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Kt details. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative phylogenetic markers, but have been mostly neglected due to technical difficulties.

A total of 61 complete mitogenomes of FOSC strains were de novo assembled and annotated. Length variations and intron zsexualidad support the separation of three phylogenetic species.

The variable region of the mitogenome that aseualidad typical for the genus Fusarium shows two new variants in the FOSC. The variant typical for Fusarium is found in members of all three clades, while variant 2 is found in clades 2 asexualidad 3 and variant 3 only in clade 2. The extended set of loci analyzed using a new implementation of the genealogical concordance species recognition method support the identification of three phylogenetic species within the FOSC.

Comparative analysis of the mitogenomes in the FOSC revealed ongoing mitochondrial recombination within, but not between phylogenetic species. The recombination indicates the presence of a parasexual cycle in F. The obstacles hindering the usage of the mitogenomes are resolved by using next generation sequencing and selective genome assemblers, such as GRAbB. Complete mitogenome sequences offer a stable basis and reference point for phylogenetic and population genetic studies.

Tm of the Fusarium oxysporum species complex FOSC are important plant pathogens causing vascular wilts, rots and damping-off asexualidad a broad range of asexualidad and horticulturally important crops [ 12 ]. Asexuaildad addition, members of this species complex are also clinically important, causing infections in both human and animal hosts [ t,4 ].

Furthermore, despite the pathogenic potential of these fungi, not all strains are virulent. Putative non-pathogenic strains asexualidad to asexualidxd group are used as biocontrol agents against pathogens asexuqlidad 5 ]. The taxonomy of Fusarium has historically been based on the morphology of the asexual reproductive structures, leading to a broad definition of F. To capture intraspecific variability within the morphospecies, formae speciales ff.

The genome of F. However, since no sexual stage has been found for this species nor could it be induced under laboratory conditions, F. The use of molecular markers revealed that multiple ff. However, asexualidad phylogenetic analysis conducted using genealogical concordance phylogenetic species recognition GCPSR based on eight loci supported the separation of only two phylogenetic species within the complex: one species corresponding to clade 1 and the other to the remaining clades [ 12 ].

After genetic isolation, two populations or species undergo the following stages: shared polymorphism apparent polyphylyloss of shared polymorphism asexualidadd fixation in one of the species and reciprocal monophyly after fixation in both species. According to GCPSR, the genetic isolation between populations phylogenetic species can be detected by a combination of genealogical concordance and non-discordance. Genealogical concordance is meant by the asexualidac reciprocal monophyly of multiple gene genealogies.

Genealogical non-discordance means that no grouping supported by high support values for one of the genes is contradicted by another gene with the same level of support assexualidad 1314 ]. Asexualidwd sequences were used for resolving phylogenetic and evolutionary relationships between fungi at all taxonomic levels [ 15 — 17 ]. The advances in sequencing technologies and the reduction of costs involved, as well as, the development of tools to selectively assemble target genomic regions, like GRAbB, made it feasible to conduct complete mitochondrial genome mitogenome sequence analysis of a large number of strains [ 18 ].

The mitochondrial genomes of Fusarium spp. The orientation and order of the genes are conserved within the genus, with the exception of some of the tRNA-encoding genes [ 17 ]. One of the introns is located in the rnl gene and encodes a small ribosomal protein Rps3.

Asexualidaf intron is conserved in the Pezizomycotina [ 20 ]. In addition to the genes with functional predictions, a large open reading asexualidda ORF was found in all Fusarium spp. The mitogenome of the representative strain for F. Although several F. Both of these mitogenome asexualidad, GenBank accession no.

KR unpublished and LT [ 18 ] Fig. Mitochondrial genome of Fusarium oxysporum f. Green blocks: tRNA coding genes, blue arrows: genes, yellow arrows: protein coding sequences, red arrows: rDNA coding sequence, purple arrows: intron encoded homing endonuclease genes, gray segment: large variable LV region with orf LV-uORF. The goals of this study asexualidad i to prove that the mitochondrial genomes of a large number of strains can be analyzed, as we suggested in an earlier study [ 18 ], ii to present a detailed analysis of these mitochondrial genomes and iii to demonstrate how a detailed analysis of these genomes can contribute to our understanding of the biology of the given organism.

To achieve these goals we present the following in this study. First, the phylogenetic relationships between 61 strains of the F. Second, a detailed analysis of the genetic diversity of the mitochondrial genomes within the complex is given. Third, an interpretation of the mitogenome diversity in the light of the phylogeny is provided. Lastly, the biological implications of our tj are discussed. Sixty-one F. The F. For the two F. Each of the libraries was loaded as part of one lane of an Illumina paired-end flowcell for cluster generation using a cBot.

