scholarly journals Comparative Genomic Analysis of Dactylonectria torresensis Strains from Grapevine, Soil and Weed Highlights Potential Mechanisms in Pathogenicity and Endophytic Lifestyle

2020 ◽  
Vol 6 (4) ◽  
pp. 255
Author(s):  
David Gramaje ◽  
Carmen Berlanas ◽  
María del Pilar Martínez-Diz ◽  
Emilia Diaz-Losada ◽  
Livio Antonielli ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Light Response ◽  
Gene Clusters ◽  
Fungal Species ◽  
Glycoside Hydrolases ◽  
White Rot ◽  
Comparative Genomic ◽  
Plant Tissues ◽  
Dactylonectria Torresensis ◽  
Foot Disease

The soil-borne fungus Dactylonectria torresensis is the most common causal agent of black-foot disease in Europe. However, there is a lack of understanding on how this fungus can provoke plant symptoms. In this study, we sequenced, annotated and analyzed the genomes of three isolates of D. torresensis collected from asymptomatic vine, weed and soil. Sequenced genomes were further compared to those of 27 fungal species including root and aerial pathogens, white rot degraders, indoor biodeterioration agents, saprotrophs, dark septate endophytes and mycorrhiza. Strains of D. torresensis present genomes with between 64 and 65 Mbp and with up to 18,548 predicted genes for each strain. Average Nucleotide Identity (ANI) shows that strains are different according to genome contents. Clusters of orthologous groups were compared, and clusters of genes related to necroses were particularly detected in all strains of D. torresensis (necrosis inducing peptides and proteins, and ethylene inducing peptides) as well as several genes involved in resistance against fungicides frequently used in viticulture such as copper. Interestingly, an expanded high number of genes related to carbohydrate-active enzymes were detected in each Dactylonectria strain, especially those related to glycoside hydrolases that could be involved in penetration of plant tissues or pathogenicity. An increased number of candidate genes for CAZyme classes AA9 and AA3-1 supports the ability of strains to efficiently degrade plant material. High numbers of genes of D. torresensis related to secretome and small secreted proteins were further characterized. Moreover, the presence of several gene clusters such as fujikurin-like genes was detected and were normally found in Fusariumfujikuroi, that have been linked to fungal pathogenicity. The phenotypes of the three strains investigated showed further difference in light response. We found that Dactylonectria strains have an increased number of photoreceptor encoding genes and we showed sequence alterations. Altogether, the results highlight several gene clusters present in D. torresensis strains that could be linked to endophytic lifestyle, pathogenicity, plant maceration and degradation of plant tissues as well as adaptation to soil contaminated with metals and metalloids and light response.

scholarly journals Comparative Genomic Analysis of Ochratoxin A Biosynthetic Cluster in Producing Fungi: New Evidence of a Cyclase Gene Involvement

2020 ◽  
Vol 11 ◽  
Author(s):  
Massimo Ferrara ◽  
Antonia Gallo ◽  
Giancarlo Perrone ◽  
Donato Magistà ◽  
Scott E. Baker
Keyword(s):  
Ochratoxin A ◽  
Cluster Structure ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Fungal Species ◽  
Comparative Genomic ◽  
New Era ◽  
Putative Role ◽  
Genome Analyses ◽  
Expression Evidence

The widespread use of Next-Generation Sequencing has opened a new era in the study of biological systems by significantly increasing the catalog of fungal genomes sequences and identifying gene clusters for known secondary metabolites as well as novel cryptic ones. However, most of these clusters still need to be examined in detail to completely understand the pathway steps and the regulation of the biosynthesis of metabolites. Genome sequencing approach led to the identification of the biosynthetic genes cluster of ochratoxin A (OTA) in a number of producing fungal species. Ochratoxin A is a potent pentaketide nephrotoxin produced by Aspergillus and Penicillium species and found as widely contaminant in food, beverages and feed. The increasing availability of several new genome sequences of OTA producer species in JGI Mycocosm and/or GenBank databanks led us to analyze and update the gene cluster structure in 19 Aspergillus and 2 Penicillium OTA producing species, resulting in a well conserved organization of OTA core genes among the species. Furthermore, our comparative genome analyses evidenced the presence of an additional gene, previously undescribed, located between the polyketide and non-ribosomal synthase genes in the cluster of all the species analyzed. The presence of a SnoaL cyclase domain in the sequence of this gene supports its putative role in the polyketide cyclization reaction during the initial steps of the OTA biosynthesis pathway. The phylogenetic analysis showed a clustering of OTA SnoaL domains in accordance with the phylogeny of OTA producing species at species and section levels. The characterization of this new OTA gene, its putative role and its expression evidence in three important representative producing species, are reported here for the first time.

