Genome and evolution of the arbuscular mycorrhizal fungus <i>Diversispora epigaea</i> (formerly <i>Glomus versiforme</i>) and its bacterial endosymbionts

Sun, Xuepeng; Chen, Wenbo; Ivanov, Sergey; MacLean, Allyson M.; Wight, Haley; Ramaraj, Thiruvarangan; Mudge, Joann; Harrison, Maria J.; Fei, Zhangjun

doi:10.1111/nph.15472

Cited by 94 publications

(112 citation statements)

References 82 publications

(115 reference statements)

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“…Comparison of AM fungal genomes with those of Mortierella elongata (Mortierellomycotina) and representative Mucoromycotina species indicates extensive copy number variations in genes involved in nutrient acquisition, developmental pathways, and primary and secondary metabolism. This study, together with the recent analyses of Chen et al (2018a,b), Kobayashi et al (2018), Maeda et al (2018) and Sun et al (2019), have expanded and refined our understanding of the genomic heritage of AM symbionts. mycelium produced on carrot root organ cultures as described by Tisserant et al (2013) and Ropars et al (2016).…”

Section: Introductionmentioning

confidence: 59%

“…Those conserved genes mainly code for cellular and signalling processes, and pathways of the primary metabolism, probably derived from those encoded by the saprotrophic MRCA. Several of these general genomic features have recently been confirmed in G. clarus (Kobayashi et al ., ) and D. epigaea (Sun et al ., ).…”

Section: Discussionmentioning

confidence: 97%

“…Multigene families were analysed for statistically significant evolutionary changes in protein family size using the Cafe and FastOrtho programs (Han et al ., ; Wattam et al ., ) with default parameters. The genomes of R. clarus (Kobayashi et al ., ) and D. epigaea (Sun et al ., ) were not included in these analyses, as they were publicly released after submission of the present manuscript.…”

Section: Methodsmentioning

confidence: 99%

“…DAOM197198 experienced the loss of several, otherwise widely conserved Mucoromycotina genes with functions related to cell wall polysaccharide degradation, and overall primary and secondary metabolism, which could explain its obligate biotrophy. These features have recently been corroborated by the sequencing of five additional isolates from R. irregularis (Chen et al ., ,), R. clarus (Kobayashi et al ., ) and D. epigaea (Sun et al ., ). Most importantly, no gene encoding multidomain de novo fatty acid synthase was detected in the genome of these species as initially suggested by Wewer et al .…”

Section: Introductionmentioning

confidence: 97%

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Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina

et al. 2019

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Summary Glomeromycotina is a lineage of early diverging fungi that establish arbuscular mycorrhizal (AM) symbiosis with land plants. Despite their major ecological role, the genetic basis of their obligate mutualism remains largely unknown, hindering our understanding of their evolution and biology. We compared the genomes of Glomerales (Rhizophagus irregularis, Rhizophagus diaphanus, Rhizophagus cerebriforme) and Diversisporales (Gigaspora rosea) species, together with those of saprotrophic Mucoromycota, to identify gene families and processes associated with these lineages and to understand the molecular underpinning of their symbiotic lifestyle. Genomic features in Glomeromycotina appear to be very similar with a very high content in transposons and protein‐coding genes, extensive duplications of protein kinase genes, and loss of genes coding for lignocellulose degradation, thiamin biosynthesis and cytosolic fatty acid synthase. Most symbiosis‐related genes in R. irregularis and G. rosea are specific to Glomeromycotina. We also confirmed that the present species have a homokaryotic genome organisation. The high interspecific diversity of Glomeromycotina gene repertoires, affecting all known protein domains, as well as symbiosis‐related orphan genes, may explain the known adaptation of Glomeromycotina to a wide range of environmental settings. Our findings contribute to an increasingly detailed portrait of genomic features defining the biology of AM fungi.

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Section: Introductionmentioning

confidence: 59%

Section: Discussionmentioning

confidence: 97%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

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Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina

et al. 2019

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“…In the three species, the protein length, the signal peptide and the CLE peptide sequences were very similar to what we observed in R. irregularis (Figs b, S1b–d). We did not find CLE peptide gene in Diversispora epigaea (Sun et al ., ), perhaps due to a lack of genome coverage.…”

Section: Resultsmentioning

confidence: 99%

Arbuscular mycorrhizal fungi possess a CLAVATA3/embryo surrounding region‐related gene that positively regulates symbiosis

2019

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Summary The arbuscular mycorrhizal (AM) symbiosis is a beneficial association established between land plants and the members of a subphylum of fungi, the Glomeromycotina. How the two symbiotic partners regulate their association is still enigmatic. Secreted fungal peptides are candidates for regulating this interaction. We searched for fungal peptides with similarities with known plant signalling peptides. We identified CLAVATA (CLV)/EMBRYO SURROUNDING REGION (ESR)‐RELATED PROTEIN (CLE) genes in phylogenetically distant AM fungi: four Rhizophagus species and one Gigaspora species. These CLE genes encode a signal peptide for secretion and the conserved CLE C‐terminal motif. They seem to be absent in the other fungal clades. Rhizophagus irregularis and Gigaspora rosea CLE genes (RiCLE1 and GrCLE1) are transcriptionally induced in symbiotic vs asymbiotic conditions. Exogenous application of synthetic RiCLE1 peptide on Medicago truncatula affects root architecture, by slowing the apical growth of primary roots and stimulating the formation of lateral roots. In addition, pretreatment of seedlings with RiCLE1 peptide stimulates mycorrhization. Our findings demonstrate for the first time that in addition to plants and nematodes, AM fungi also possess CLE genes. These results pave the way for deciphering new mechanisms by which AM fungi modulate plant cellular responses during the establishment of AM symbiosis.

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Life of Microbes Inside the Plant: Beneficial Fungal Endophytes and Mycorrhizal Fungi

Lanfranco¹,

Fiorilli²

2022

Good Microbes in Medicine, Food Production, Biotechnology, Bioremediation, and Agriculture

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Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme) and its bacterial endosymbionts

Cited by 94 publications

References 82 publications

Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina

Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina

Arbuscular mycorrhizal fungi possess a CLAVATA3/embryo surrounding region‐related gene that positively regulates symbiosis

Life of Microbes Inside the Plant: Beneficial Fungal Endophytes and Mycorrhizal Fungi

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