Data for transcriptome and proteome analysis of Eucalyptus infected with Calonectria pseudoreteaudii.
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ABSTRACT:
SUBMITTER: Chen Q
PROVIDER: S-EPMC4509981 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundLeaf blight caused by Calonectria spp. is one of the most destructive diseases to affect Eucalyptus nurseries and plantations. These pathogens mainly attack Eucalyptus, a tree with a diversity of secondary metabolites employed as defense-related phytoalexins. To unravel the fungal adaptive mechanisms to various phytoalexins, we examined the genome of C. pseudoreteaudii, which is one of the most aggressive pathogens in southeast Asia.ResultsA 63.7 Mb genome with 14,355 coding genes of C. pseudoreteaudii were assembled. Genomic comparisons identified 1785 species-specific gene families in C. pseudoreteaudii. Most of them were not annotated and those annotated genes were enriched in peptidase activity, pathogenesis, oxidoreductase activity, etc. RNA-seq showed that 4425 genes were differentially expressed on the eucalyptus(the resistant cultivar E. grandis×E.camaldulensis M1) tissue induced medium. The annotation of GO term and KEGG pathway indicated that some of the differential expression genes were involved in detoxification and transportation, such as genes encoding ABC transporters, degrading enzymes of aromatic compounds and so on.ConclusionsPotential genomic determinants of phytoalexin detoxification were identified in C. pseudoreteaudii by comparison with 13 other fungi. This pathogen seems to employ membrane transporters and degradation enzymes to detoxify Eucalyptus phytoalexins. Remarkably, the Calonectria genome possesses a surprising number of secondary metabolism backbone enzyme genes involving toxin biosynthesis. It is also especially suited for cutin and lignin degradation. This indicates that toxin and cell wall degrading enzymes may act important roles in the establishment of Calonectria leaf blight. This study provides further understanding on the mechanism of pathogenesis in Calonectria.
| S-EPMC5946483 | biostudies-literature
Project description:Eucalyptus leaf blight caused by Calonectria spp. is a serious disease in Eucalyptus seedling and plantations. However, the molecular mechanisms of the infection process and pathogenesis of Calonectria to Eucalyptus is not well-studied. In this study, we analyzed the transcriptomes of C. pseudoreteaudii at three stages of Eucalyptus leaf infection, and in mycelium grown in potato dextrose broth using Illumina RNA-Seq technology. We identified 161 differentially expressed genes between C. pseudoreteaudii from leaf and mycelium grown in potato dextrose broth. GO and KEGG enrichment analyses of these genes suggested that they were mainly involved in oxidoreductase activity, hydrolase activity, and transmembrane transporter activity. Most of the differentially expressed genes at the early infection stage were upregulated. These upregulated genes were mainly involved in cell wall hydrolysis and toxin synthesis, suggesting a role for toxin and cell wall hydrolases in the establishment of Calonectria leaf blight. Genes related to detoxification of phytoalexins were continually upregulated during infection. The candidate effectors and putative pathogenicity determinants identified in this study will help in the functional analysis of C. pseudoreteaudii virulence and pathogenicity.
| S-EPMC5224884 | biostudies-literature
Project description:Decline in the productivity of Eucalyptus hybrid cutting production in the Guangdong Province of China is linked to cutting rot associated with several Calonectria spp. The aim of this study was to identify these fungi using morphological and DNA sequence comparisons. Two previously undescribed Calonectria spp., Ca. pseudoreteaudii sp. nov. and Ca. cerciana sp. nov. were identified together with Ca. pauciramosa. Calonectria pseudoreteaudii resides in the Ca. reteaudii complex and Ca. cerciana is closely related to Ca. morganii. Connected to the discovery of Ca. pseudoreteaudii, species in the Ca. reteaudii complex were re-considered and the group is shown to accommodate two cryptic species. These originate from Australia and are described as Ca. queenslandica sp. nov. and Ca. terrae-reginae sp. nov.
| S-EPMC2890164 | biostudies-literature
Project description:Here, we report the draft genome sequence of Calonectria pteridis, the causal agent of Calonectria leaf blight in eucalyptus plantations in Brazil. The 58,373,473-bp genome assembly consists of 1,167 scaffolds, with a GC content of 50.21%. These genomic data can contribute to future studies involving the biology, adaptability, and pathogenicity of C. pteridis.
