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

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.

Download Full-text

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

Journal of Fungi ◽

10.3390/jof7050337 ◽

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.

Download Full-text

Comparative Analysis of Whole-Genome and Methylome Profiles of a Smooth and a Rough Mycobacterium abscessus Clinical Strain

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400737 ◽

2019 ◽

Vol 10 (1) ◽

pp. 13-22 ◽

Cited By ~ 2

Author(s):

Chiranjibi Chhotaray ◽

Shuai Wang ◽

Yaoju Tan ◽

Amjad Ali ◽

Muhammad Shehroz ◽

...

Keyword(s):

Single Molecule ◽

Gene Clusters ◽

Mycobacterium Abscessus ◽

Clinical Strain ◽

Comparative Genomic ◽

Illumina Hiseq ◽

Clinical Strains ◽

Synonymous Mutations ◽

Pan Genome ◽

Genome Wide

Mycobacterium abscessus is a fast growing Mycobacterium species mainly causing skin and respiratory infections in human. M. abscessus is resistant to numerous drugs, which is a major challenge for the treatment. In this study, we have sequenced the genomes of two clinical M. abscessus strains having rough and smooth morphology, using the single molecule real-time and Illumina HiSeq sequencing technology. In addition, we reported the first comparative methylome profiles of a rough and a smooth M. abscessus clinical strains. The number of N4-methylcytosine (4mC) and N6-methyladenine (6mA) modified bases obtained from smooth phenotype were two-fold and 1.6 fold respectively higher than that of rough phenotype. We have also identified 4 distinct novel motifs in two clinical strains and genes encoding antibiotic-modifying/targeting enzymes and genes associated with intracellular survivability having different methylation patterns. To our knowledge, this is the first report about genome-wide methylation profiles of M. abscessus strains and identification of a natural linear plasmid (15 kb) in this critical pathogen harboring methylated bases. The pan-genome analysis of 25 M. abscessus strains including two clinical strains revealed an open pan genome comprises of 7596 gene clusters. Likewise, structural variation analysis revealed that the genome of rough phenotype strain contains more insertions and deletions than the smooth phenotype and that of the reference strain. A total of 391 single nucleotide variations responsible for the non-synonymous mutations were detected in clinical strains compared to the reference genome. The comparative genomic analysis elucidates the genome plasticity in this emerging pathogen. Furthermore, the detection of genome-wide methylation profiles of M. abscessus clinical strains may provide insight into the significant role of DNA methylation in pathogenicity and drug resistance in this opportunistic pathogen.

Download Full-text

Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma)

BMC Genomics ◽

10.1186/s12864-020-07042-7 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Pingping Liang ◽

Hafiz Sohaib Ahmed Saqib ◽

Xiaomin Ni ◽

Yingjia Shen

Keyword(s):

Dna Repair ◽

Positive Selection ◽

Single Molecule ◽

Genome Assembly ◽

De Novo ◽

Gene Families ◽

Comparative Genomic ◽

De Novo Genome Assembly ◽

Marine Medaka ◽

Oryzias Melastigma

Abstract Background Marine medaka (Oryzias melastigma) is considered as an important ecotoxicological indicator to study the biochemical, physiological and molecular responses of marine organisms towards increasing amount of pollutants in marine and estuarine waters. Results In this study, we reported a high-quality and accurate de novo genome assembly of marine medaka through the integration of single-molecule sequencing, Illumina paired-end sequencing, and 10X Genomics linked-reads. The 844.17 Mb assembly is estimated to cover more than 98% of the genome and is more continuous with fewer gaps and errors than the previous genome assembly. Comparison of O. melastigma with closely related species showed significant expansion of gene families associated with DNA repair and ATP-binding cassette (ABC) transporter pathways. We identified 274 genes that appear to be under significant positive selection and are involved in DNA repair, cellular transportation processes, conservation and stability of the genome. The positive selection of genes and the considerable expansion in gene numbers, especially related to stimulus responses provide strong supports for adaptations of O. melastigma under varying environmental stresses. Conclusions The highly contiguous marine medaka genome and comparative genomic analyses will increase our understanding of the underlying mechanisms related to its extraordinary adaptation capability, leading towards acceleration in the ongoing and future investigations in marine ecotoxicology.

