Complete mitochondrial genome sequence of Aspergillus flavus SRRC1009: insight of intraspecific variations on A. flavus mitochondrial genomes.
ABSTRACT: The mitogenome of Aspergillus flavus SRRC1009 was sequenced to investigate intraspecific variations on mitochondrial genomes of A. flavus. It shows 29,202 bp with a typical configuration of Aspergillus mitogenome. Sixteen SNPs and 22 INDELs and 17 SNPs and 27 INDELs were identified against AflaGuard® and JQ355000, respectively. Phylogenetic trees present in the three A. flavus mitochondrial genomes were clustered with A. oryzae mitochondrial genome in one clade.
Project description:Afla-Guard<sup>®</sup> is a commercial non-toxigenic <i>Aspergillus flavus</i> strain used to decrease aflatoxin contamination level in field. Its mitochondrial genome was sequenced, showing that its length is 29,208 bp with typical configuration of <i>Aspergillus</i> mitochondrial genome. 17 SNPs and 27 INDELs were identified by comparing with previous <i>A. flavus</i> mitochondrial genome. Phylogenetic trees present that <i>A. flavus</i> of Afla-Guard<sup>®</sup> was clustered with the previous <i>A. flavus</i> mitochondrial genome.
Project description:We have determined a mitochondrial genome of <i>Ricania speculum</i> (Walker, 1851) collected in Jeollabuk-do, Republic of Korea. The circular mitogenome of <i>R. speculum</i> is 15,530 bp long which is shorter than that of the previous mitogenome of <i>R. speculum</i> by 199 bp. It includes 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNAs. Intraspecific variation between two mitogenome of <i>R. speculum</i> was investigated: 171 SNPs and 18 INDELs were identified, presenting a high level of intraspecific variations on mitochondrial genome.
Project description:Aspergillus flavus is an important zoonotic pathogen and a well-known aflatoxin producer. Aspergillus flavus strains that are prevalent in Japanese environments are reported to be non-aflatoxigenic, although their aflatoxin productivity, especially among clinical isolates, has not been thoroughly investigated to date. In this study, we sequenced the genomes of ten strains of A. flavus isolated in Japan and compared their sequences with each other as well as with those of Aspergillus oryzae RIB40 and A. flavus NRRL3357. The phylogenetic analysis based on identified SNPs indicated that five strains were closer to A. oryzae RIB40 than to A. flavus NRRL3357. In contrast, of those isolates that were closer to A. flavus NRRL3357 than to A. oryzae RIB40, three were found to possess either the entire or partial aflatoxin biosynthesis gene cluster of NRRL3357-type. Furthermore, two of the three actually produced either aflatoxin B1 or an intermediate of the reaction leading to aflatoxin formation. Three of the ten strains we isolated were identified to possess part of the aflatoxin gene cluster, while five others retained the A. oryzae RIB40-type cluster. The genome data thus obtained may be further explored and utilized for comparative analysis of aflatoxin production in environmental and clinical isolates of A. flavus.
Project description:ABSTRACT Nuclear genome sequences incompletely characterize the genomic content and thus the genetic diversity of fungal species. Here, we present the complete mitochondrial genome sequences of nine Aspergillus flavus strains, providing useful information for inter- and intraspecific analyses.
Project description:Iron is an essential component for growth and development. Despite relative abundance in the environment, bioavailability of iron is limited due to oxidation by atmospheric oxygen into insoluble ferric iron. Filamentous fungi have developed diverse pathways to uptake and use iron. In the current study, a putative iron utilization gene cluster (IUC) in <i>Aspergillus flavus</i> was identified and characterized. Gene analyses indicate <i>A. flavus</i> may use reductive as well as siderophore-mediated iron uptake and utilization pathways. The ferroxidation and iron permeation process, in which iron transport depends on the coupling of these two activities, mediates the reductive pathway. The IUC identified in this work includes six genes and is located in a highly polymorphic region of the genome. Diversity among <i>A. flavus</i> genotypes is manifested in the structure of the IUC, which ranged from complete deletion to a region disabled by multiple indels. Molecular profiling of <i>A. flavus</i> populations suggests lineage-specific loss of IUC. The observed variation among A. flavus genotypes in iron utilization and the lineage-specific loss of the iron utilization genes in several <i>A. flavus</i> clonal lineages provide insight on evolution of iron acquisition and utilization within <i>Aspergillus</i> section <i>Flavi</i>. The potential divergence in capacity to acquire iron should be taken into account when selecting <i>A. flavus</i> active ingredients for biocontrol in niches where climate change may alter iron availability.
