Nuclear and mitochondrial genomes of the hybrid fungal plant pathogen Verticillium longisporum display a mosaic structure

TL;DR: In conclusion, the nuclear and mitochondrial genomes of V. longisporum parents interacted dynamically in the hybridization aftermath, and novel combinations of DNA sequence of different parental origin facilitated genome stability after hybridization and consecutive niche adaptation ofV.

Abstract: Allopolyploidization, genome duplication through interspecific hybridization, is an important evolutionary mechanism that can enable organisms to adapt to environmental changes or stresses. This increased adaptive potential of allopolyploids can be particularly relevant for plant pathogens in their quest for host immune response evasion. Allodiploidization likely caused the shift in host range of the fungal pathogen plant Verticillium longisporum, as V. longisporum mainly infects Brassicaceae plants in contrast to haploid Verticillium spp. In this study, we investigated the allodiploid genome structure of V. longisporum and its evolution in the hybridization aftermath. The nuclear genome of V. longisporum displays a mosaic structure, as numerous contigs consists of sections of both parental origins. V. longisporum encountered extensive genome rearrangements, whereas the contribution of gene conversion is negligible. Thus, the mosaic genome structure mainly resulted from genomic rearrangements between parental chromosome sets. Furthermore, a mosaic structure was also found in the mitochondrial genome, demonstrating its bi-parental inheritance. In conclusion, the nuclear and mitochondrial genomes of V. longisporum parents interacted dynamically in the hybridization aftermath. Conceivably, novel combinations of DNA sequence of different parental origin facilitated genome stability after hybridization and consecutive niche adaptation of V. longisporum.

Summary

INTRODUCTION

• Nonetheless, allopolyploidization impacted the evolution of numerous fungal species, including the economically important baker's yeast Saccharomyces cerevisiae (Marcet-Houben & Gabaldón 2015) .
• V. longisporum is assumed to have largely conserved its allodiploid state as the sizes of its sub-genomes resemble those of haploid Verticillium spp.
• Nevertheless, not all genes are present in heterozygous copies, as its nuclear ribosomal internal transcribed spacer region is derived only from one of the parents (Inderbitzin et al. 2011b ). certified by peer review) is the author/funder.

Genome analysis

• Genome assemblies of the two V. longisporum strains (VLB2 and VL20) and V. dahliae strain JR2 were previously published (Faino et al.
• Telomeric regions were determined based on the telomeric repeat pattern: TAACCC/GGGTTA (minimum three repetitions).
• Furthermore, additional repeats were identified and characterized using RepeatModeler (v1.0.8).
• Genome-wide sequence identities between Verticillium strains were calculated with dnadiff (Kurtz et al. 2004 ).
• Here, only hits with a minimal coverage of 80% with each other were selected.

Parental origin determination

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• ; https://doi.org/10.1101/249565 doi: bioRxiv preprint Sub-genomes were divided based on the differences in sequence identities between species A1 and D1 with V. dahliae.
• Here, only 1-to-1 alignments longer than 10kb and a minimum of 80% identity were retained.
• Here, hits with a minimum subject and query coverage of 80% were used.

Phylogenetic tree construction

• The phylogenetic tree of the nuclear DNA was based on the nucleotide sequences of the ascomycete set BUSCO orthologs present in clade Flavnonexudans Verticillium spp. (Simão et al. 2015) .
• Nuclear and mitochondrial genomes of Verticillium spp. other than V. longisporum were previously sequenced and assembled (Shi-Kunne et al. forthcoming; Faino et al. 2015; Jelen et al. 2016) .
• Whole-genome alignments for tree construction were performed by mafft (v7.271) (default settings) (Katoh & Standley 2013; Katoh et al. 2002) , and subsequently the likelihood phylogenetic tree was reconstricted using RAxML with the GTRGAMMA substitution model (v8.2.0) (Stamatakis 2014) . certified by peer review) is the author/funder.

