Comment on 'Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi'

Auxier, Ben; Bazzicalupo, Anna

doi:10.7554/elife.47301

Cited by 12 publications

(21 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The discovery of inter-nuclear recombination in AMF was, however, challenged. Specifically, it was suggested that recombination events in AMF drop significantly once heterozygous, duplicated regions covering SNPs and sites supported by less than five reads are removed from available datasets from single nuclei (Auxier and Bazzicalupo, 2019). Here, we show that the removal of duplicates, heterozygous positions and sites supported by less than five reads still retrieves significant inter-nuclear recombination within available datasets (Chen et al, 2018b).…”

Section: Introductionmentioning

confidence: 59%

“…To this end, plans are underway to sequence individual AMF nuclei using long-read sequencing technologies, and perform single nuclei genotyping using complete, phased genome references for all dikaryotic AMF isolates. Long-read sequencing will be important to reveal the exact origin of the heterozygous sites in single nuclei datasets – i.e., whether some of these represent miss-mapped reads, sequence errors, aneuploidy or contaminants - as these are often found along recombination tracts (see paper and Auxier and Bazzicalupo, 2019 ). Lastly, producing a recombining progeny by crossing compatible homokaryotic AMF isolates will be key to conclusively demonstrate how/when sexual reproduction (meiosis) occurs in AMF.…”

Section: Discussionmentioning

confidence: 99%

“…This view is supported by data available for the two dikaryotic isolates A4 and A5. Specifically, the genotypes of single nuclei isolated from these two isolates were mainly produced from positions with low read depth (Auxier and Bazzicalupo, 2019). However, despite the overabundance of low coverage sites, the 150 base pairs paired-end Illumina reads from single nuclei still did their job well, mapping with high fidelity to their genome assemblies to generate a clear dikaryotic patterns for these isolates (see Figure 2a,b in Chen et al, 2018b).…”

Section: Recombination In Low Coverage and High-coverage Sitesmentioning

confidence: 99%

“…Using PCR and sequencing, Chen et al (2018b) found that Nucleus 07 of SL1 (SL1_07) carries the MAT-locus 1, even though its nuclear genotype often resembles that of co-existing MAT-5 nuclei. It was noted that Illumina reads covering the MAT-locus 1 are not present in the in SL1_07 single nucleus data, and it was thus suggested that this specific sample may have been mixed-up (Auxier and Bazzicalupo, 2019).…”

Section: Confirming That Nucleus 07 (Sl1) Carries the Mat-5 Locus Woumentioning

confidence: 99%

“…This data can be found here: ID LLXH00000000, LLXI00000000, LLXJ00000000, LLXK00000000, LLXL00000000, and PRJNA477348. Chen et al (2018b) and Auxier and Bazzicalupo (2019) removed, and single-copy regions. Yellow and Green colors highlight the two co-existing genotypes.…”

Section: Data Availability Statementmentioning

confidence: 99%

See 4 more Smart Citations

More Filtering on SNP Calling Does Not Remove Evidence of Inter-Nucleus Recombination in Dikaryotic Arbuscular Mycorrhizal Fungi

et al. 2020

View full text Add to dashboard Cite

Evidence for the existence of dikaryote-like strains, low nuclear sequence diversity and inter-nuclear recombination in arbuscular mycorrhizal fungi has been recently reported based on single nucleus sequencing data. Here, we aimed to support evidence of internuclear recombination using an approach that filters SNP calls more conservatively, keeping only positions that are exclusively single copy and homozygous, and with at least five reads supporting a given SNP. This methodology recovers hundreds of putative inter-nucleus recombination events across publicly available sequence data from individual nuclei. Challenges related to the acquisition and analysis of sequence data from individual nuclei are highlighted and discussed, and ways to address these issues in future studies are presented.

