scholarly journals Early steps in the evolution of vertical transmission revealed by a plant-bacterium symbiosis

2019 ◽  
Author(s):  
Frédéric De Meyer ◽  
Bram Danneels ◽  
Tessa Acar ◽  
Rado Rasolomampianina ◽  
Mamy Tiana Rajaonah ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Genome Sequencing ◽  
Vertical Transmission ◽  
Potential Role ◽  
Phenotypic Characterization ◽  
Whole Genome ◽  
Vertical Mode ◽  
Mode Of Transmission ◽  
Nodule Symbiosis ◽  
Wild Yam

ABSTRACTVarious plant species establish intimate symbioses with bacteria within their aerial organs. The bacteria are contained within nodules or glands often present in distinctive patterns on the leaves in what is commonly referred to as leaf nodule symbiosis. We describe here a highly specific symbiosis between a wild yam species from Madagascar, Dioscorea sansibarensis and bacteria of the species Orrella dioscoreae. Using whole genome sequencing of plastid and bacteria from wild-collected samples, we show phylogenetic patterns consistent with a vertical transmission of the symbionts. Unique among leaf nodule symbioses, the bacteria can be cultured and are amenable to comparative transcriptomics and phenotypic characterization, revealing a potential role in complementing the host’s arsenal of secondary metabolites. We propose a very recent acquisition of the vertical mode of transmission in this symbiosis which, together with a large effective populations size explain the cultivability and remarkable lack of genome reductive evolution in O. dioscoreae. We leverage these unique features to reveal pathways and functions under positive selection in these specialized endophytes, highlighting the mechanisms enabling a permanent association in the phyllosphere.

scholarly journals Whole-genome sequencing of the endemic Antarctic fungus Antarctomyces pellizariae reveals an ice-binding protein, a scarce set of secondary metabolites gene clusters and provides insights on Thelebolales phylogeny

Genomics ◽  
2020 ◽  
Vol 112 (5) ◽  
pp. 2915-2921 ◽  
Author(s):  
Thiago Mafra Batista ◽  
Heron Oliveira Hilario ◽  
Gabriel Antônio Mendes de Brito ◽  
Rennan Garcias Moreira ◽  
Carolina Furtado ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Binding Protein ◽  
Protein A ◽  
Gene Clusters ◽  
Whole Genome ◽  
Ice Binding ◽  
Ice Binding Protein

scholarly journals A Genetic Screen to Identify New Molecular Players Involved in Photoprotection qH in Arabidopsis thaliana

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1565
Author(s):  
Pierrick Bru ◽  
Sanchali Nanda ◽  
Alizée Malnoë
Keyword(s):  
Arabidopsis Thaliana ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Screen ◽  
Phenotypic Characterization ◽  
Photochemical Quenching ◽  
Transcriptional Level ◽  
Whole Genome ◽  
Non Photochemical Quenching

Photosynthesis is a biological process which converts light energy into chemical energy that is used in the Calvin–Benson cycle to produce organic compounds. An excess of light can induce damage to the photosynthetic machinery. Therefore, plants have evolved photoprotective mechanisms such as non-photochemical quenching (NPQ). To focus molecular insights on slowly relaxing NPQ processes in Arabidopsis thaliana, previously, a qE-deficient line—the PsbS mutant—was mutagenized and a mutant with high and slowly relaxing NPQ was isolated. The mutated gene was named suppressor of quenching 1, or SOQ1, to describe its function. Indeed, when present, SOQ1 negatively regulates or suppresses a form of antenna NPQ that is slow to relax and is photoprotective. We have now termed this component qH and identified the plastid lipocalin, LCNP, as the effector for this energy dissipation mode to occur. Recently, we found that the relaxation of qH1, ROQH1, protein is required to turn off qH. The aim of this study is to identify new molecular players involved in photoprotection qH by a whole genome sequencing approach of chemically mutagenized Arabidopsis thaliana. We conducted an EMS-mutagenesis on the soq1 npq4 double mutant and used chlorophyll fluorescence imaging to screen for suppressors and enhancers of qH. Out of 22,000 mutagenized plants screened, the molecular players cited above were found using a mapping-by-sequencing approach. Here, we describe the phenotypic characterization of the other mutants isolated from this genetic screen and an additional 8000 plants screened. We have classified them in several classes based on their fluorescence parameters, NPQ kinetics, and pigment content. A high-throughput whole genome sequencing approach on 65 mutants will identify the causal mutations thanks to allelic mutations from having reached saturation of the genetic screen. The candidate genes could be involved in the formation or maintenance of quenching sites for qH, in the regulation of qH at the transcriptional level, or be part of the quenching site itself.

