scholarly journals A Small Horizontally Transferred Gene Cluster Contributes to the Sporulation of Alternaria alternata

2019 ◽  
Vol 11 (12) ◽  
pp. 3436-3444 ◽  
Author(s):  
Mingshuang Wang ◽  
Huilan Fu ◽  
Ruoxin Ruan
Keyword(s):  
Gene Cluster ◽  
Alternaria Alternata ◽  
Phylogenetic Trees ◽  
Single Gene ◽  
Growth Stress ◽  
Spore Production ◽  
Brown Spot ◽  
Plant Materials ◽  
Asexual Spore ◽  
Protein Encoding

Abstract Horizontal gene transfer (HGT) has been identified as an important source of genomic innovation in fungi. However, how HGT drove the evolution of Alternaria alternata, a necrotrophic fungus which can be ubiquitously isolated from soil and various plants and decaying plant materials is largely known. In this study, we identified 12 protein-encoding genes that are likely acquired from lineages outside Pezizomycotina. Phylogenetic trees and approximately unbiased comparative topology tests strongly supported the evolutionary origin of these genes. According to their predicted functions, these HGT candidates are involved in nitrogen and carbohydrate metabolism. Especially, five genes of them were likely transferred as a physically linked cluster from Tremellales (Basidiomycota). Functionally knocking out the five-gene cluster in an A. alternata isolate causing citrus brown spot resulted in an 80% decrease in asexual spore production in the deletion mutant. We further knocked out each of these five genes in this cluster and the resultant single-gene deletion mutants exhibited a various degree of reduction in spore production. Except for conidiation, functions of these genes associated with vegetative growth, stress tolerance, and virulence are very limited. Our results provide new evidence that HGT has played important roles over the course of the evolution of filamentous fungi.

scholarly journals Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata

2017 ◽  
Author(s):  
Mingshuang Wang ◽  
Huilan Fu ◽  
Xing-Xing Shen ◽  
Ruoxin Ruan ◽  
Nicholas Pun ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Cluster ◽  
Alternaria Alternata ◽  
Deletion Mutant ◽  
Metabolic Process ◽  
Brown Spot ◽  
P Value ◽  
Dispensable Chromosome ◽  
Cdc Genes

AbstractThe tangerine pathotype of the ascomycete fungus Alternaria alternata is the causal agent of citrus brown spot, which can result in significant losses of both yield and marketability for tangerines and tangerine hybrids worldwide. A conditionally dispensable chromosome (CDC), which harbors the host-selective ACT toxin gene cluster, is required for tangerine pathogenicity of A. alternata. To understand the genetic makeup and evolution of the tangerine pathotype CDC, we analyzed the function and evolution of the CDC genes present in the A. alternata Z7 strain. The 1.84Mb long CDC contains 512 predicted protein-coding genes, which are enriched in functional categories associated with ‘metabolic process’ (132 genes, p-value = 0.00192) including ‘oxidation-reduction process’ (48 genes, p-value = 0.00021) and ‘lipid metabolic process’ (11 genes, p-value = 0.04591). Relatively few of the CDC genes can be classified as CAZymes (13), kinases (3) and transporters (20). Differential transcriptome analysis of H2O2 treatment and control conditions revealed that 29 CDC genes were significantly up-regulated and 14 were significantly down-regulated, suggesting that CDC genes may play a role in coping with oxidative stress. Evolutionary analysis of the 512 CDC proteins showed that their evolutionary conservation tends to be restricted within the genus Alternaria and that the CDC genes evolve faster than genes in the essential chromosomes. Interestingly, phylogenetic analysis suggested that the genes of 13 enzymes and one sugar transporter residing in the CDC were likely horizontally transferred from distantly related species. Among these, one carboxylesterase gene was transferred from bacteria but functionally knocking out this gene revealed no obvious biological role. Another 4 genes might have been transferred from Colletotrichum (Sordariomycetes) and 5 were likely transferred as a physically linked cluster of genes from Cryptococcus (Basidiomycota) or Penicillium (Eurotiomycetes). Functionally knocking out the 5-gene cluster resulted in an 80% decrease in asexual spore production in the deletion mutant. These results provide new insights into the function and evolution of CDC genes in Alternaria.Author SummaryMany fungal phytopathogens harbor conditionally dispensable chromosomes (CDCs). CDCs are variable in size, contain many genes involved in virulence, but their evolution remains obscure. In this study, we investigated the origin of the CDC present in the tangerine pathotype of Alternaria alternata Z7 strain. We found that most of the Z7 CDC proteins are highly conserved within the genus Alternaria but poorly conserved outside the genus. We also discovered that a small number of genes originated via horizontal gene transfer (HGT) from distantly related fungi and bacteria. These horizontally transferred genes include a carboxylesterase gene that was likely acquired from bacteria, a cluster of 4 physically linked genes likely transferred from Colletotrichum, and a cluster of 5 physically linked genes likely transferred from Cryptococcus (Basidiomycota) or Penicillium (Eurotiomycetes). To gain insight into the functions of these transferred genes, we knocked out the bacterial carboxylesterase and the 5-gene cluster. Whereas the carboxylesterase deletion mutant showed no obvious phenotype, the 5-gene cluster mutant showed a dramatically reduced production of asexual spores (conidia). The results of our study suggest that Alternaria CDCs are largely comprised from rapidly evolving native genes; although only a few genes were acquired via horizontal gene transfer, some of them appear to be involved in functions critical to the phytopathogenic lifestyle.

