Complete mitochondrial genome sequence of Fusarium tricinctum.
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ABSTRACT:
SUBMITTER: Xie K
PROVIDER: S-EPMC7782290 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The genome of the phytopathogenic fungus Fusarium tricinctum strain INRA104 was sequenced at a fold-coverage of more than 500×. This led to 23 scaffolds, including one scaffold for the mitochondrial genome, for a total genome size of 42.8?Mb, with an average GC content of 45% and 13,387 predicted genes.
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Project description:In summer 2019, during a survey on the health status of a hazelnut orchard located in the Tuscia area (the province of Viterbo, Latium, Italy), nuts showing symptoms, such as brown-grayish spots at the bottom of the nuts progressing upward to the apex, and necrotic patches on the bracts and, sometimes, on the petioles, were found and collected for further studies. This syndrome is associated with the nut gray necrosis (NGN), whose main causal agent is Fusarium lateritium. Aiming to increase knowledge about this fungal pathogen, the whole-genome sequencing of a strain isolated from symptomatic hazelnut was performed using long Nanopore reads technology in combination with the higher precision of the Illumina reads, generating a high-quality genome assembly. The following phylogenetic and comparative genomics analysis suggested that this isolate is caused by the F. tricinctum species complex rather than F. lateritium one, as initially hypothesized. Thus, this study demonstrates that different Fusarium species can infect Corylus avellana producing the same symptomatology. In addition, it sheds light onto the genetic features of the pathogen in subject, clarifying facets about its biology, epidemiology, infection mechanisms, and host spectrum, with the future objective to develop specific and efficient control strategies.
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Project description:We report here the complete mitochondrial genome sequence of a Rocky Mountain bighorn sheep (Ovis canadensis) in the United States. The circular genome has a size of 16,466?bp and contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes.
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Project description:The 13,647-bp complete mitochondrial genome of Mansonella perstans was sequenced and is syntenic to the mitochondrial genome of Mansonella ozzardi Phylogenetic analysis of the mitochondrial genome is consistent with the known phylogeny of ONC5 group filarial nematodes.
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Project description:Fusarium oxysporum f. sp. lactucae 016-086 is a plant pathogenic filamentous fungus isolated from wilted lettuce in Korea. We reported complete mitochondrial genome sequence of F. oxysporum f. sp. lactucae 016-086. Total length of this mitogenome is 41,826?bp and it encoded 42 genes (14 protein-coding genes, 2 rRNAs, and 26 tRNAs). Nucleotide sequence of coding region takes over 30.6%, and overall GC content is 32.5%. Phylogenetic tree of Fusarium mitochondrial genomes presented distinct clades along with nine formae speciales. This mitogenome will contribute distinguishing formae speciales of F. oxysoporum claearly with additional mitogenomes sequenced in the near future.
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Project description:Fusarium oxysporum is a famous plant pathogenic filamentous fungus. Here, we report the complete mitochondrial genome sequence of F. oxysporum f. sp. lactucae isolated from the lettuce field in Suwon area, Korea. Total length of the mitochondrial genome is 45,020 bp and it encodes 42 genes (15 protein-coding genes, two rRNAs, and 25 tRNAs). Nucleotide sequence of coding region takes over 32.7%, and overall GC content is 32.4%. Phylogenetic tree presented that F. oxysporum f. sp. lactucae 09-002 was clustered with Fusarium commune not like another F. oxysporum mitochondrial genomes, requiring further analyses.
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Project description:Plant pathogenic fungi such as Fusarium tricinctum cause various plant diseases worldwide, especially in temperate regions. In cereals, F. tricinctum is one of the most common species causing Fusarium head blight (FHB) and root rot. Infection with F. tricinctum results in high yield losses and reduction in quality, mainly due to mycotoxin contamination of grain. Mycotoxins produced by F. tricinctum, such as enniatins (ENs) and moniliformin (MON), which are the most studied mycotoxins, have been reported to have multiple toxic effects on humans and animals. Although chemical control of Fusarium infection has been applied to grains, it is not always effective in controlling disease or reducing the level of mycotoxins in wheat grains. To the contrary, chemical control may significantly increase infection of F. tricinctum in fungicide-treated plots after treatment. Our studies show that the bacterium Bacillus amyloliquefaciens, has good control effects against F. tricinctum. Therefore, its use as a biological control agent against various plant pathogens may be an effective strategy to control the spread of Fusarium pathogens. Here, we conduct a review of the literature involving this plant pathogen, its diversity, virulence, and methods to control.