Sequencing was done on an Illumina HiSeq instrument using7, flow cycles for forward, index and reverse reads respectively. De-multiplexing of resulting data was done using Casava 1.

The remaining strains were sequenced by other research groups or as part of asexualidaad studies [ 22 asexuqlidad 24 ]. The eight loci used by Laurence et al. A set of eight complete protein coding genes were used in zsexualidad study, which have been traditionally used as barcoding genes or have recently been suggested as such [ 25 ]: actasexualidarcalrpl10aRPB2tef1atef3 and top1.

The barcoding regions and genes were each aligned per locus. The alignment of the mitochondrial genome required a different approach. The mitochondrial genome sequences were split into two regions: the large variable region between the trnT tgt and the nad2 genes and remaining part of the mitochondrial genome, which we refer to as the conserved part of the mitochondrial genome. Since the conserved part of the mitogenome and the variants of the large variable region were too long for MUSCLE to handle in a single run, we used the following approach.

First, the given sequences were divided into non-overlapping homologous blocks — bp. Finally, the individual aligned blocks were concatenated in the original order. Sequence variability of each region was calculated by aligning the sequences, then the asexuaidad of characters with multiple character states was calculated and divided by the total number of characters in the alignment. The most appropriate substitution evolution model was determined using jModelTest 2 [ 33 ] for each of the single locus data aseualidad.

Phylogenetic reconstruction has been conducted using MrBayes 3. The MCMC algorithm was run for 4, generations with four incrementally-heated chains, starting from random trees and sampling one out every generations. Burn-in was set to a relative value, 0. Genealogical concordance phylogenetic species recognition GCPSR was implemented in two steps: i identifying independent evolutionary lineages IELs and ii exhaustive subdivision of strains into phylogenetic species.

Independent evolutionary lineages Rk have two criteria: concordance and non-discordance. In our implementation, we used these two criteria in a sequential order: First, identifying asexualdiad clades, then comparing concordant clades and removing those that were discordant with each other. The concordant clades obtained in this manner define an unambiguous tree topology.

This tree can be visualized and the number of loci supporting each clade can be used as a support value for the given clade. This tree can asexualudad used for exhaustive subdivision. Each isolate must be classified within a putative phylogenetic species. This is referred to as exhaustive subdivision, which ensures that all phylogenetic species are monophyletic and there are no paraphyletic species. The clades that are kept after this step are recognized as phylogenetic species.

Sixty-one strains belonging to Fusarium oxysporum species complex, one F. Applying genealogical concordance phylogenetic species recognition GCPSR on the eight single copy nuclear complete protein coding genes actcalRPB2rpl10atef1atef3asexyalidad and tub2 resulted in the recognition of three phylogenetic species within the FOSC.

Half of the single locus phylogenies still aswxualidad the three species when the rDNA repeat region and the conserved part of the mitogenome were added besides the eight genes Fig. Genealogical concordance phylogenetic species recognition based on the 10 qsexualidad data set.

The 10 loci used in the analysis were: acttub2caltef1atef3rpl10arpb2top1rDNA repeat and the conserved part of the mitogenome. The three clades within the FOSC were recognized as phylogenetic species and shown in the tree. Only tef1a showed high support for all three clades data not shown.

The mitogenomes of all 64 strains 61 FOSC and the 3 outgroup strains were successfully assembled into single contigs each showing circular topology Fig.

All of the strains analyzed contained an intron in the rnl gene mtLSU that is conserved in the Pezizomycotina and contains a gene coding for a ribosomal protein, Rps3. The asrxualidad F. The members of clade 2 could be differentiated from all other strains based on their intron patterns.

Intron patterns xsexualidad almost no asexualidad aeexualidad clades 2 and 3, the only exception being strain FOSC3-a in clade 3.

Clade 1 showed marked variation asexualidad intron pattern. The mitogenomes of Fusarium spp. In this paragraph, we present the analysis of the genetic diversity of the mitochondrial sequences located asxeualidad the LV region, the analysis of the LV region can be found asexualdiad the next subsection. Strains that belong to clades 2 and 3 had clearly different lengths of the conserved region of the mitogenome. This is partially due to the difference in intron patterns, but even after these introns were excluded, the asexualiddad populations, clades 2 and 3, had significantly different lengths, The significant difference between lengths of the conserved part of mitogenome suggests that these two populations have been genetically isolated.

The variation observed in clade 1 was larger than in the two other clades. There were only 5 strains within clade 1, thus, further grouping of the strains based on mitogenome length within this t, would not produce statistically supported results. Re-sequencing of F. Although the three variants contained asexualidad genes with identical asexuapidad sequences asexualidad a similar order Fig.

The variant that is typical for Fusarium spp. This variant was present in all three major clades of the FOSC. Finally, variant 3 zsexualidad or bp long and it was found only in clade 2.

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