scholarly journals Diverse Horizontally-Acquired Gene Clusters Confer Sucrose Utilization to Different Lineages of the Marine Pathogen Photobacterium damselae subsp. damselae

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1244
Author(s):  
Saqr Abushattal ◽  
Ana Vences ◽  
Alba V. Barca ◽  
Carlos R. Osorio
Keyword(s):  
Comparative Genomics ◽  
Horizontal Transfer ◽  
Hot Spot ◽  
Housekeeping Genes ◽  
Gene Clusters ◽  
Marine Animals ◽  
The Family ◽  
Photobacterium Damselae ◽  
Comparative Genomics Analysis ◽  
Sucrose Utilization

The ability to metabolize sucrose is a variable trait within the family Vibrionaceae. The marine bacterium Photobacterium damselae subsp. damselae (Pdd), pathogenic for marine animals and humans, is generally described as negative for sucrose utilization (Scr−). Previous studies have reported sucrose-utilizing isolates (Scr+), but the genetic basis of this variable phenotype remains uncharacterized. Here, we carried out the genome sequencing of five Scr+ and two Scr−Pdd isolates and conducted a comparative genomics analysis with sixteen additional Pdd genomes sequenced in previous studies. We identified two different versions of a four-gene cluster (scr cluster) exclusive of Scr+ isolates encoding a PTS system sucrose-specific IIBC component (scrA), a fructokinase (scrK), a sucrose-6-phosphate hydrolase (scrB), and a sucrose operon repressor (scrR). A scrA deletion mutant did not ferment sucrose and was impaired for growth with sucrose as carbon source. Comparative genomics analyses suggested that scr clusters were acquired by horizontal transfer by different lineages of Pdd and were inserted into a recombination hot-spot in the Pdd genome. The incongruence of phylogenies based on housekeeping genes and on scr genes revealed that phylogenetically diverse gene clusters for sucrose utilization have undergone extensive horizontal transfer among species of Vibrio and Photobacterium.

scholarly journals Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity

2021 ◽  
Vol 7 (5) ◽  
pp. 337
Author(s):  
Daniel Peterson ◽  
Tang Li ◽  
Ana M. Calvo ◽  
Yanbin Yin
Keyword(s):  
Comparative Genomics ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Phytopathogenic Fungi ◽  
Secreted Proteins ◽  
Economic Losses ◽  
Comparative Genomic ◽  
Signal Peptides ◽  
Comparative Genomics Analysis

Phytopathogenic Ascomycota are responsible for substantial economic losses each year, destroying valuable crops. The present study aims to provide new insights into phytopathogenicity in Ascomycota from a comparative genomic perspective. This has been achieved by categorizing orthologous gene groups (orthogroups) from 68 phytopathogenic and 24 non-phytopathogenic Ascomycota genomes into three classes: Core, (pathogen or non-pathogen) group-specific, and genome-specific accessory orthogroups. We found that (i) ~20% orthogroups are group-specific and accessory in the 92 Ascomycota genomes, (ii) phytopathogenicity is not phylogenetically determined, (iii) group-specific orthogroups have more enriched functional terms than accessory orthogroups and this trend is particularly evident in phytopathogenic fungi, (iv) secreted proteins with signal peptides and horizontal gene transfers (HGTs) are the two functional terms that show the highest occurrence and significance in group-specific orthogroups, (v) a number of other functional terms are also identified to have higher significance and occurrence in group-specific orthogroups. Overall, our comparative genomics analysis determined positive enrichment existing between orthogroup classes and revealed a prediction of what genomic characteristics make an Ascomycete phytopathogenic. We conclude that genes shared by multiple phytopathogenic genomes are more important for phytopathogenicity than those that are unique in each genome.

scholarly journals Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yang Yang ◽  
Xiaobao Liu ◽  
Jimiao Cai ◽  
Yipeng Chen ◽  
Boxun Li ◽  
...  
Keyword(s):  
Cell Wall ◽  
Comparative Genomics ◽  
Antifungal Activity ◽  
Endophytic Fungus ◽  
Gene Clusters ◽  
Comparative Genomic ◽  
Cell Wall Degradation ◽  
Brachiaria Brizantha ◽  
Helvolic Acid ◽  
Comparative Genomics Analysis