V. longisporum displays a mosaic genome structure

• The genomes of two V. longisporum strains were analysed to investigate the impact of hybridization on the genome structure.
• The V. longisporum genomes were also screened for telomere-specific repeats (TAACCC/GGGTTA) to estimate the number of chromosomes.
• In allopolyploid organisms, parental origin determination is elementary to investigate genome evolution in the hybridization aftermath.
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Genomic rearrangements are responsible for the mosaic genome

• Typically, a mosaic structure of a hybrid genome can originate from gene conversion or from chromosomal rearrangements between DNA strands of different parental origin (Mixão & Gabaldón 2018) .
• To aid gene annotation with the BRAKER1 1.9 pipeline (Hoff et al. 2016 ), ~2 Gb of filtered RNA-seq reads were generated from fungal certified by peer review) is the author/funder.
• Over 80% of the V. longisporum genes are present in two copies whereas, similar to V. dahliae, almost all genes (97-98%) are present in one copy within each of the V. longisporum sub-genomes.
• Moreover, of the 7,620 genes that are present in two copies in VLB2 and VL20, only 5 genes were found to be highly identical (<1%, nucleotide sequence identity) in VLB2, whereas the corresponding gene pair in VL20 was more diverse (>1%, nucleotide sequence identity) .
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Also the mitochondrial genome has a bi-parental origin

• To determine how Verticillium species A1 and D1 relate to other species in the clade Flavnonexudans, a phylogenetic tree was constructed based on 1,194 Ascomycota Benchmarking Universal Single-Copy Orthologs that are present in all members of Verticillium clade Flavnonexudans .
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• In addition to genomic DNA, the V. longisporum clade Flavnonexudans phylogeny was also determined based on mitochondrial DNA .
• The hybrid nature of the V. longisporum mtDNA was furthermore confirmed with a phylogenetic analysis based on a 3.5 kb region that displays 0.7% higher average sequence identity to V. dahliae than to V. nonalfalfae.

DISCUSSION

• Divergent evolution often fixates genomic incompatibilities between populations, leading to reproductive isolation and eventually even speciation (Seehausen et al. 2014) .
• Conceivably, extensive genome alterations occurred after hybridization, facilitating the V. longisporum genome to reach a stable equilibrium.
• Genomic rearrangements often result from double-strand DNA breaks that are erroneously repaired based on templates that display high sequence similarity (Seidl & Thomma 2014) .
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• Mitochondrial DNA is subjected to laws different from the Mendelian principles of segregation and independent assortment as it is maternally inherited in most sexual eukaryotes, including numerous fungal species (Basse 2010) .

Conclusion

• The V. longisporum genome consists of two near to complete genomes of its haploid parents.
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• The relative difference in GC content (dGC) between genes in double copy, also known as Lane 5.
• Gene pairs that encountered gene conversion (purple dots in the red zones) have sequence divergence of more than one percent in one V. longisporum strain and less than one percent in the other strain.
• In other cases, pairs that differ less than one percent are depicted as a black dot, whereas a difference higher than one percent is depicted as a blue dot.

Figures

Table 1: Comparison V. longisporum and V. dahliae genomes.

Fig. 4: The contribution of genomic rearrangements to V. longisporum genome evolution. The ten largest contigs of the V. longisporum strains VLB2 (displayed in grey) and VL20 (displayed in white) are depicted with complete chromosomes indicated by asterisks. Ribbons indicate syntenic genome regions between the two strains. Red bars on the contigs indicate synteny breaks that are confirmed by discontinuity in alignment of VLB2 reads to VL20 genome.

Fig. 3: The contribution of gene conversion to V. longisporum genome evolution. Sequence identities between double-copy genes, present in V. longisporum VLB2 and VL20, are depicted. Gene pairs that encountered gene conversion (purple dots in the red zones) have sequence divergence of more than one percent in one V. longisporum strain and less than one percent in the other strain. In other cases, pairs that differ less than one percent are depicted as a black dot, whereas a difference higher than one percent is depicted as a blue dot.

Fig. 2: Gene copy number distribution within Verticillium (sub-)genomes. “(A1)” and “(D1)” represent species A1 and D1 sub-genomes, respectively, of the V. longisporum strains VLB2 and VL20. For V. dahliae, the strain JR2 was used.

Fig. 1: Determination of parental origin of Verticillium longisporum genome sections. The ten largest contigs of the genome assemblies of V. longisporum strains VLB2 and VL20 are depicted. Lane 1: regions with a sequence identity of at least 96% were assigned to Species D1 (orange), whereas ones with lower sequence identity to Species A1 (purple). Lane 2: sequence identity of V. longisporum alignments to V. dahliae. Lane 3: Sequence identity between exonic regions of V. longisporum and V. dahliae orthologs. Lane 4: Difference in

Fig. 5: Phylogenetic positioning of Verticillium longisporum nuclear sub-genomes and mitochondrial genome to other Verticillium species of clade Flavnonexudans. The nuclear phylogenetic tree was constructed with 1,194 orthologous genes, whereas the mitochondrial phylogenetic tree was based on complete mitochondrial genomes. Maximum-likelihood phylogeny analysis of Verticillium spp. was rooted on Verticillium nubilum and the robustness of the tree was assessed using 100 bootstrap replicates.