Download Full-text

SMRT sequencing of the Oryza rufipogon genome reveals the genomic basis of rice adaptation

10.1101/2020.01.14.905281 ◽

2020 ◽

Cited By ~ 1

Author(s):

Wei Li ◽

Kui Li ◽

Ying Huang ◽

Cong Shi ◽

Wu-Shu Hu ◽

...

Keyword(s):

Single Molecule ◽

Wild Rice ◽

De Novo ◽

Rice Genome ◽

Gene Families ◽

Oryza Rufipogon ◽

Genomic Diversity ◽

Comparative Genomic ◽

Cultivated Rice ◽

Reproductive Process

AbstractAsian cultivated rice is believed to have been domesticated from an immediate ancestral progenitor, Oryza rufipogon, which provides promising sources of novel alleles for world rice improvement. Here we first present a high-quality de novo assembly of the typical O. rufipogon genome through the integration of single-molecule sequencing (SMRT), 10× and Hi-C technologies. This chromosome-based reference genome allows a multi-species comparative analysis of the annual selfing O. sativa and its two wild progenitors, the annual selfing O. nivara and perennial outcrossing O. rufipogon, identifying massive numbers of dispensable genes that are functionally enriched in reproductive process. Comparative genomic analyses identified millions of genomic variants, of which large-effect mutations (e.g., SVs, CNV and PAVs) may affect the variation of agronomically significant traits. We demonstrate how lineage-specific expansion of rice gene families may have contributed to the formation of reproduction isolation (e.g., the recognition of pollen and male sterility), thus brightening the role in driving mating system evolution during the evolutionary process of recent speciation. We document thousands of positively selected genes that are mainly involved in flower development, ripening, pollination, reproduction and response to biotic- and abiotic stresses. We show that selection pressures may serve as crucial forces to govern substantial genomic alterations among the three rice species that form the genetic basis of rapid evolution of mating and reproductive systems under diverse habitats. This first chromosome-based wild rice genome in the genus Oryza will become powerful to accelerate the exploration of untapped genomic diversity from wild rice for the enhancement of elite rice cultivars.

Download Full-text

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

BMC Genomics ◽

10.1186/s12864-019-6095-1 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 2

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.

Download Full-text

Purification and characterization of cassiicolin, the toxin produced by Corynespora cassiicola, causal agent of the leaf fall disease of rubber tree

Journal of Chromatography B ◽

10.1016/j.jchromb.2006.10.051 ◽

2007 ◽

Vol 849 (1-2) ◽

pp. 357-362 ◽

Cited By ~ 17

Author(s):

Frédéric de Lamotte ◽

Marie-Pierre Duviau ◽

Christine Sanier ◽

Robert Thai ◽

Joël Poncet ◽

...

Keyword(s):

Rubber Tree ◽

Causal Agent ◽

Corynespora Cassiicola ◽

Leaf Fall ◽

Purification And Characterization

Download Full-text

Endophytes from Wild Rubber Trees as Antagonists of the Pathogen Corynespora cassiicola

Phytopathology ◽

10.1094/phyto-03-19-0093-r ◽

2019 ◽

Vol 109 (11) ◽

pp. 1888-1899 ◽

Cited By ~ 3

Author(s):

Valérie Pujade-Renaud ◽

Marine Déon ◽

Romina Gazis ◽

Sébastien Ribeiro ◽

Florence Dessailly ◽

...

