Subtelomeres as Specialized Chromatin Domains

Hocher, Antoine; Taddei, Angela

doi:10.1002/bies.201900205

Cited by 8 publications

(8 citation statements)

References 79 publications

(95 reference statements)

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“…The largest duplications or absences in WA isolates relative to SN15 were predominantly located near telomeric regions or on AC23 (Fig 4). This is consistent with the known enrichment of structural rearrangement in subtelomeres (Hocher and Taddei 2020) and proposed prevalence of BFB- mediated rearrangement across the Dothideomycetes (Croll et al 2013). Complete and partial absences of SN15 AC23 were observed in some Western Australian isolates, suggesting that large structural mutations are occurring in the field (Fig 4).…”

Section: Discussionsupporting

confidence: 89%

Pathogenicity effector candidates and accessory genome revealed by pan-genomic analysis of Parastagonospora nodorum

Jones

Rybak

Bertazzoni

et al. 2021

Preprint

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The wheat pathogen Parastagonospora nodorum has emerged as a model necrotrophic fungal species with growing genomic resources. Recent population-level pan-genome studies were leveraged to provide novel insights into pathogen evolution and effector-like gene contents relevant to local crop disease outbreaks. In this study, we examined 156 isolates representing a regional population from the Western Australian (WA) wheat-belt region, and 17 internationally sourced isolates. We observed a highly diverse local population, within which were numerous small and highly similar clusters of isolates from hotter and drier regions. Pan-genome assembly and orthologous gene datasets resulted in 3579 predicted effector candidates, 2291 of which exhibited presence-absence variation (PAV) across the population, and 1362 were specific to WA isolates. There was an abundance of mutations (including repeat-induced point mutation (RIP)), distributed in 'hot-spots' within the pan-genomic landscape that were rich in effector candidates. Three characterised effector loci (ToxA, Tox1 and Tox3) were located within sub-telomeric regions of lower diversity, but were nestled within larger high-diversity regions. RIP was widespread across the genome, but non-synonymous RIP-like mutations were strongly selected against. These improved bioinformatic resources for P. nodorum, represent progressive advancements in fungal pan-genomics, with a view towards supporting region-specific surveillance of host-pathogen interactions.

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Section: Discussionsupporting

confidence: 89%

Pathogenicity effector candidates and accessory genome revealed by pan-genomic analysis of Parastagonospora nodorum

Jones

Rybak

Bertazzoni

et al. 2021

Preprint

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“…While heterochromatin is thought to be a general property of subtelomeres in many organisms, chromatin organization at subtelomeres might be more complex ( 27 ) and for instance, its nature in plants is still a matter of debate ( 25 , 26 , 91 ). Here, we find that chromatin in C. reinhardtii might follow a simple organization.…”

Section: Discussionmentioning

confidence: 99%

“…This is less clear in plant subtelomeres where signatures of both euchromatin and heterochromatin have been reported ( 25 , 26 ). An emerging view proposes that subtelomeres might be associated with a specific type of chromatin, alongside canonical heterochromatin ( 27 ), which can lead to reversible transcriptional silencing, a property called telomere position effect. Additionally, specific non-coding transcripts have been detected in these regions, including the telomeric repeat-containing RNA (TERRA), which plays multiple roles in telomere biology ( 28 , 29 ).…”

Section: Introductionmentioning

confidence: 99%

Architecture and evolution of subtelomeres in the unicellular green algaChlamydomonas reinhardtii

Chaux-Jukic

O’Donnell

Craig

et al. 2021

Nucleic Acids Research

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In most eukaryotes, subtelomeres are dynamic genomic regions populated by multi-copy sequences of different origins, which can promote segmental duplications and chromosomal rearrangements. However, their repetitive nature has complicated the efforts to sequence them, analyse their structure and infer how they evolved. Here, we use recent genome assemblies of Chlamydomonas reinhardtii based on long-read sequencing to comprehensively describe the subtelomere architecture of the 17 chromosomes of this model unicellular green alga. We identify three main repeated elements present at subtelomeres, which we call Sultan, Subtile and Suber, alongside three chromosome extremities with ribosomal DNA as the only identified component of their subtelomeres. The most common architecture, present in 27 out of 34 subtelomeres, is a heterochromatic array of Sultan elements adjacent to the telomere, followed by a transcribed Spacer sequence, a G-rich microsatellite and transposable elements. Sequence similarity analyses suggest that Sultan elements underwent segmental duplications within each subtelomere and rearranged between subtelomeres at a much lower frequency. Analysis of other green algae reveals species-specific repeated elements that are shared across subtelomeres, with an overall organization similar to C. reinhardtii. This work uncovers the complexity and evolution of subtelomere architecture in green algae.

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“…Furthermore, TE activities are generally suppressed by host defense processes. These processes include DNA methylation ( Selker et al 2003 ; Zemach et al 2010 ), histone modifications associated with highly condensed heterochromatin ( Slotkin and Martienssen 2007 ; Hocher et al 2018 ; Hocher and Taddei 2020 ), targeted processes such as RNA-silencing ( Lippman and Martienssen 2004 ; Nicolas et al 2013 ; Yadav et al 2018 ), or repeat-induced point (RIP) mutation, a fungal specific process in in which duplicated or repetitive sequences are targeted by C to T mutations ( Cambareri et al 1989 ; Galagan and Selker 2004 ; Fudal et al 2009 ; Wang et al 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant PathogenVerticillium dahliae

Torres

Thomma

Seidl

2021

Genome Biology and Evolution

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Transposable elements (TEs) are a major source of genetic and regulatory variation in their host genome and are consequently thought to play important roles in evolution. Many fungal and oomycete plant pathogens have evolved dynamic and TE-rich genomic regions containing genes that are implicated in host colonization and adaptation. TEs embedded in these regions have typically been thought to accelerate the evolution of these genomic compartments, but little is known about their dynamics in strains that harbor them. Here, we used whole-genome sequencing data of 42 strains of the fungal plant pathogen Verticillium dahliae to systematically identify polymorphic TEs that may be implicated in genomic as well as in gene expression variation. We identified 2,523 TE polymorphisms and characterize a subset of 8% of the TEs as polymorphic elements that are evolutionary younger, less methylated, and more highly expressed when compared with the remaining 92% of the total TE complement. As expected, the polyrmorphic TEs are enriched in the adaptive genomic regions. Besides, we observed an association of polymorphic TEs with pathogenicity-related genes that localize nearby and that display high expression levels. Collectively, our analyses demonstrate that TE dynamics in V. dahliae contributes to genomic variation, correlates with expression of pathogenicity-related genes, and potentially impacts the evolution of adaptive genomic regions.

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Subtelomeres as Specialized Chromatin Domains

Cited by 8 publications

References 79 publications

Pathogenicity effector candidates and accessory genome revealed by pan-genomic analysis of Parastagonospora nodorum

Pathogenicity effector candidates and accessory genome revealed by pan-genomic analysis of Parastagonospora nodorum

Architecture and evolution of subtelomeres in the unicellular green algaChlamydomonas reinhardtii

Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant PathogenVerticillium dahliae

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