Full text

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Research Article
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Nuclear and mitochondrial genomes of the hybrid fungal plant pathogen
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Verticillium longisporum display a mosaic structure
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Authors: Jasper R.L. Depotter
1,2†
, Fabian van Beveren
1†
, Grardy C.M. van den Berg
1
, Thomas
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A. Wood
2‡
, Bart P.H.J. Thomma
1*‡
, Michael F. Seidl
1*‡
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Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB
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Wageningen, The Netherlands
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2
Department of Crops and Agronomy, National Institute of Agricultural Botany, Huntingdon
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Road, CB3 0LE Cambridge, United Kingdom
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† These authors contributed equally to this work
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‡ These authors contributed equally to this work
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*For correspondence:
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Bart P.H.J. Thomma, Laboratory of Phytopathology, Wageningen
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University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands. Tel. 0031-317-
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484536, e-mail: bart.thomma@wur.nl
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Michael F. Seidl, Laboratory of Phytopathology, Wageningen
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University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands. Tel. 0031-317-
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484536, e-mail: michael.seidl@wur.nl
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certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
The copyright holder for this preprint (which was notthis version posted January 17, 2018. ; https://doi.org/10.1101/249565doi: bioRxiv preprint

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ABSTRACT
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Allopolyploidization, genome duplication through interspecific hybridization, is an important
23
evolutionary mechanism that can enable organisms to adapt to environmental changes or
24
stresses. This increased adaptive potential of allopolyploids can be particularly relevant for
25
plant pathogens in their quest for host immune response evasion. Allodiploidization likely
26
caused the shift in host range of the fungal pathogen plant Verticillium longisporum, as V.
27
longisporum mainly infects Brassicaceae plants in contrast to haploid Verticillium spp. In this
28
study, we investigated the allodiploid genome structure of V. longisporum and its evolution in
29
the hybridization aftermath. The nuclear genome of V. longisporum displays a mosaic
30
structure, as numerous contigs consists of sections of both parental origins. V. longisporum
31
encountered extensive genome rearrangements, whereas the contribution of gene conversion
32
is negligible. Thus, the mosaic genome structure mainly resulted from genomic
33
rearrangements between parental chromosome sets. Furthermore, a mosaic structure was also
34
found in the mitochondrial genome, demonstrating its bi-parental inheritance. In conclusion,
35
the nuclear and mitochondrial genomes of V. longisporum parents interacted dynamically in
36
the hybridization aftermath. Conceivably, novel combinations of DNA sequence of different
37
parental origin facilitated genome stability after hybridization and consecutive niche
38
adaptation of V. longisporum.
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Key words: whole-genome duplication, allopolyploidy, genomic rearrangement, Verticillium
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stem striping, Verticillium wilt, Brassica
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certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
The copyright holder for this preprint (which was notthis version posted January 17, 2018. ; https://doi.org/10.1101/249565doi: bioRxiv preprint

