far more commonly than would be expected by chance, and that certain TS/CYP pairings predominate, providing signals for key events that are likely to have shaped terpene diversity. We recover TS/CYP gene pairs for previously characterized terpene metabolic gene clusters and demonstrate new functional pairing of TSs and CYPs within previously uncharacterized clusters. Unexpectedly, we find evidence for different mechanisms of pathway assembly in eudicots and monocots; in the former, microsyntenic blocks of TS/CYP gene pairs duplicate and provide templates for the evolution of new pathways, whereas in the latter, new pathways arise by mixing and matching of individual TS and CYP genes through dynamic genome rearrangements. This is, to our knowledge, the first documented observation of the unique pattern of TS and CYP assembly in eudicots and monocots.

scholarly journals Genome Sequence of Streptomyces caatingaensis CMAA 1322, a New Abiotic Stress-Tolerant Actinomycete Isolated from Dried Lake Bed Sediment in the Brazilian Caatinga Biome

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Suikinai Nobre Santos ◽  
Ranko Gacesa ◽  
Rodrigo Gouvêa Taketani ◽  
Paul F. Long ◽  
Itamar Soares Melo
Keyword(s):  
Abiotic Stress ◽  
Environmental Stress ◽  
Stress Tolerance ◽  
Genome Sequence ◽  
Gene Clusters ◽  
Bed Sediment ◽  
Metabolic Gene ◽  
Caatinga Biome

The genome sequence of the first Streptomyces species isolated from the Brazilian Caatinga is reported here. Genes related to environmental stress tolerance were prevalent and included many secondary metabolic gene clusters.

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