scholarly journals Resistance Gene-Directed Genome Mining of 50 Aspergillus Species

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Inge Kjærbølling ◽  
Tammi Vesth ◽  
Mikael R. Andersen
Keyword(s):  
Secondary Metabolites ◽  
Whole Genome Sequencing ◽  
Resistance Gene ◽  
Secondary Metabolite ◽  
Genome Sequencing ◽  
Bioactive Compounds ◽  
Genome Mining ◽  
Whole Genome ◽  
Metabolite Production ◽  
Genetic Potential

Species belonging to the Aspergillus genus are known to produce a large number of secondary metabolites; some of these compounds are used as pharmaceuticals, such as penicillin, cyclosporine, and statin. With whole-genome sequencing, it became apparent that the genetic potential for secondary metabolite production is much larger than expected. As an increasing number of species are whole-genome sequenced, thousands of secondary metabolite genes are predicted, and the question of how to selectively identify novel bioactive compounds from this information arises. To address this question, we have created a pipeline to predict genes involved in the production of bioactive compounds based on a resistance gene hypothesis approach.

Whole genome sequencing of melanomas in adolescent and young adults reveals distinct mutation landscapes and the potential role of germline variants in disease susceptibility

2018 ◽  
Vol 144 (5) ◽  
pp. 1049-1060 ◽  
Author(s):  
James S. Wilmott ◽  
Peter A. Johansson ◽  
Felicity Newell ◽  
Nicola Waddell ◽  
Peter Ferguson ◽  
...  
Keyword(s):  
Young Adults ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Potential Role ◽  
Disease Susceptibility ◽  
Whole Genome ◽  
Germline Variants ◽  
Adolescent And Young Adults

scholarly journals Secondary metabolites from hypocrealean entomopathogenic fungi: genomics as a tool to elucidate the encoded parvome

2020 ◽  
Vol 37 (9) ◽  
pp. 1164-1180 ◽  
Author(s):  
Liwen Zhang ◽  
Qun Yue ◽  
Chen Wang ◽  
Yuquan Xu ◽  
István Molnár
Keyword(s):  
Secondary Metabolites ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bioactive Compounds ◽  
Entomopathogenic Fungi ◽  
Gene Clusters ◽  
Whole Genome ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters

Whole genome sequencing allows the cataloguing of the parvome (secondary metabolome) of hypocrealean entomopathogenic fungi, uncovering biosynthetic gene clusters for known and novel bioactive compounds with ecological and pharmaceutical significance.

scholarly journals Genetic and Phenotypic Characterization of in-Host Developed Azole-Resistant Aspergillus flavus Isolates

2021 ◽  
Vol 7 (3) ◽  
pp. 164
Author(s):  
Jochem B. Buil ◽  
Jos Houbraken ◽  
Monique H. Reijers ◽  
Jan Zoll ◽  
Maurizio Sanguinetti ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Aspergillus Flavus ◽  
Prolonged Exposure ◽  
Major Facilitator Superfamily ◽  
Phenotypic Characterization ◽  
Azole Resistance ◽  
Whole Genome ◽  
Pulmonary Aspergillosis ◽  
Resistant Strains

Aspergillus flavus is a pathogenic fungal species that can cause pulmonary aspergillosis, and triazole compounds are used for the treatment of these infections. Prolonged exposure to azoles may select for compensatory mutations in the A. flavus genome, resulting in azole resistance. Here, we characterize a series of 11 isogenic A. flavus strains isolated from a patient with pulmonary aspergillosis. Over a period of three months, the initially azole-susceptible strain developed itraconazole and voriconazole resistance. Short tandem repeat analysis and whole-genome sequencing revealed the high genetic relatedness of all isolates, indicating an infection with one single isolate. In contrast, the isolates were macroscopically highly diverse, suggesting an adaptation to the environment due to (epi)genetic changes. The whole-genome sequencing of susceptible and azole-resistant strains showed a number of mutations that might be associated with azole resistance. The majority of resistant strains contain a Y119F mutation in the Cyp51A gene, which corresponds to the Y121F mutation found in A. fumigatus. One azole-resistant strain demonstrated a divergent set of mutations, including a V99A mutation in a major facilitator superfamily (MSF) multidrug transporter (AFLA 083950).