scholarly journals Effect of Lesion Age, Humidity, and Fungicide Application on Sporulation of Alternaria alternata, the Cause of Brown Spot of Tangerine

Plant Disease ◽  
2006 ◽  
Vol 90 (8) ◽  
pp. 1051-1054 ◽  
Author(s):  
R. F. Reis ◽  
A. de Goes ◽  
S. N. Mondal ◽  
T. Shilts ◽  
F. C. Brentu ◽  
...  
Keyword(s):  
Alternaria Alternata ◽  
Unit Area ◽  
Spore Production ◽  
Brown Spot ◽  
Yield Losses ◽  
Conidial Production ◽  
Leaf Lesion ◽  
Inoculum Production ◽  
The World ◽  
Alternaria Brown Spot

Alternaria brown spot, caused by Alternaria alternata, causes yield losses and fruit blemishes on many tangerines and their hybrids in most citrus areas of the world where susceptible cultivars are grown. Although the conditions affecting infection and disease severity are known, little information is available on inoculum production on infected tissue. We found that sporulation on leaves began about 10 days after symptoms developed, was abundant from 20 to 40 days, and declined thereafter. Conidial production was far greater on leaf than on fruit or twig lesions. Spore production per unit area of leaf lesion was greater on the more susceptible hybrids, Minneola and Orlando tangelos, than on the less susceptible Murcott tangor. At 74% relative humidity, conidial production on leaf lesions was low, but it was abundant at 85, 92.5, 96, and 100%. Application of QoI or copper fungicides, but not ferbam, suppressed sporulation on leaf lesions for about 14 to 21 days after application. Additional applications did not appear to be more effective than a single spray in reducing inoculum production.

scholarly journals High-resolution analysis of cis -acting regulatory networks at the α-globin locus

2013 ◽  
Vol 368 (1620) ◽  
pp. 20120361 ◽  
Author(s):  
Jim R. Hughes ◽  
Karen M. Lower ◽  
Ian Dunham ◽  
Stephen Taylor ◽  
Marco De Gobbi ◽  
...  
Keyword(s):  
High Resolution ◽  
Gene Cluster ◽  
Regulatory Networks ◽  
Single Gene ◽  
Regulatory Elements ◽  
Circular Chromosome ◽  
Chromosome Conformation ◽  
Cis Acting ◽  
High Resolution Analysis ◽  
Resolution Analysis

We have combined the circular chromosome conformation capture protocol with high-throughput, genome-wide sequence analysis to characterize the cis -acting regulatory network at a single locus. In contrast to methods which identify large interacting regions (10–1000 kb), the 4C approach provides a comprehensive, high-resolution analysis of a specific locus with the aim of defining, in detail, the cis -regulatory elements controlling a single gene or gene cluster. Using the human α-globin locus as a model, we detected all known local and long-range interactions with this gene cluster. In addition, we identified two interactions with genes located 300 kb (NME4) and 625 kb (FAM173a) from the α-globin cluster.