Project description:The argentine ant, <i>Linepithema humile</i> (Mayr, 1867), is an invasive ant species that has spread across the world. We have determined the mitochondrial genome of <i>L. humile</i> collected in South Korea, which is 15,934 bp containing 10 SNPs and 5 INDELs compared to the previous mitogenome. Most SNPs were found in <i>cox3</i>, followed by <i>cytb</i>. From SNPs our mitogenome was identified as a H3 haplotype, which was previously recorded in Japan and the U.S. while the previous mitogenome was H1 haplotype. Phylogenetic analysis was congruent to previous study within the tribe Leptomyrmecini but not between other tribes of subfamily Dolichoderinae.
Project description:We have determined mitochondrial genome of <i>A. gossypii</i> isolated from <i>Plantago asiatica</i> in Korea. The circular mitogenome of <i>A. gossypii</i> is 16,045 bp including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single control region of 798 bp. Its AT ratio is 83.8%. In comparison this mitogenome to Chinese and Korean <i>A. gossypii</i> mitogenomes, 66 single nucleotide polymorphisms (SNPs) and 176 insertions and deletions (INDELs) and 11 SNPs and 173 INDELs are identified, respectively, presenting similar level to those of <i>Nilaparvata lugens</i>, <i>Laodelphax striatellus</i>, and <i>Spodoptera frugiperda</i> and lower than that of <i>Chilo suppresallis</i>.
Project description:Metabolism of fatty acids is a critical requirement for the pathogenesis of oil seed pathogens including the fungus Aspergillus flavus Previous studies have correlated decreased ability to grow on fatty acids with reduced virulence of this fungus on host seed. Two fatty acid metabolism regulatory transcription factors, FarA and FarB, have been described in other filamentous fungi. Unexpectedly, we find A. flavus possesses three Far homologs, FarA, FarB, and FarC, with FarA and FarC showing a greater protein similarity to each other than FarB. farA and farB are located in regions of colinearity in all Aspergillus spp. sequenced to date, whereas farC is limited to a subset of species where it is inserted in an otherwise colinear region in Aspergillus genomes. Deletion and overexpression (OE) of farA and farB, but not farC, yielded mutants with aberrant growth patterns on specific fatty acids as well as altered expression of genes involved in fatty acid metabolism. Marked differences included significant growth defects of both ∆farA and ∆farB on medium-chain fatty acids and decreased growth of OE::farA on unsaturated fatty acids. Loss of farA diminished expression of mitochondrial β-oxidation genes whereas OE::farA inhibited expression of genes involved in unsaturated fatty acid catabolism. FarA also positively regulated the desaturase genes required to generate polyunsaturated fatty acids. Aflatoxin production on toxin-inducing media was significantly decreased in the ∆farB mutant and increased in the OE::farB mutant, with gene expression data supporting a role for FarB in tying β-oxidation processes with aflatoxin accumulation.
Project description:<i>Riccia fluitans</i> L. is the most common species in <i>Riccia</i> genus. To investigate intraspecific variations on mitochondrial genomes of <i>R. fluitans</i>, we completed mitochondrial genome of <i>R. fluitans</i>. Its length is 185,640 bp, longer than that of NC_043906 by 19 bp and it contains 74 genes (42 protein-coding genes, 3 rRNAs, 28 tRNAs, and 1 pseudogene). 18 single nucleotide polymorphisms (SNPs) and 19 insertions and deletions are identified, higher than that of <i>Marchantia polymorpha</i> subsp. <i>ruderalis</i>. One non-synonymous SNP is found in <i>ccmFN.</i> Phylogenetic trees show that <i>R. fluitans</i> is clustered with <i>Dumortiera hirsuta</i>, requiring additional mitogenome to clarify the phylogenetic relationship.
Project description:Aspergillus flavus and A. oryzae represent two unique species predicted to have spent centuries in vastly different environments. A. flavus is an important opportunistic plant pathogen known for contaminating crops with the carcinogenic mycotoxin, aflatoxin and A. oryzae is a domesticated fungus used in food fermentations. Remarkably, the genomes of these two species are still nearly identical. We have used the recently sequenced genomes of A. oryzae RIB40 and A. flavus NRRL3357 along with array based comparative genome hybridization (CGH) as a tool to compare genomes across several strains of these two species. A comparison of three strains from each species by CGH revealed only 42 and 129 genes unique to A. flavus and A. oryzae, respectively. Further, only 709 genes were identified as being polymorphic between the species. Despite the high degree of similarity between these two species, correlation analysis among all data from the CGH arrays for all strains used in this study reveals a species split. However, this view of species demarcation becomes muddled when focused on only those genes for secondary metabolism. CGH comparison between 3 strains of A. flavus and 3 strains of A. oryzae, analyzed at the probe level