Abstract Background Sarocladium brachiariae is a newly identified endophytic fungus isolated from Brachiaria brizantha. A previous study indicated that S. brachiariae had antifungal activity; however, limited genomic information restrains further study. Therefore, we sequenced the genome of S. brachiariae and compared it with the genome of S. oryzae to identify differences between a Sarocladium plant pathogen and an endophyte. Results In this study, we reported a gapless genome sequence of a newly identified endophytic fungus Sarocladium brachiariae isolated from Brachiaria brizantha. The genome of S. brachiariae is 31.86 Mb, with a contig N50 of 3.27 Mb and 9903 protein coding genes. Phylogenomic analysis based on single copy orthologous genes provided insights into the evolutionary relationships of S. brachiariae and its closest species was identified as S. oryzae. Comparative genomics analysis revealed that S. brachiaria has 14.9% more plant cell wall degradation related CAZymes to S. oryzae, and 33.3% more fungal cell wall degradation related CAZymes, which could explain the antifungal activity of S. brachiaria. Based on Antibiotics & Secondary Metabolite Analysis Shell (antiSMASH) analysis, we identified a contact helvolic acid biosynthetic gene cluster (BGC) for the first time in S. oryzae. However, S. brachiaria had seven fewer terpene gene clusters, including helvolic acid BGC, compared with S. oryzae and this may be associated with adaptation to an endophytic lifestyle. Synteny analysis of polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and hybrid (PKS-NRPS) gene clusters between S. brachiariae and S. oryzae revealed that just 37.5% of tested clusters have good synteny, while 63.5% have no or poor synteny. This indicated that the S. brachiariae could potentially synthesize a variety of unknown-function secondary metabolites, which may play an important role in adaptation to its endophytic lifestyle and antifungal activity. Conclusions The data provided a better understanding of the Sarocladium brachiariae genome. Further comparative genomic analysis provided insight into the genomic basis of its endophytic lifestyle and antifungal activity.

scholarly journals Genomic and Metabolic Profiling of Nonulosonic Acids in Vibrionaceae Reveal Biochemical Phenotypes of Allelic Divergence in Vibrio vulnificus

2011 ◽  
Vol 77 (16) ◽  
pp. 5782-5793 ◽  
Author(s):  
Amanda L. Lewis ◽  
Jean-Bernard Lubin ◽  
Shilpa Argade ◽  
Natasha Naidu ◽  
Biswa Choudhury ◽  
...  
Keyword(s):  
Vibrio Vulnificus ◽  
Hot Spot ◽  
Gene Clusters ◽  
Human Pathogens ◽  
Environmental Isolates ◽  
Content Type ◽  
The Family ◽  
Domains Of Life ◽  
Biochemical Analyses ◽  
And Function

ABSTRACTNonulosonic acids (NulOs) encompass a large group of structurally diverse nine-carbon backbone α-keto sugars widely distributed among the three domains of life. Mammals express a specialized version of NulOs called sialic acids, which are displayed in prominent terminal positions of cell surface and secreted glycoconjugates. Within bacteria, the ability to synthesize NulOs has been demonstrated in a number of human pathogens and is phylogenetically widespread. Here we examine the distribution, diversity, evolution, and function of NulO biosynthesis pathways in members of the familyVibrionaceae. Among 27 species ofVibrionaceaeexamined at the genomic level, 12 species containednabgene clusters. We document examples of duplication, divergence, horizontal transfer, and recombination ofnabgene clusters in differentVibrionaceaelineages. Biochemical analyses, including mass spectrometry, confirmed that many species do, in fact, produce di-N-acetylated NulOs. A library of clinical and environmental isolates ofVibrio vulnificusserved as a model for further investigation ofnaballele genotypes and levels of NulO expression. The data show that lineage I isolates produce about 20-fold higher levels of NulOs than lineage II isolates. Moreover,nabgene alleles found in a subset ofV. vulnificusclinical isolates express 40-fold higher levels of NulOs thannaballeles associated with environmental isolates. Taken together, the data implicate the familyVibrionaceaeas a “hot spot” of NulO evolution and suggest that these molecules may have diverse roles in environmental persistence and/or animal virulence.