scholarly journals Genome Reduction and Secondary Metabolism of the Marine Sponge-Associated Cyanobacterium Leptothoe

Marine Drugs ◽  
2021 ◽  
Vol 19 (6) ◽  
pp. 298
Author(s):  
Despoina Konstantinou ◽  
Rafael V. Popin ◽  
David P. Fewer ◽  
Kaarina Sivonen ◽  
Spyros Gkelis
Keyword(s):  
Natural Products ◽  
Microbial Communities ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Marine Sponges ◽  
Genome Reduction ◽  
Extracellular Polysaccharides ◽  
Comparative Genomic ◽  
Symbiotic Relationships ◽  
Genes Encoding

Sponges form symbiotic relationships with diverse and abundant microbial communities. Cyanobacteria are among the most important members of the microbial communities that are associated with sponges. Here, we performed a genus-wide comparative genomic analysis of the newly described marine benthic cyanobacterial genus Leptothoe (Synechococcales). We obtained draft genomes from Le. kymatousa TAU-MAC 1615 and Le. spongobia TAU-MAC 1115, isolated from marine sponges. We identified five additional Leptothoe genomes, host-associated or free-living, using a phylogenomic approach, and the comparison of all genomes showed that the sponge-associated strains display features of a symbiotic lifestyle. Le. kymatousa and Le. spongobia have undergone genome reduction; they harbored considerably fewer genes encoding for (i) cofactors, vitamins, prosthetic groups, pigments, proteins, and amino acid biosynthesis; (ii) DNA repair; (iii) antioxidant enzymes; and (iv) biosynthesis of capsular and extracellular polysaccharides. They have also lost several genes related to chemotaxis and motility. Eukaryotic-like proteins, such as ankyrin repeats, playing important roles in sponge-symbiont interactions, were identified in sponge-associated Leptothoe genomes. The sponge-associated Leptothoe stains harbored biosynthetic gene clusters encoding novel natural products despite genome reduction. Comparisons of the biosynthetic capacities of Leptothoe with chemically rich cyanobacteria revealed that Leptothoe is another promising marine cyanobacterium for the biosynthesis of novel natural products.

scholarly journals Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica

2018 ◽  
Vol 19 (8) ◽  
pp. 2379 ◽  
Author(s):  
Young-Jin Park ◽  
Yong-Un Jeong ◽  
Won-Sik Kong
Keyword(s):  
Gene Prediction ◽  
Gc Content ◽  
Industrial Applications ◽  
Fungal Species ◽  
Amino Acid Sequences ◽  
Glycoside Hydrolases ◽  
White Rot ◽  
White Rot Fungus ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules

Next-generation sequencing (NGS) of the Flammulina elastica (wood-rotting basidiomycete) genome was performed to identify carbohydrate-active enzymes (CAZymes). The resulting assembly (31 kmer) revealed a total length of 35,045,521 bp (49.7% GC content). Using the AUGUSTUS tool, 12,536 total gene structures were predicted by ab initio gene prediction. An analysis of orthologs revealed that 6806 groups contained at least one F. elastica protein. Among the 12,536 predicted genes, F. elastica contained 24 species-specific genes, of which 17 genes were paralogous. CAZymes are divided into five classes: glycoside hydrolases (GHs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycosyltransferases (GTs), and auxiliary activities (AA). In the present study, annotation of the predicted amino acid sequences from F. elastica genes using the dbCAN CAZyme database revealed 508 CAZymes, including 82 AAs, 218 GHs, 89 GTs, 18 PLs, 59 CEs, and 42 carbohydrate binding modules in the F. elastica genome. Although the CAZyme repertoire of F. elastica was similar to those of other fungal species, the total number of GTs in F. elastica was larger than those of other basidiomycetes. This genome information elucidates newly identified wood-degrading machinery in F. elastica, offers opportunities to better understand this fungus, and presents possibilities for more detailed studies on lignocellulosic biomass degradation that may lead to future biotechnological and industrial applications.