Keyword(s):

Fungal Endophytes ◽

Rubber Tree ◽

The Philippines ◽

Corynespora Cassiicola ◽

Yield Losses ◽

Promising Candidate ◽

Trichoderma Spp ◽

Trichoderma Isolates ◽

Mycelial Development

The Corynespora leaf fall disease of rubber trees, caused by the necrotrophic fungus Corynespora cassiicola, is responsible for important yield losses in Asian and African plantations, whereas its impact is negligible in South America. The objective of this study was to identify potential antagonists of C. cassiicola among fungal endophytes (i.e., Pestalotiopsis, Colletotrichum, and Trichoderma spp.) isolated from wild and cultivated rubber trees distributed in the Peruvian Amazon. We first tested the endophytes in dual in vitro confrontation assays against a virulent C. cassiicola isolate (CCP) obtained from diseased rubber trees in the Philippines. All Trichoderma isolates overran the CCP colony, suggesting some antagonistic mechanism, while species from the other genera behaved as mutual antagonists. Trichoderma isolates were then tested through antibiosis assays for their capacity to produce growth-inhibiting molecules. One isolate (LA279), recovered as an endophyte from a wild Hevea guianensis specimen and identified as Trichoderma koningiopsis, showed significant antibiosis capacity. We demonstrated that LA279 was also able to endophytically colonize the cultivated rubber tree species (H. brasiliensis). Under controlled laboratory conditions, rubber plants were inoculated with three Trichoderma strains, including LA279, in combination with the pathogenic CCP. Results showed that 1 week preinoculation with the endophytes differentially reduced CCP mycelial development and symptoms. In conclusion, this study suggests that T. koningiopsis isolate LA279—and derivate compounds—could be a promising candidate for the biological control of the important rubber tree pathogen C. cassiicola.

Download Full-text

Rhodococcus comparative genomics reveals a phylogenomic-dependent non-ribosomal peptide synthetase distribution: insights into biosynthetic gene cluster connection to an orphan metabolite

Microbial Genomics ◽

10.1099/mgen.0.000621 ◽

2021 ◽

Vol 7 (7) ◽

Author(s):

Agustina Undabarrena ◽

Ricardo Valencia ◽

Andrés Cumsille ◽

Leonardo Zamora-Leiva ◽

Eduardo Castro-Nallar ◽

...

Keyword(s):

Comparative Genomics ◽

Gene Cluster ◽

Sequence Similarity ◽

Gene Clusters ◽

Biosynthetic Gene Cluster ◽

Chemical Diversity ◽

Comparative Genomic ◽

Biosynthetic Gene ◽

Content Type ◽

Link Type

Natural products (NPs) are synthesized by biosynthetic gene clusters (BGCs), whose genes are involved in producing one or a family of chemically related metabolites. Advances in comparative genomics have been favourable for exploiting huge amounts of data and discovering previously unknown BGCs. Nonetheless, studying distribution patterns of novel BGCs and elucidating the biosynthesis of orphan metabolites remains a challenge. To fill this knowledge gap, our study developed a pipeline for high-quality comparative genomics for the actinomycete genus Rhodococcus , which is metabolically versatile, yet understudied in terms of NPs, leading to a total of 110 genomes, 1891 BGCs and 717 non-ribosomal peptide synthetases (NRPSs). Phylogenomic inferences showed four major clades retrieved from strains of several ecological habitats. BiG-SCAPE sequence similarity BGC networking revealed 44 unidentified gene cluster families (GCFs) for NRPS, which presented a phylogenomic-dependent evolution pattern, supporting the hypothesis of vertical gene transfer. As a proof of concept, we analysed in-depth one of our marine strains, Rhodococcus sp. H-CA8f, which revealed a unique BGC distribution within its phylogenomic clade, involved in producing a chloramphenicol-related compound. While this BGC is part of the most abundant and widely distributed NRPS GCF, corason analysis unveiled major differences regarding its genetic context, co-occurrence patterns and modularity. This BGC is composed of three sections, two well-conserved right/left arms flanking a very variable middle section, composed of nrps genes. The presence of two non-canonical domains in H-CA8f’s BGC may contribute to adding chemical diversity to this family of NPs. Liquid chromatography-high resolution MS and dereplication efforts retrieved a set of related orphan metabolites, the corynecins, which to our knowledge are reported here for the first time in Rhodococcus . Overall, our data provide insights to connect BGC uniqueness with orphan metabolites, by revealing key comparative genomic features supported by models of BGC distribution along phylogeny.

Download Full-text