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INTRODUCTION
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Whole-genome duplication (WGD) is an important evolutionary mechanism that facilitates
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environmental adaptation (Van de Peer et al. 2017; Mallet 2005). The duplication of genomic
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content increases genomic plasticity, leading to an augmented adaptive potential of organisms
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that underwent WGD. Consequently, polyploids have been associated with increased
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invasiveness (te Beest et al. 2012) and resistance to environmental stresses (Lohaus & Van de
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Peer 2016). For instance, numerous plant species that survived the Cretaceous-Palaeogene
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mass extinction, 66 million years ago, underwent a WGD which is thought to have
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contributed to their increased survival rates (Vanneste et al. 2014a; Vanneste et al. 2014b).
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Both genome copies involved in WGD may have the same species origin, i.e.
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autopolyploidization, or originate from different species as a result of interspecific
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hybridization, i.e. allopolyploidization. In general, allopolyploids are believed to have a
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higher adaptive potential than autopolyploids due to the increased genetic divergence between
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the chromosome sets.
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The impact of allopolyploidization has mainly been investigated in plants, as
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approximately a tenth of all plant species consists of allopolyploids (Barker et al. 2015). In
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contrast, allopolyploidization in fungi is far less intensively investigated (Campbell et al.
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2016). Nonetheless, allopolyploidization impacted the evolution of numerous fungal species,
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including the economically important baker’s yeast Saccharomyces cerevisiae (Marcet-
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Houben & Gabaldón 2015). The increased adaptive potential enabled allopolyploid fungi to
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develop desirable traits that can be exploited in industrial bioprocessing (Peris et al. 2017).
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For instance, at least two recent hybridization events between S. cerevisiae and its close
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relative Saccharomyces eubayanus gave rise to Saccharomyces pastorianus, a species with
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high cold tolerance and good maltose/maltotriose utilization capabilities, which is exploited in
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the production of lager beer that requires barley to be malted at low temperatures (Gibson &
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Liti 2015).
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Allopolyploid genomes experience a so-called “genome shock” upon hybridization,
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inciting major genomic reorganizations that can manifest by genome rearrangements,
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extensive gene loss, transposon activation, and alterations in gene expression (Doyle et al.
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2008). These early stage alterations are primordial for hybrid survival, as divergent evolution
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is principally associated with incompatibilities between the parental genomes (Matute et al.
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2010). Allopolyploids benefit from a thorough re-organization where negative interactions
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between the parental genomes are purged. Frequently, heterozygosity is lost for many regions
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in the allopolyploid genome (Mixão & Gabaldón 2018). This can be a result of the direct loss
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of a duplicated gene copy through deletion or gene conversion, a process where one of the
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copies substitutes its homeologous counterpart (McGrath et al. 2014). Gene conversion and
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the homogenization of complete chromosomes played a pivotal role in the evolution of the
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osmotolerant yeast species Pichia sorbitophila (Louis et al. 2012). In total, two of its seven
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chromosome pairs consist of partly heterozygous, partly homozygous sections, whereas two
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chromosome pairs are completely homozygous. Gene conversion may eventually result in
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chromosomes consisting of sections of both parental origins as “mosaic genomes”
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(Stukenbrock et al. 2012). However, mosaic genomes can also arise through recombination
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between chromosomes of the different parents, such as in the hybrid yeast
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Zygosaccharomyces parabailii (Ortiz-Merino et al. 2017).
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Plant pathogens are often thought to evolve while being engaged in arms races with
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their hosts; pathogens evolve to evade host immunity while plant hosts attempt to intercept
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pathogen ingress (Cook et al. 2015). Due to the increased adaptation potential,
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allopolyploidization has been proposed as a potent driver in pathogen evolution (Depotter et
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al. 2016b). Allopolyploids often have different pathogenic traits than their parental lineages,
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such as higher virulence (Husson et al. 2015; Brasier & Kirk 2001) and shifted host ranges
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(Inderbitzin et al. 2011b; Zeise & Tiedemann 2002). Within the fungal genus Verticillium,
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allodiploidization resulted in the emergence of a novel pathogen on brassicaceous plants;
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Verticillium longisporum (Inderbitzin et al. 2011b; Depotter et al. 2017b). Similar to haploid
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Verticillium spp., V. longisporum is thought to have a predominant asexual reproduction as a
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sexual cycle has never been described and populations are not outcrossing (Depotter et al.
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2017b; Short et al. 2014). V. longisporum is sub-divided into three lineages, each representing
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a separate hybridization event (Inderbitzin et al. 2011b). The economically most important
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lineage is A1/D1 that originates from hybridization between Verticillium species A1 and D1
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that have hitherto not been found in their haploid states. V. longisporum lineage A1/D1 is the
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main causal agent of Verticillium stem striping on oilseed rape (Novakazi et al. 2015) and its
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economic importance as emerging pathogen is increasing worldwide (Depotter et al. 2017a).
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A recent study revealed that lineage A1/D1 can be further divided into two genetically distinct
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populations, which have been named ‘A1/D1 West’ and ‘A1/D1 East’ after their geographic
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occurrence in Europe (Depotter et al. 2017b). Nevertheless, both populations were shown to
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originate the same hybridization event (Depotter et al. 2017b).
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V. longisporum is assumed to have largely conserved its allodiploid state as the sizes
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of its sub-genomes resemble those of haploid Verticillium spp. (Depotter et al. 2017b; Shi-
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Kunne et al. forthcoming; Fogelqvist et al. 2018). Nevertheless, not all genes are present in
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heterozygous copies, as its nuclear ribosomal internal transcribed spacer region is derived
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only from one of the parents (Inderbitzin et al. 2011b). Here, we investigated the evolution of
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the allodiploid genome of V. longisporum and determined to what extent heterozygosity is
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lost.
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certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
The copyright holder for this preprint (which was notthis version posted January 17, 2018. ; https://doi.org/10.1101/249565doi: bioRxiv preprint