The expression of a baculovirus-derived chitinase gene increased resistance of tobacco cultivars to brown spot (Alternaria alternata)

2000 ◽  
Vol 136 (1) ◽  
pp. 1-8 ◽  
Author(s):  
J SHI ◽  
C J THOMAS ◽  
L A KING ◽  
C R HAWES ◽  
R D POSSEE ◽  
...  
Keyword(s):  
Alternaria Alternata ◽  
Chitinase Gene ◽  
Brown Spot

scholarly journals A Single Gene Cluster Controls Incompatibility and Partial Resistance to Various Melampsora larici-populina Races in Hybrid Poplars

1998 ◽  
Vol 88 (2) ◽  
pp. 156-163 ◽  
Author(s):  
F. Lefèvre ◽  
M. C. Goué-Mourier ◽  
P. Faivre-Rampant ◽  
M. Villar
Keyword(s):  
Gene Cluster ◽  
Partial Resistance ◽  
Random Amplified Polymorphic Dna ◽  
Single Gene ◽  
Field Resistance ◽  
Clonal Variation ◽  
Multiple Alleles ◽  
Hybrid Poplars ◽  
Genetic Background Effect ◽  
Trait Locus

Complete cosegregation for race-specific incompatibility with three Melampsora larici-populina rust races was observed in five F1 hybrid progenies of Populus, with different patterns among the various progenies. A single gene cluster could explain these segregations: one locus with multiple alleles or two tightly linked loci controlling complete resistance to E1 and E3, and two tightly linked loci for E2. The random amplified polymorphic DNA marker OPM03/04_480 was linked to that cluster in all families (<1 cM). This marker accounted for more than 70% of the genetic variation for field resistance in each family (heritability ≈ 0.40). The same marker accounted for up to 64% of the clonal variation for growth in the nursery under natural inoculum pressure; the weak tolerance to rust of F1 interspecific hybrids was attributed to a genetic background effect. Partial resistance was split into epidemiological components (heritability ranged from 0.35 to 0.87). Genotypic correlations among resistance traits for the different races were high (0.73 to 0.90). However, correlations among different resistance components for a single race were not all significant. A major quantitative trait locus for all components of partial resistance to E2 was associated to the cluster controlling incompatibility to E1 and E3 and marked by OPM03/04_480 (R2from 48 to 68%).

scholarly journals A Single Gene on the Staphylococcal Multiresistance Plasmid pSK1 Encodes a Novel Partitioning System

2003 ◽  
Vol 185 (7) ◽  
pp. 2143-2152 ◽  
Author(s):  
Alice E. Simpson ◽  
Ronald A. Skurray ◽  
Neville Firth
Keyword(s):  
Single Gene ◽  
Replication Initiation ◽  
Plasmid Replication ◽  
Rolling Circle ◽  
Plasmid Segregation ◽  
Segregational Stability ◽  
Protein Encoding ◽  
Single Protein ◽  
Encoding Gene ◽  
Postsegregational Killing

ABSTRACT The orf245 gene is located immediately upstream of, and divergently transcribed from, the replication initiation gene, rep, of the Staphylococcus aureus multiresistance plasmid pSK1, and related genes have been found in association with a range of evolutionarily distinct replication genes on plasmids from various gram-positive genera. orf245 has been shown previously to extend the segregational stability of a pSK1 minireplicon. Here we describe an investigation into the basis of orf245-mediated stabilization. orf245 was not found to influence transcription of pSK1 rep, indicating that it is not directly involved in plasmid replication. This was confirmed by demonstrating that orf245 is able to enhance the segregational stability of heterologous theta- and rolling-circle-replicating replicons, suggesting that it encodes a plasmid maintenance function. Evidence inconsistent with postsegregational killing and multimer resolution mechanisms was obtained; however, the intergenic region upstream of orf245 was found to mediate orf245-dependent incompatibility, as would be expected if it encodes a cis-acting centromere-like site. Taken together, these findings implicate active partitioning as the probable basis of the activity of orf245, which is therefore redesignated par. Since it is unrelated to any gene known to play a role in plasmid segregation, it seems likely that pSK1 par potentially represents the prototype of a novel class of active partitioning systems that are distinguished by their capacity to enhance plasmid segregational stability via a single protein-encoding gene.

scholarly journals Brown spot of tangerine hybrid cultivars Minneola, Page and Fortune caused by Alternaria alternata in Iran

2006 ◽  
Vol 55 (4) ◽  
pp. 578-578 ◽  
Author(s):  
M. Golmohammadi ◽  
M. Andrew ◽  
T. L. Peever ◽  
N. A. Peres ◽  
L. W. Timmer
Keyword(s):  
Alternaria Alternata ◽  
Brown Spot

scholarly journals A New Subclade of Leptosphaeria biglobosa Identified from Brassica rapa