scholarly journals Comparative Genomic Analysis of Bifidobacterium Catenulatum Reveal the Genetic Divergence of its Two Subspecies from Infant and Adult Gut

2021 ◽  
Author(s):  
Jiaqi Liu ◽  
Weicheng Li ◽  
Caiqing Yao ◽  
Jie Yu ◽  
Heping Zhang
Keyword(s):  
Genetic Divergence ◽  
Gc Content ◽  
Genomic Analysis ◽  
Glycoside Hydrolases ◽  
Comparative Genomic ◽  
Carbohydrate Binding ◽  
Functional Difference ◽  
Carbohydrate Utilization ◽  
Carbohydrate Binding Modules ◽  
Genomic Studies

Abstract Background: Bifidobacterium catenulatum, which includes two subspecies that B. catenulatum subsp. kashiwanohense and B. catenulatum subsp. catenulatum are usually from infant and adult gut respectively, while the genomic studies of functional difference and genetic divergence in them have been rarely reported. In this study, we analyzed 16 B. catenulatum strains through comparative genomics, including two novel sequenced strains. Results: A phylogenetic tree based on 785 core genes indicated that the two subspecies of B. catenulatum were significantly separated and confirmed their colonizing bias in infants and adults. Comparison of general genomic characteristics revealed that the two subspecies had significantly different genomic sizes but similar GC content. Functional annotations found that they peculiarly differ in utilization of carbohydrates and amino acid. Among them, we found that carbohydrate metabolism seems to play an important role in the divergence because of their carbohydrate-active enzymes (CAZyme) present two different clustering patterns. B. catenulatum subsp. kashiwanohense have functional genes that specifically adapted to the infant gut for glycoside hydrolases 95 (GH95) and carbohydrate-binding modules 51 (CBM51), which specifically participated in the metabolism of Human Milk Oligosaccharides (HMOs), and specific genes fuc that related to HMOs were also detected. While B. catenulatum subsp. catenulatum rich in GH3 and glycosyltransferases 4 (GT4) tended to metabolize plant-derived glycan that may help it metabolize more complex carbohydrates (eg. xylan) in the adult intestine. Conclusions: Our findings revealed genomic evidence of carbohydrate utilization bias which may be a key leading to the genetic divergence of two subspecies of B. catenulatum.

scholarly journals Insights into the cultured bacterial fraction of corals

2020 ◽  
Author(s):  
Michael Sweet ◽  
Helena Villela ◽  
Tina Keller-Costa ◽  
Rodrigo Costa ◽  
Stefano Romano ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Gene Clusters ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Comprehensive Overview ◽  
Associated Bacteria ◽  
Reef Restoration ◽  
Coral Holobiont ◽  
Metabolic Interactions ◽  
And Function

Abstract Bacteria associated with coral hosts are diverse and abundant, with recent studies suggesting involvement of these symbionts in host resilience to anthropogenic stress. Despite the putative importance of bacteria, the work dedicated to culturing coral-associated bacteria has received little attention. Combining published and unpublished data, here we report a comprehensive overview of the diversity and function of culturable, coral-associated bacteria. A total of 3055 isolates from 52 studies were considered by our meta-survey. Of these, 1045 had full length 16S rRNA gene sequences, spanning 138 formally described and 12 putatively novel bacterial genera across the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria phyla. We performed comparative genomic analysis using the available genomes of 74 strains and identified potential signatures of beneficial bacterial-coral symbioses among them. Our analysis revealed >400 biosynthetic gene clusters that underlie the biosynthesis of antioxidant, antimicrobial, cytotoxic, and other secondary metabolites. Moreover, we uncovered genomic features - not previously described for coral-bacterial symbioses - involved in host colonization and host-symbiont recognition, antiviral defence mechanisms, and/or integrated metabolic interactions, which we suggest as novel targets for the screening of coral probiotics. Our results highlight the importance of bacterial cultures to elucidate coral holobiont functioning, and guide the selection of probiotic candidates to promote coral resilience and improve reef restoration efforts.

