A comparative genome analysis of Cercospora sojina with other members of the pathogen genus Mycosphaerella on different plant hosts

Zeng, Fanchang; Lian, Xin; Zhang, Guirong; Yu, Xiaoman; Bradley, Carl A.; Ming, Ray

doi:10.1016/j.gdata.2017.07.007

Cited by 16 publications

(11 citation statements)

References 33 publications

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“…However, the relative abundances of other microbial taxa that include some plant pathogens, such as Mycosphaerella , were enhanced in R soils (Figure 7G). Mycosphaerella species can cause leaf-spot disease in economically important crops including wheat, soybean, banana, citrus, and eucalyptus (Stukenbrock et al, 2011; Ohm et al, 2012; Zeng et al, 2017). In addition, the relative abundance of the bacterial order Xanthomonadales was increased in R soils (Figure 7C).…”

Section: Discussionmentioning

confidence: 99%

Wheat Straw Return Influences Nitrogen-Cycling and Pathogen Associated Soil Microbiota in a Wheat–Soybean Rotation System

Yang

Rong

et al. 2019

Front. Microbiol.

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Returning straw to soil is an effective way to sustain or improve soil quality and crop yields. However, a robust understanding of the impact of straw return on the composition of the soil microbial communities under field conditions has remained elusive. In this study, we characterized the effects of wheat straw return on soil bacterial and fungal communities in a wheat–soybean rotation system over a 3-year period, using Illumina-based 16S rRNA, and internal transcribed region (ITS) amplicon sequencing. Wheat straw return significantly affected the α-diversity of the soil bacterial, but not fungal, community. It enhanced the relative abundance of the bacterial phylum Proteobacteria and the fungal phylum Zygomycota, but reduced that of the bacterial phylum Acidobacteria, and the fungal phylum Ascomycota. Notably, it enriched the relative abundance of nitrogen-cycling bacterial genera such as Bradyrhizobium and Rhizobium . Preliminary analysis of soil chemical properties indicated that straw return soils had significantly higher total nitrogen (TN) contents than no straw return soils. In addition, the relative abundance of fungal genera containing pathogens was significantly lower in straw return soils relative to control soils, such as Fusarium , Alternaria , and Myrothecium . These results suggested a selection effect from the 3-year continuous straw return treatment and the soil bacterial and fungal communities were moderately changed.

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Section: Discussionmentioning

confidence: 99%

Wheat Straw Return Influences Nitrogen-Cycling and Pathogen Associated Soil Microbiota in a Wheat–Soybean Rotation System

Yang

Rong

et al. 2019

Front. Microbiol.

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“…Genome organizational changes have significant implications in coordinated gene expression ( 29 ), genome-specific specialization, ( 30 ) and the discovery of orthologous genes ( 31 ). CoGe’s provides powerful tools for exploring changes in genome structure and sequence evolution across multiple species, and making inferences on the evolutionary mechanisms and forces behind them.…”

Section: The Coge Web-based Platformmentioning

confidence: 99%

A tutorial of diverse genome analysis tools found in the CoGe web-platform usingPlasmodiumspp. as a model

et al. 2018

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Integrated platforms for storage, management, analysis and sharing of large quantities of omics data have become fundamental to comparative genomics. CoGe (https://genomevolution.org/coge/) is an online platform designed to manage and study genomic data, enabling both data- and hypothesis-driven comparative genomics. CoGe’s tools and resources can be used to organize and analyse both publicly available and private genomic data from any species. Here, we demonstrate the capabilities of CoGe through three example workflows using 17 Plasmodium genomes as a model. Plasmodium genomes present unique challenges for comparative genomics due to their rapidly evolving and highly variable genomic AT/GC content. These example workflows are intended to serve as templates to help guide researchers who would like to use CoGe to examine diverse aspects of genome evolution. In the first workflow, trends in genome composition and amino acid usage are explored. In the second, changes in genome structure and the distribution of synonymous (Ks) and non-synonymous (Kn) substitution values are evaluated across species with different levels of evolutionary relatedness. In the third workflow, microsyntenic analyses of multigene families’ genomic organization are conducted using two Plasmodium-specific gene families—serine repeat antigen, and cytoadherence-linked asexual gene—as models. In general, these example workflows show how to achieve quick, reproducible and shareable results using the CoGe platform. We were able to replicate previously published results, as well as leverage CoGe’s tools and resources to gain additional insight into various aspects of Plasmodium genome evolution. Our results highlight the usefulness of the CoGe platform, particularly in understanding complex features of genome evolution. Database URL: https://genomevolution.org/coge/

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“…A broad comparative genomic study of three Trichoderma species has also been reported, which included comparison of their CAZyme genome content ( Schmoll et al. 2016 ), as well as a study in which genomes of five plant pathogenic species of the genus Mycosphaerella were compared ( Zeng et al. 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli

Mäkelä¹,

DiFalco²,

McDonnell³

et al. 2018

Studies in Mycology

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We classified the genes encoding carbohydrate-active enzymes (CAZymes) in 17 sequenced genomes representing 16 evolutionarily diverse Aspergillus species. We performed a phylogenetic analysis of the encoding enzymes, along with experimentally characterized CAZymes, to assign molecular function to the Aspergilli CAZyme families and subfamilies. Genome content analysis revealed that the numbers of CAZy genes per CAZy family related to plant biomass degradation follow closely the taxonomic distance between the species. On the other hand, growth analysis showed almost no correlation between the number of CAZyme genes and the efficiency in polysaccharide utilization. The exception is A. clavatus where a reduced number of pectinolytic enzymes can be correlated with poor growth on pectin. To gain detailed information on the enzymes used by Aspergilli to breakdown complex biomass, we conducted exoproteome analysis by mass spectrometry. These results showed that Aspergilli produce many different enzymes mixtures in the presence of sugar beet pulp and wheat bran. Despite the diverse enzyme mixtures produced, species of section Nigri, A. aculeatus, A. nidulans and A. terreus, produce mixtures of enzymes with activities that are capable of digesting all the major polysaccharides in the available substrates, suggesting that they are capable of degrading all the polysaccharides present simultaneously. For the other Aspergilli, typically the enzymes produced are targeted to a subset of polysaccharides present, suggesting that they can digest only a subset of polysaccharides at a given time.

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A comparative genome analysis of Cercospora sojina with other members of the pathogen genus Mycosphaerella on different plant hosts

Cited by 16 publications

References 33 publications

Wheat Straw Return Influences Nitrogen-Cycling and Pathogen Associated Soil Microbiota in a Wheat–Soybean Rotation System

Wheat Straw Return Influences Nitrogen-Cycling and Pathogen Associated Soil Microbiota in a Wheat–Soybean Rotation System

A tutorial of diverse genome analysis tools found in the CoGe web-platform usingPlasmodiumspp. as a model

Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli

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