scholarly journals Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae

2008 ◽  
Vol 190 (10) ◽  
pp. 3494-3504 ◽  
Author(s):  
Henryk Urbanczyk ◽  
Jennifer C. Ast ◽  
Allison J. Kaeding ◽  
James D. Oliver ◽  
Paul V. Dunlap
Keyword(s):  
Phylogenetic Analysis ◽  
Horizontal Transfer ◽  
Vibrio Vulnificus ◽  
Housekeeping Genes ◽  
Housekeeping Gene ◽  
Vibrio Splendidus ◽  
Photobacterium Leiognathi ◽  
Photobacterium Damselae ◽  
Phylogenetic Divergence ◽  
Distinctive Phenotype

ABSTRACT Horizontal gene transfer (HGT) is thought to occur frequently in bacteria in nature and to play an important role in bacterial evolution, contributing to the formation of new species. To gain insight into the frequency of HGT in Vibrionaceae and its possible impact on speciation, we assessed the incidence of interspecies transfer of the lux genes (luxCDABEG), which encode proteins involved in luminescence, a distinctive phenotype. Three hundred three luminous strains, most of which were recently isolated from nature and which represent 11 Aliivibrio, Photobacterium, and Vibrio species, were screened for incongruence of phylogenies based on a representative housekeeping gene (gyrB or pyrH) and a representative lux gene (luxA). Strains exhibiting incongruence were then subjected to detailed phylogenetic analysis of horizontal transfer by using multiple housekeeping genes (gyrB, recA, and pyrH) and multiple lux genes (luxCDABEG). In nearly all cases, housekeeping gene and lux gene phylogenies were congruent, and there was no instance in which the lux genes of one luminous species had replaced the lux genes of another luminous species. Therefore, the lux genes are predominantly vertically inherited in Vibrionaceae. The few exceptions to this pattern of congruence were as follows: (i) the lux genes of the only known luminous strain of Vibrio vulnificus, VVL1 (ATCC 43382), were evolutionarily closely related to the lux genes of Vibrio harveyi; (ii) the lux genes of two luminous strains of Vibrio chagasii, 21N-12 and SB-52, were closely related to those of V. harveyi and Vibrio splendidus, respectively; (iii) the lux genes of a luminous strain of Photobacterium damselae, BT-6, were closely related to the lux genes of the lux-rib 2 operon of Photobacterium leiognathi; and (iv) a strain of the luminous bacterium Photobacterium mandapamensis was found to be merodiploid for the lux genes, and the second set of lux genes was closely related to the lux genes of the lux-rib 2 operon of P. leiognathi. In none of these cases of apparent HGT, however, did acquisition of the lux genes correlate with phylogenetic divergence of the recipient strain from other members of its species. The results indicate that horizontal transfer of the lux genes in nature is rare and that horizontal acquisition of the lux genes apparently has not contributed to speciation in recipient taxa.

scholarly journals Evolutionary Origins of the Fumonisin Secondary Metabolite Gene Cluster in Fusarium verticillioides and Aspergillus niger

2011 ◽  
Vol 2011 ◽  
pp. 1-7 ◽  
Author(s):  
Nora Khaldi ◽  
Kenneth H. Wolfe
Keyword(s):  
Comparative Genomics ◽  
Aspergillus Niger ◽  
Gene Cluster ◽  
Secondary Metabolite ◽  
Horizontal Transfer ◽  
Fusarium Verticillioides ◽  
Gene Clusters ◽  
Evolutionary Origins ◽  
Species Specific ◽  
Secondary Metabolite Gene Cluster

The secondary metabolite gene clusters of euascomycete fungi are among the largest known clusters of functionally related genes in eukaryotes. Most of these clusters are species specific or genus specific, and little is known about how they are formed during evolution. We used a comparative genomics approach to study the evolutionary origins of a secondary metabolite cluster that synthesizes a polyketide derivative, namely, the fumonisin (FUM) cluster of Fusarium verticillioides, and that of Aspergillus niger another fumonisin (fumonisin B) producing species. We identified homologs in other euascomycetes of the Fusarium verticillioides FUM genes and their flanking genes. We discuss four models for the origin of the FUM cluster in Fusarium verticillioides and argue that two of these are plausible: (i) assembly by relocation of initially scattered genes in a recent Fusarium verticillioides; or (ii) horizontal transfer of the FUM cluster from a distantly related Sordariomycete species. We also propose that the FUM cluster was horizontally transferred into Aspergillus niger, most probably from a Sordariomycete species.