| S-EPMC9476984 | biostudies-literature
Project description:Diseases caused by species of Calonectria (Ca.) represent a serious threat to the growth and sustainability of Eucalyptus plantations in China. Symptoms caused by these fungi mainly include leaf blight on trees in plantations and rotting of stems and leaves in nurseries. Extensive surveys have recently been conducted where Calonectria species were collected in Eucalyptus plantations and nurseries in the FuJian, GuangDong, GuangXi, and YunNan Provinces of South China. Additional isolates were baited from soil samples in the Hong Kong Region. The aim of this study was to identify the 115 Calonectria isolates obtained using comparisons of DNA sequence data for the β-tubulin (tub2), calmodulin (cmdA), histone H3 (his3) and partial translation elongation factor-1α (tef1) gene regions as well as their morphological features. Seven known species were identified, including Calonectria arbusta, Ca. asiatica, Ca. chinensis, Ca. eucalypti, Ca. hongkongensis, Ca. mossambicensis and Ca. pentaseptata. In addition, six novel taxa were collected and are described here as Ca. aciculata, Ca. honghensis, Ca. lantauensis, Ca. pseudoturangicola, Ca. pseudoyunnanensis, and Ca. yunnanensis spp. nov. Overall, the results reflect a high diversity of Calonectria species in China.
| S-EPMC5729712 | biostudies-literature
Project description:Eucalyptus leaf polyphenols extract (EPE) has been proved to have various bioactivities, but few reports focus on its antioxidant mechanism in vivo. The purpose of this study was to elucidate the effect and mechanism of EPE dietary supplements on antioxidant capacity in chicken. A total of 216 chickens were randomly selected for a 40-day experiment. Four treatment groups received diets including the control diet only, the control diet + low EPE (0.6 g/kg), the control diet + moderate EPE (0.9 g/kg), and the control diet + high EPE (1.2 g/kg). Compared with control group, the glutathione peroxidase (GSH-Px) activity and glutathione (GSH) content in the breast muscle of the moderate EPE treatment group was significantly higher (p < 0.05), while the malonaldehyde (MDA) content in the moderate EPE group was reduced (p < 0.05). Moreover, proteomic and transcriptomic analyses of the breast muscle revealed that glutathione metabolism and the peroxisome were the two crucial metabolic pathways responsible for increased antioxidant capacity of the muscle. Accordingly, nine candidate genes and two candidate proteins were identified related to improved antioxidant status induced by EPE supplements. This research provides new insights into the molecular mechanism of antioxidant capacity in chickens treated with EPE dietary supplements.
| S-EPMC7313108 | biostudies-literature
Project description:The lily (Lilium spp.) anther contains a lot of pollen. It is not known if lily pollen contains allergens, and therefore screening pollen allergy-related proteins and genes is necessary. The pollen development period of lily 'Siberia' was determined by microscope observation. Early mononuclear microspores and mature pollens were used as sequencing materials. The analysis of the pollen transcriptome identified differentially expressed genes (DEGs), e.g., Profilin, Phl p 7 (Polcalcin), Ole e 1, and Phl p 11, which are associated with pollen allergens. The proteome analysis positively verified a significant increase in pollen allergenic protein content. The expression levels of LoProfiilin and LoPolcalcin, annotated as allergen proteins, gradually increased in mature pollen. LoProfiilin and LoPolcalcin were cloned and their open reading frame lengths were 396 bp and 246 bp, which encoded 131 and 81 amino acids, respectively. Amino acid sequence and structure alignment indicated that the protein sequences of LoProfilin and LoPolcalcin were highly conserved. Subcellular localization analysis showed that LoProfilin protein was localized in the cell cytoplasm and nucleus. LoProfilin and LoPolcalcin were highly expressed in mature pollen at the transcriptional and protein levels. A tertiary structure prediction analysis identified LoProfilin and LoPolcalcin as potential allergens in lily pollen.