scholarly journals Whole Genome Sequencing Based Taxonomic Classification, and Comparative Genomic Analysis of Potentially Human Pathogenic Enterobacter spp. Isolated from Chlorinated Wastewater in the North West Province, South Africa

2021 ◽  
Vol 9 (9) ◽  
pp. 1928
Author(s):  
Tawanda E. Maguvu ◽  
Cornelius C. Bezuidenhout
Keyword(s):  
Bacterial Species ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Comparative Genomic Analysis ◽  
Taxonomic Classification ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Human Pathogens ◽  
Wastewater Treatment Process ◽  
North West

Comparative genomics, in particular, pan-genome analysis, provides an in-depth understanding of the genetic variability and dynamics of a bacterial species. Coupled with whole-genome-based taxonomic analysis, these approaches can help to provide comprehensive, detailed insights into a bacterial species. Here, we report whole-genome-based taxonomic classification and comparative genomic analysis of potential human pathogenic Enterobacter hormaechei subsp. hoffmannii isolated from chlorinated wastewater. Genome Blast Distance Phylogeny (GBDP), digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANI) confirmed the identity of the isolates. The algorithm PathogenFinder predicted the isolates to be human pathogens with a probability of greater than 0.78. The potential pathogenic nature of the isolates was supported by the presence of biosynthetic gene clusters (BGCs), aerobactin, and aryl polyenes (APEs), which are known to be associated with pathogenic/virulent strains. Moreover, analysis of the genome sequences of the isolates reflected the presence of an arsenal of virulence factors and antibiotic resistance genes that augment the predictions of the algorithm PathogenFinder. The study comprehensively elucidated the genomic features of pathogenic Enterobacter isolates from wastewaters, highlighting the role of wastewaters in the dissemination of pathogenic microbes, and the need for monitoring the effectiveness of the wastewater treatment process.

scholarly journals Comparative Genomic Analysis of Lactiplantibacillus plantarum Isolated from Different Niches

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 241
Author(s):  
Bingyong Mao ◽  
Ruimin Yin ◽  
Xiaoshu Li ◽  
Shumao Cui ◽  
Hao Zhang ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Expression Patterns ◽  
Genomic Analysis ◽  
Genomic Diversity ◽  
Glycoside Hydrolases ◽  
Comparative Genomic ◽  
Carbohydrate Active Enzymes ◽  
Different Strains ◽  
Many Sources ◽  
Different Sources

Lactiplantibacillus plantarum can adapt to a variety of niches and is widely distributed in many sources. We used comparative genomics to explore the differences in the genome and in the physiological characteristics of L. plantarum isolated from pickles, fermented sauce, and human feces. The relationships between genotypes and phenotypes were analyzed to address the effects of isolation source on the genetic variation of L. plantarum. The comparative genomic results indicate that the numbers of unique genes in the different strains were niche-dependent. L. plantarum isolated from fecal sources generally had more strain-specific genes than L. plantarum isolated from pickles. The phylogenetic tree and average nucleotide identity (ANI) results indicate that L. plantarum in pickles and fermented sauce clustered independently, whereas the fecal L. plantarum was distributed more uniformly in the phylogenetic tree. The pan-genome curve indicated that the L. plantarum exhibited high genomic diversity. Based on the analysis of the carbohydrate active enzyme and carbohydrate-use abilities, we found that L. plantarum strains isolated from different sources exhibited different expression of the Glycoside Hydrolases (GH) and Glycosyl Transferases (GT) families and that the expression patterns of carbohydrate active enzymes were consistent with the evolution relationships of the strains. L. plantarum strains exhibited niche-specific characteristicsand the results provided better understating on genetics of this species.

scholarly journals Whole-Genome Sequencing of Corallococcus sp. Strain EGB Reveals the Genetic Determinants Linking Taxonomy and Predatory Behavior