The family Orthotrichaceae (Bryophyta) in flora of Russia: results of revision and biogeographical review

2018 ◽  
Vol 52 (2) ◽  
pp. 519-534 ◽  
Author(s):  
V. E. Fedosov
Keyword(s):  
Hot Spots ◽  
Latitudinal Gradient ◽  
Hot Spot ◽  
Spatial Differentiation ◽  
Taxonomic Composition ◽  
Undescribed Species ◽  
Longitudinal Gradient ◽  
Biogeographic Pattern ◽  
The Family ◽  
North Pacific Region

Recent studies on Orthotrichoid mosses in Russia are summarized genus by genus. Orthotrichum furcatum Otnyukova is synonymized with Nyholmiella obtusifolia. Orthotrichum vittii is excluded from the Russian moss flora. Description of O. dagestanicum is amended. Fifty four currently recognized species from 9 genera of the Orthotrichaceae are presently known to occur in Russia; list of species with common synonyms and brief review of distribution in Russia is presented. Numerous problematic specimens with unresolved taxonomy were omitted for future. Revealed taxonomical inconsistencies in the genera Zygodon, Ulota, Lewinskya, Nyholmiella, Orthotrichum are briefly discussed. Main regularities of spatial differentiation of the family Orthotrichaceae in Russia are considered. Recently presented novelties contribute to the certain biogeographic pattern, indicating three different centers of diversity of the family, changing along longitudinal gradient. Unlike European one, continental Asian diversity of Orthotrichaceae is still poorly known, the Siberian specimens which were previously referred to European species in most cases were found to represent other, poorly known or undescribed species. North Pacific Region houses peculiar and poorly understood hot spot of diversity of Orthotrichoid mosses. Thus, these hot spots are obligatory to be sampled in course of revisions of particular groups, since they likely comprise under-recorded cryptic- or semi-cryptic species. Latitudinal gradient also contributes to the spatial differentiation of the revealed taxonomic composition of Orthotrichaceae.

scholarly journals Genomic Characteristics and Comparative Genomics Analysis of Two Chinese Corynespora cassiicola Strains Causing Corynespora Leaf Fall (CLF) Disease

2021 ◽  
Vol 7 (6) ◽  
pp. 485
Author(s):  
Boxun Li ◽  
Yang Yang ◽  
Jimiao Cai ◽  
Xianbao Liu ◽  
Tao Shi ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Single Molecule ◽  
Rubber Tree ◽  
Gene Families ◽  
Gene Clusters ◽  
The Philippines ◽  
Tree Plantations ◽  
Comparative Genomic ◽  
Corynespora Cassiicola ◽  
Leaf Fall

Rubber tree Corynespora leaf fall (CLF) disease, caused by the fungus Corynespora cassiicola, is one of the most damaging diseases in rubber tree plantations in Asia and Africa, and this disease also threatens rubber nurseries and young rubber plantations in China. C. cassiicola isolates display high genetic diversity, and virulence profiles vary significantly depending on cultivar. Although one phytotoxin (cassicolin) has been identified, it cannot fully explain the diversity in pathogenicity between C. cassiicola species, and some virulent C. cassiicola strains do not contain the cassiicolin gene. In the present study, we report high-quality gapless genome sequences, obtained using short-read sequencing and single-molecule long-read sequencing, of two Chinese C. cassiicola virulent strains. Comparative genomics of gene families in these two stains and a virulent CPP strain from the Philippines showed that all three strains experienced different selective pressures, and metabolism-related gene families vary between the strains. Secreted protein analysis indicated that the quantities of secreted cell wall-degrading enzymes were correlated with pathogenesis, and the most aggressive CCP strain (cassiicolin toxin type 1) encoded 27.34% and 39.74% more secreted carbohydrate-active enzymes (CAZymes) than Chinese strains YN49 and CC01, respectively, both of which can only infect rubber tree saplings. The results of antiSMASH analysis showed that all three strains encode ~60 secondary metabolite biosynthesis gene clusters (SM BGCs). Phylogenomic and domain structure analyses of core synthesis genes, together with synteny analysis of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters, revealed diversity in the distribution of SM BGCs between strains, as well as SM polymorphisms, which may play an important role in pathogenic progress. The results expand our understanding of the C. cassiicola genome. Further comparative genomic analysis indicates that secreted CAZymes and SMs may influence pathogenicity in rubber tree plantations. The findings facilitate future exploration of the molecular pathogenic mechanism of C. cassiicola.

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