show abstract

Section: Introductionmentioning

confidence: 59%

Section: Discussionmentioning

confidence: 99%

Section: Recombination In Low Coverage and High-coverage Sitesmentioning

confidence: 99%

Section: Confirming That Nucleus 07 (Sl1) Carries the Mat-5 Locus Woumentioning

confidence: 99%

Section: Data Availability Statementmentioning

confidence: 99%

See 3 more Smart Citations

More Filtering on SNP Calling Does Not Remove Evidence of Inter-Nucleus Recombination in Dikaryotic Arbuscular Mycorrhizal Fungi

et al. 2020

View full text Add to dashboard Cite

show abstract

Coexistence of genetically different Rhizophagus irregularis isolates induces genes involved in a putative fungal mating response

et al. 2020

View full text Add to dashboard Cite

Arbuscular mycorrhizal fungi (AMF) are of great ecological importance because of their effects on plant growth. Closely related genotypes of the same AMF species coexist in plant roots. However, almost nothing is known about the molecular interactions occurring during such coexistence. We compared in planta AMF gene transcription in single and coinoculation treatments with two genetically different isolates of Rhizophagus irregularis in symbiosis independently on three genetically different cassava genotypes. Remarkably few genes were specifically upregulated when the two fungi coexisted. Strikingly, almost all of the genes with an identifiable putative function were known to be involved in mating in other fungal species. Several genes were consistent across host plant genotypes but more upregulated genes involved in putative mating were observed in host genotype (COL2215) compared with the two other host genotypes. The AMF genes that we observed to be specifically upregulated during coexistence were either involved in the mating pheromone response, in meiosis, sexual sporulation or were homologs of MAT-locus genes known in other fungal species. We did not observe the upregulation of the expected homeodomain genes contained in a putative AMF MAT-locus, but observed upregulation of HMG-box genes similar to those known to be involved in mating in Mucoromycotina species. Finally, we demonstrated that coexistence between the two fungal genotypes in the coinoculation treatments explained the number of putative mating response genes activated in the different plant host genotypes. This study demonstrates experimentally the activation of genes involved in a putative mating response and represents an important step towards the understanding of coexistence and sexual reproduction in these important plant symbionts.

show abstract

Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198

Manyara,

Sánchez-García,

Montoliu-Nerin

et al. 2024

G3: Genes, Genomes, Genetics

View full text Add to dashboard Cite

Identifying genuine polymorphic variants is a significant challenge in sequence data analysis, although detecting low-frequency variants in sequence data is essential for estimating demographic parameters and investigating genetic processes, such as selection, within populations. Arbuscular mycorrhizal (AM) fungi are multinucleate organisms, in which individual nuclei collectively operate as a population, and the extent of genetic variation across nuclei has long been an area of scientific interest. In this study, we investigated the patterns of polymorphism discovery and the alternate allele frequency distribution by comparing polymorphism discovery in 2 distinct genomic sequence datasets of the AM fungus model species, Rhizophagus irregularis strain DAOM197198. The 2 datasets used in this study are publicly available and were generated either from pooled spores and hyphae or amplified single nuclei from a single spore. We also estimated the intraorganismal variation within the DAOM197198 strain. Our results showed that the 2 datasets exhibited different frequency patterns for discovered variants. The whole-organism dataset showed a distribution spanning low-, intermediate-, and high-frequency variants, whereas the single-nucleus dataset predominantly featured low-frequency variants with smaller proportions in intermediate and high frequencies. Furthermore, single nucleotide polymorphism density estimates within both the whole organism and individual nuclei confirmed the low intraorganismal variation of the DAOM197198 strain and that most variants are rare. Our study highlights the methodological challenges associated with detecting low-frequency variants in AM fungal whole-genome sequence data and demonstrates that alternate alleles can be reliably identified in single nuclei of AM fungi.

show abstract

Comment on 'Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi'

Cited by 12 publications

References 17 publications

More Filtering on SNP Calling Does Not Remove Evidence of Inter-Nucleus Recombination in Dikaryotic Arbuscular Mycorrhizal Fungi

More Filtering on SNP Calling Does Not Remove Evidence of Inter-Nucleus Recombination in Dikaryotic Arbuscular Mycorrhizal Fungi

Coexistence of genetically different Rhizophagus irregularis isolates induces genes involved in a putative fungal mating response

Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198

Contact Info

Product

Resources

About