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1421
Author(s):  
Yuqiang Zhao ◽  
Yanxin Wang ◽  
Chengyao Xia ◽  
Xu Li ◽  
Xianfeng Ye ◽  
...  
Keyword(s):  
Extracellular Enzymes ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Predatory Behavior ◽  
Phytopathogenic Fungi ◽  
Plant Diseases ◽  
Comparative Genomic ◽  
Comprehensive Overview ◽  
Circular Chromosome ◽  
Pan Genome

Corallococcus sp. strain EGB is a Gram-negative myxobacteria isolated from saline soil, and has considerable potential for the biocontrol of phytopathogenic fungi. However, the detailed mechanisms related to development and predatory behavior are unclear. To obtain a comprehensive overview of genetic features, the genome of strain EGB was sequenced, annotated, and compared with 10 other Corallococcus species. The strain EGB genome was assembled as a single circular chromosome of 9.4 Mb with 7916 coding genes. Phylogenomics analysis showed that strain EGB was most closely related to Corallococcus interemptor AB047A, and it was inferred to be a novel species within the Corallococcus genus. Comparative genomic analysis revealed that the pan-genome of Corallococcus genus was large and open. Only a small proportion of genes were specific to strain EGB, and most of them were annotated as hypothetical proteins. Subsequent analyses showed that strain EGB produced abundant extracellular enzymes such as chitinases and β-(1,3)-glucanases, and proteases to degrade the cell-wall components of phytopathogenic fungi. In addition, 35 biosynthetic gene clusters potentially coding for antimicrobial compounds were identified in the strain EGB, and the majority of them were present in the dispensable pan-genome with unexplored metabolites. Other genes related to secretion and regulation were also explored for strain EGB. This study opens new perspectives in the greater understanding of the predatory behavior of strain EGB, and facilitates a potential application in the biocontrol of fungal plant diseases in the future.

scholarly journals Oxygenation properties of hemoglobin and the evolutionary origins of isoform multiplicity in an amphibious air-breathing fish, the blue-spotted mudskipper (Boleophthalmus pectinirostris)

2019 ◽  
Author(s):  
Jay F. Storz ◽  
Chandrasekhar Natarajan ◽  
Magnus K. Grouleff ◽  
Michael Vandewege ◽  
Federico G. Hoffmann ◽  
...  
Keyword(s):  
Globin Gene ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Comparative Genomic ◽  
Air Breathing ◽  
Aerial Respiration ◽  
Evolutionary Origins ◽  
Amino Acid Divergence ◽  
Boleophthalmus Pectinirostris ◽  
And Function

ABSTRACTAmong the numerous lineages of teleost fish that have independently transitioned from obligate water-breathing to facultative air-breathing, evolved properties of hemoglobin (Hb)-O2 transport may have been shaped by the prevalence and severity of aquatic hypoxia (which influences the extent to which fish are compelled to switch to aerial respiration) as well as the anatomical design of air-breathing structures and the cardiovascular system. Here we examine the structure and function of Hbs in an amphibious, facultative air-breathing fish, the blue-spotted mudskipper (Boleophthalmus pectinirostris). We also characterized the genomic organization of the globin gene clusters of the species and we integrated phylogenetic and comparative genomic analyses to unravel the duplicative history of the genes that encode the subunits of structurally distinct mudskipper Hb isoforms (isoHbs). The B. pectinirostris isoHbs exhibit high intrinsic O2-affinities, similar to those of hypoxia-tolerant, water-breathing teleosts, and remarkably large Bohr effects. Genomic analysis of conserved synteny revealed that the genes that encode the α-type subunits of the two main adult isoHbs are members of paralogous gene clusters that represent products of the teleost-specific whole-genome duplication. Experiments revealed no appreciable difference in the oxygenation properties of co-expressed isoHbs in spite of extensive amino acid divergence between the alternative α-chain subunit isoforms. It therefore appears that the ability to switch between aquatic and aerial respiration does not necessarily require a division of labor between functionally distinct isoHbs with specialized oxygenation properties.Summary statementThe blue-spotted mudskipper routinely switches between aquatic and aerial respiration. This respiratory versatility is associated with properties of hemoglobin-oxygen transport that are similar to those found in hypoxia-adapted water-breathing fishes.

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