Nuclear and mitochondrial genomes of the hybrid fungal plant pathogen Verticillium longisporum display a mosaic structure
Summary (3 min read)
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) .
- The copyright holder for this preprint (which was not this version posted January 17, 2018.
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 .
- The copyright holder for this preprint (which was not this version posted January 17, 2018.
- 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) .
- The copyright holder for this preprint (which was not this version posted January 17, 2018.
- 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.
- The copyright holder for this preprint (which was not this version posted January 17, 2018.
- 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.
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...New fungal hybrids are reported on a regular basis (Depotter et al., 2018; Giordano et al., 2018)....
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...Comparisons between nuclear and mitochondrial genomes are useful to identify hybridization, introgression or incomplete lineage sorting among other evolutionary events (Depotter et al., 2018; Gonthier et al., 2018)....
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References
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Additional excerpts
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...26.0) to calculate the significance of the break/repeat association (Quinlan & Hall 2010)....
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