Abstract C38: Whole-genome sequencing of paired androgen-dependent and -independent prostate cancer cell lines: Potential role of novel targets in PI3K and Notch signaling pathways in resistance to hormonal therapy

2012 ◽  
Vol 72 (4 Supplement) ◽  
pp. C38-C38
Author(s):  
Gillian L. Dalgliesh ◽  
Joanne L. Hartley ◽  
Cary H. O'Donnell ◽  
James R. Bradford ◽  
Iain McKendrick ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Notch Signaling ◽  
Genome Sequencing ◽  
Hormonal Therapy ◽  
Potential Role ◽  
Prostate Cancer Cell ◽  
Whole Genome ◽  
Prostate Cancer Cell Lines ◽  
Novel Targets

scholarly journals Resistance Gene-Directed Genome Mining of 50 Aspergillus species

2018 ◽  
Author(s):  
Inge Kjærbølling ◽  
Tammi Vesth ◽  
Mikael R. Andersen
Keyword(s):  
Secondary Metabolites ◽  
Resistance Gene ◽  
Genome Sequencing ◽  
Genome Mining ◽  
Gene Clusters ◽  
Rational Approach ◽  
Whole Genome ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Valuable Compounds

AbstractFungal secondary metabolites are a rich source of valuable natural products. Genome sequencing have revealed an enormous potential from predicted biosynthetic gene clusters. It is however currently a time consuming task and an unfeasible task to characterize all biosynthetic gene cluster and to identify possible uses of the compounds. A rational approach is needed to identify promising gene clusters responsible for producing valuable compounds. Several valuable bioactive clusters have been shown to include a resistance gene which is a paralog of the target gene inhibited by the compound. This mechanism can be used to design a rational approach selecting those clusters.We have developed a pipeline FRIGG (Fungal Resistance Gene-directed Genome mining) identifying putative resistance genes found in biosynthetic gene clusters based on homology patterns of the cluster genes. The FRIGG pipeline has been run using 51 Aspergillus and Penicillium genomes, identifying 72 unique protein families with putative resistance genes using various settings in the pipeline. The pipeline was also able to identify the characterized resistance gene inpE from the Fellutamide B cluster thereby validating the approach.We have successfully developed an approach identifying putative valuable bio-active clusters based on a specific resistance mechanism. This approach will be highly useful as an ever increasing amount of genomic data becomes available — the art of identifying and selecting clusters producing novel valuable compounds will only become more crucial.ImportanceSpecies belonging to the Aspergillus genus are known to produce a large number of secondary metabolites, some of these compounds are bioactive and used as pharmaceuticals such as penicillin, cyclosporin and statin. With whole genome sequencing it became apparent that the genetic potential for secondary metabolite production is much bigger than expected. As an increasing number of species are whole genome sequenced an immense number of secondary metabolite genes are predicted and the question of how to selectively identify novel bioactive compounds from this information arises. To address this question, we have created a pipeline identifying genes likely involved in the production of bioactive compounds based on a resistance gene hypothesis approach.

Utility of Whole Genome Sequencing in diagnosing complex disorders: lesson from renal tubular disorders

2018 ◽  
Author(s):  
Mark Stevenson ◽  
Alistair T Pagnamenta ◽  
Heather G Mack ◽  
Judith A Savige ◽  
Kate E Lines ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Complex Disorders ◽  
Tubular Disorders ◽  
Renal Tubular Disorders ◽  
Renal Tubular

1722-P: Colocalization of TOPMed Whole Genome Sequencing Analysis and Tissue-Specific eQTL Signals Detects Target Genes for Type 2 Diabetes Risk

Diabetes ◽  
2019 ◽  
Vol 68 (Supplement 1) ◽  
pp. 1722-P
Author(s):  
MINDY D. SZETO ◽  
HEATHER M. HIGHLAND ◽  
ALISA MANNING ◽  
Keyword(s):  
Type 2 Diabetes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Target Genes ◽  
Diabetes Risk ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Tissue Specific
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