| S-EPMC6929097 | biostudies-literature
Project description:The genus Calonectria includes pathogens of various agricultural, horticultural, and forestry crops. Species of Calonectria are commonly collected from soils, fruits, leaves, stems, and roots. Some species of Calonectria isolated from soils are considered as important plant pathogens. Understanding the species diversity and distribution characteristics of Calonectria species in different soil layers will help us to clarify their long-term potential harm to plants and their patterns of dissemination. To our knowledge, no systematic research has been conducted concerning the species diversity and distribution characteristics of Calonectria in different soil layers. In this study, 1000 soil samples were collected from five soil layers (0-20, 20-40, 40-60, 60-80, and 80-100 cm) at 100 sampling points in one 15-year-old Eucalyptus urophylla hybrid plantation in southern China. A total of 1037 isolates of Calonectria present in all five soil layers were obtained from 93 of 100 sampling points. The 1037 isolates were identified based on DNA sequence comparisons of the translation elongation factor 1-alpha (tef1), β-tubulin (tub2), calmodulin (cmdA), and histone H3 (his3) gene regions, as well as the combination of morphological characteristics. These isolates were identified as C. hongkongensis (665 isolates; 64.1%), C. aconidialis (250 isolates; 24.1%), C. kyotensis (58 isolates; 5.6%), C. ilicicola (47 isolates; 4.5%), C. chinensis (2 isolates; 0.2%), and C. orientalis (15 isolates; 1.5%). With the exception of C. orientalis, which resides in the C. brassicae species complex, the other five species belonged to the C. kyotensis species complex. The results showed that the number of sampling points that yielded Calonectria and the number (and percentage) of Calonectria isolates obtained decreased with increasing depth of the soil. More than 84% of the isolates were obtained from the 0-20 and 20-40 cm soil layers. The deeper soil layers had comparatively lower numbers but still harbored a considerable number of Calonectria. The diversity of five species in the C. kyotensis species complex decreased with increasing soil depth. The genotypes of isolates in each Calonectria species were determined by tef1 and tub2 gene sequences. For each species in the C. kyotensis species complex, in most cases, the number of genotypes decreased with increasing soil depth. The 0-20 cm soil layer contained all of the genotypes of each species. To our knowledge, this study presents the first report of C. orientalis isolated in China. This species was isolated from the 40-60 and 60-80 cm soil layers at only one sampling point, and only one genotype was present. This study has enhanced our understanding of the species diversity and distribution characteristics of Calonectria in different soil layers.
| S-EPMC8541508 | biostudies-literature
Project description:Plantation forestry is expanding rapidly in China to meet an increasing demand for wood and pulp products globally. Fungal pathogens including species of Calonectria represent a serious threat to the growth and sustainability of this industry. Surveys were conducted in the Guangdong, Guangxi and Hainan Provinces of South China, where Eucalyptus trees in plantations or cuttings in nurseries displayed symptoms of leaf blight. Isolations from symptomatic leaves and soils collected close to infected trees resulted in a large collection of Calonectria isolates. These isolates were identified using the Consolidated Species Concept, employing morphological characters and DNA sequence comparisons for the β-tubulin, calmodulin, histone H3 and translation elongation factor 1-alpha gene regions. Twenty-one Calonectria species were identified of which 18 represented novel taxa. Of these, 12 novel taxa belonged to Sphaero-Naviculate Group and the remaining six to the Prolate Group. Southeast Asia appears to represent a centre of biodiversity for the Sphaero-Naviculate Group and this fact could be one of the important constraints to Eucalyptus forestry in China. The remarkable diversity of Calonectria species in a relatively small area of China and associated with a single tree species is surprising.
| S-EPMC4779793 | biostudies-literature
Project description:BackgroundEucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood in the world due to its increasing importance for fiber and energy. Somatic embryogenesis (SE) is one large-scale method to provide commercial use of the vegetative propagation of Eucalyptus and dedifferentiation is a key step for plant cells to become meristematic. However, little is known about the molecular changes during the Eucalyptus SE.ResultsWe compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus species - E. camaldulensis (high embryogenetic potential) and E. grandis x urophylla (low embryogenetic potential). Initially, we identified 18,777 to 20,240 genes in all samples. Compared to the differentiated tissues, we identified 9229 and 8989 differentially expressed genes (DEGs) in the dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla, respectively, and 2687 up-regulated and 2581 down-regulated genes shared. Next, we identified 2003 up-regulated and 1958 down-regulated genes only in E. camaldulensis, including 6 somatic embryogenesis receptor kinase, 17 ethylene, 12 auxin, 83 ribosomal protein, 28 zinc finger protein, 10 heat shock protein, 9 histone, 122 cell wall related and 98 transcription factor genes. Genes from other families like ABA, arabinogalactan protein and late embryogenesis abundant protein were also found to be specifically dysregulated in the dedifferentiation process of E. camaldulensis. Further, we identified 48,447 variants (SNPs and small indels) specific to E. camaldulensis, including 13,434 exonic variants from 4723 genes (e.g., annexin, GN, ARF and AP2-like ethylene-responsive transcription factor). qRT-PCR was used to confirm the gene expression patterns in both E. camaldulensis and E. grandis x urophylla.ConclusionsThis is the first time to study the somatic embryogenesis of Eucalyptus using transcriptome sequencing. It will improve our understanding of the molecular mechanisms of somatic embryogenesis and dedifferentiation in Eucalyptus. Our results provide a valuable resource for future studies in the field of Eucalyptus and will benefit the Eucalyptus breeding program.
| S-EPMC7672952 | biostudies-literature