2019 ◽  
Vol 20 (7) ◽  
pp. 1668 ◽  
Author(s):  
Zhongwei Zou ◽  
Xuehua Zhang ◽  
Paula Parks ◽  
Lindsey du Toit ◽  
Angela Van de Wouw ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Phylogenetic Trees ◽  
Single Gene ◽  
Leptosphaeria Maculans ◽  
Stem Canker ◽  
Willamette Valley ◽  
Gene Sequences ◽  
Distance Analysis ◽  
Pathogenicity Tests ◽  
Leptosphaeria Biglobosa

Blackleg (Phoma stem canker) of crucifers is a globally important disease caused by the ascomycete species complex comprising of Leptosphaeria maculans and Leptosphaeria biglobosa. Six blackleg isolates recovered from Brassica rapa cv. Mizspoona in the Willamette Valley of Oregon were characterized as L. biglobosa based on standard pathogenicity tests and molecular phylogenetic analysis. These isolates were compared to 88 characterized L. biglobosa isolates from western Canada, 22 isolates from Australia, and 6 L. maculans isolates from Idaho, USA using maximum parsimony and distance analysis of phylogenetic trees generated from the ITS rDNA (internal transcribed spacer rDNA) sequence, and the actin and β-tubulin gene sequences. The L. biglobosa isolates derived from B. rapa collected in Oregon formed a separate subclade based on concatenated gene sequences or a single gene sequence, regardless of the analyses. Pathogenicity tests showed that these isolates failed to infect either resistant or susceptible B. napus cultivars, but caused severe symptoms on three B. rapa cultivars (Accession number: UM1113, UM1112, and UM1161), a B. oleracea var. capitata (cabbage) cultivar (Copenhagen Market), and two B. juncea cultivars (CBM, a common brown Mustard, and Forge). These findings demonstrated that the L. biglobosa isolates derived from a B. rapa crop in Oregon were genetically distinct from existing species of L. biglobosa, and constitute a new subclade, herein proposed as L. biglobosa ‘americensis’.

scholarly journals Distribution and Characterization of AKT Homologs in the Tangerine Pathotype of Alternaria alternata

2000 ◽  
Vol 90 (7) ◽  
pp. 762-768 ◽  
Author(s):  
A. Masunaka ◽  
A. Tanaka ◽  
T. Tsuge ◽  
T. L. Peever ◽  
L. W. Timmer ◽  
...  
Keyword(s):  
Alternaria Alternata ◽  
Sequence Similarity ◽  
Structural Similarity ◽  
Toxin Production ◽  
Brown Spot ◽  
Japanese Pear ◽  
Black Rot ◽  
Acid Moiety ◽  
High Sequence Similarity ◽  
Rough Lemon

The tangerine pathotype of Alternaria alternata produces a host-selective toxin (HST), known as ACT-toxin, and causes Alternaria brown spot disease of citrus. The structure of ACT-toxin is closely related to AK- and AF-toxins, which are HSTs produced by the Japanese pear and strawberry pathotypes of A. alternata, respectively. AC-, AK-, and AF-toxins are chemically similar and share a 9,10-epoxy-8-hydroxy-9-methyl-decatrienoic acid moiety. Two genes controlling AK-toxin biosynthesis (AKT1 and AKT2) were recently cloned from the Japanese pear pathotype of A. alternata. Portions of these genes were used as heterologous probes in Southern blots, that detected homologs in 13 isolates of A. alternata tangerine pathotype from Minneola tangelo in Florida. Partial sequencing of the homologs in one of these isolates demonstrated high sequence similarity to AKT1 (89.8%) and to AKT2 (90.7%). AKT homologs were not detected in nine isolates of A. alternata from rough lemon, six isolates of nonpathogenic A. alternata, and one isolate of A. citri that causes citrus black rot. The presence of homologs in the Minneola isolates and not in the rough lemon isolates, nonpathogens or black rot isolates, correlates perfectly to pathogenicity on Iyo tangerine and ACT-toxin production. Functionality of the homologs was demonstrated by detection of transcripts using reverse transcription-polymerase chain reaction (RT-PCR) in total RNA of the tangerine pathotype of A. alternata. The high sequence similarity of AKT and AKT homologs in the tangerine patho-type, combined with the structural similarity of AK-toxin and ACT-toxin, may indicate that these homologs are involved in the biosynthesis of the decatrienoic acid moiety of ACT-toxin.

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