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Project description:The complete sequence of honeybee (Apis mellifera) mitochondrial DNA is reported being 16,343 bp long in the strain sequenced. Relative to their positions in the Drosophila map, 11 of the tRNA genes are in altered positions, but the other genes and regions are in the same relative positions. Comparisons of the predicted protein sequences indicate that the honeybee mitochondrial genetic code is the same as that for Drosophila; but the anticodons of two tRNAs differ between these two insects. The base composition shows extreme bias, being 84.9% AT (cf. 78.6% in Drosophila yakuba). In protein-encoding genes, the AT bias is strongest at the third codon positions (which in some cases lack guanines altogether), and least in second codon positions. Multiple stepwise regression analysis of the predicted products of the protein-encoding genes shows a significant association between the numbers of occurrences of amino acids and %T in codon family, but not with the number of codons per codon family or other parameters associated with codon family base composition. Differences in amino acid abundances are apparent between the predicted Apis and Drosophila proteins, with a relative abundance in the Apis proteins of lysine and a relative deficiency of alanine. Drosophila alanine residues are as often replaced by serine as conserved in Apis. The differences in abundances between Drosophila and Apis are associated with %AT in the codon families, and the degree of divergence in amino acid composition between proteins correlates with the divergence in %AT at the second codon positions. Overall, transversions are about twice as abundant as transitions when comparing Drosophila and Apis protein-encoding genes, but this ratio varies between codon positions. Marked excesses of transitions over chance expectation are seen for the third positions of protein-coding genes and for the gene for the small subunit of ribosomal RNA. For the third codon positions the excess of transitions is adequately explained as due to the restriction of observable substitutions to transitions for conserved amino acids with two-codon families; the excess of transitions over expectation for the small ribosomal subunit suggests that the conservation of nucleotide size is favored by selection.
| S-EPMC1205303 | biostudies-other
Project description:BackgroundIncreased contamination of European and Asian wheat and barley crops with "emerging" mycotoxins such as enniatins or beauvericin, produced by Fusarium avenaceum and Fusarium tricinctum, suggest that these phylogenetically close species could be involved in future food-safety crises.ResultsThe mitochondrial genomes of F. tricinctum strain INRA104 and F. avenaceum strain FaLH27 have been annotated. A comparative analysis was carried out then extended to a set of 25 wild strains. Results show that they constitute two distinct species, easily distinguished by their mitochondrial sequences. The mitochondrial genetic variability is mainly located within the intergenic regions. Marks of variations show they have evolved (i) by Single Nucleotide Polymorphisms (SNPs), (ii) by length variations mediated by insertion/deletion sequences (Indels), and (iii) by length mutations generated by DNA sliding events occurring in mononucleotide (A)n or (T)n microsatellite type sequences arranged in a peculiar palindromic organization. The optionality of these palindromes between both species argues for their mobility. The presence of Indels and SNPs in palindrome neighbouring regions suggests their involvement in these observed variations. Moreover, the intraspecific and interspecific variations in the presence/absence of group I introns suggest a high mobility, resulting from several events of gain and loss during short evolution periods. Phylogenetic analyses of intron orthologous sequences suggest that most introns could have originated from lateral transfers from phylogenetically close or distant species belonging to various Ascomycota genera and even to the Basidiomycota fungal division.ConclusionsMitochondrial genome evolution between F. tricinctum and F. avenaceum is mostly driven by two types of mobile genetic elements, implicated in genome polymorphism. The first one is represented by group I introns. Indeed, both genomes harbour optional (inter- or intra-specifically) group I introns, all carrying putatively functional hegs, arguing for a high mobility of these introns during short evolution periods. The gain events were shown to involve, for most of them, lateral transfers between phylogenetically distant species. This study has also revealed a new type of mobile genetic element constituted by a palindromic arrangement of (A) n and (T) n microsatellite sequences whose presence was related to occurrence of SNPs and Indels in the neighbouring regions.
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