The population genetic structure approach adds new insights into the evolution of plant LTR retrotransposon lineages

Suguiyama, Vanessa Fuentes; Vasconcelos, Luiz Augusto Baciega; Rossi, Maria Magdalena; Biondo, Cibele; Setta, Nathalia de

doi:10.1371/journal.pone.0214542

Cited by 9 publications

(6 citation statements)

References 77 publications

(122 reference statements)

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“…In A. saccharum , the CHH methylation frequencies of Oryco/Ivana and Ale/Retrofit were even lower than Sire , and while the copy number of Oryco/Ivana was also lower, Ale/Retrofit was interesting in its overall prevalence in the genome, with 4035 and 3488 divergent copies for A. negundo and A. saccharum , respectively. This pattern of high Ale sequence diversity and more even distribution through the genome was observed in a population level assessment of Setaria italica (Suguiyama et al., 2019 ). The low CHH methylation observed for Ale/Retrofit elements could be a reflection of sufficient suppression by CG and CHG elements, or it could be ascribed to the inherent structure of these TEs which may influence methylation levels.…”

Section: Resultssupporting

confidence: 54%

Profiling genome‐wide methylation in two maples: Fine‐scale approaches to detection with nanopore technology

McEvoy,

Grady,

Pauloski

et al. 2024

Evolutionary Applications

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DNA methylation is critical to the regulation of transposable elements and gene expression and can play an important role in the adaptation of stress response mechanisms in plants. Traditional methods of methylation quantification rely on bisulfite conversion that can compromise accuracy. Recent advances in long‐read sequencing technologies allow for methylation detection in real time. The associated algorithms that interpret these modifications have evolved from strictly statistical approaches to Hidden Markov Models and, recently, deep learning approaches. Much of the existing software focuses on methylation in the CG context, but methylation in other contexts is important to quantify, as it is extensively leveraged in plants. Here, we present methylation profiles for two maple species across the full range of 5mC sequence contexts using Oxford Nanopore Technologies (ONT) long‐reads. Hybrid and reference‐guided assemblies were generated for two new Acer accessions: Acer negundo (box elder; 65x ONT and 111X Illumina) and Acer saccharum (sugar maple; 93x ONT and 148X Illumina). The ONT reads generated for these assemblies were re‐basecalled, and methylation detection was conducted in a custom pipeline with the published Acer references (PacBio assemblies) and hybrid assemblies reported herein to generate four epigenomes. Examination of the transposable element landscape revealed the dominance of LTR Copia elements and patterns of methylation associated with different classes of TEs. Methylation distributions were examined at high resolution across gene and repeat density and described within the broader angiosperm context, and more narrowly in the context of gene family dynamics and candidate nutrient stress genes.

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Section: Resultssupporting

confidence: 54%

Profiling genome‐wide methylation in two maples: Fine‐scale approaches to detection with nanopore technology

McEvoy,

Grady,

Pauloski

et al. 2024

Evolutionary Applications

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“…We thus used a genetic structure approach based on full-length long terminal repeat retrotransposons (fl-LTR-RT) as an alternative strategy. A total of 11 fl-LTR-RT families with more than 30 elements were identified and defined as a 'populations', allowing us to apply genetic structure analyses that are often used in population genomics 30 . We searched for fl-LTR-RT clusters that only appeared in one of the two homoeologous sub-genomes.…”

Section: Resultsmentioning

confidence: 99%

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

et al. 2020

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Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.

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“…We thus used a genetic structure approach based on full-length long terminal repeat retrotransposons (fl-LTR-RT). A total of eleven fl-LTR-RT families with more than 30 elements were identified and defined as a ‘populations’, allowing us to apply genetic structure analyses that are often used in population genomics 29 . We searched for fl-LTR-RT clusters that only appeared in one of the two homoeologous sub-genomes.…”

Section: Resultsmentioning

confidence: 99%

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Abrouk

Ahmed

Cubry

et al. 2020

Preprint

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33Sustainable food production in the context of climate change necessitates diversification of 34 agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria 35 exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we 36 established high-quality genomic resources to facilitate fonio improvement through molecular 37 breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 38 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population 39 structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic 40 factors. Two genes associated with seed size and shattering showed signatures of selection. Most 41 known domestication genes from other cereal models however have not experienced strong 42 selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and 43 dry environments. 44 45 agriculture 1-3 . The Food and Agriculture Organization of the United Nations (FAO) stated that arid 50 and semi-arid regions are the most vulnerable environments to increasing uncertainties in regional 51 and global food production 4 . In most countries of Africa and the Middle East, agricultural 52 productivity will decline in the near future 4 , because of climate change, land degradation, and 53 groundwater depletion 5 . Agricultural selection, from the early steps of domestication to modern-54 day crop breeding, has resulted in a marked decrease in agrobiodiversity 6,7 . Today, three cereal 55 4 crops alone, bread wheat (Triticum aestivum), maize (Zea mays), and rice (Oryza sativa) account 56 for more than half of the globally consumed calories 8 . 57Many of today's major cereal crops, including rice and maize, originated in relatively humid 58 tropical and sub-tropical regions 9,10 . Although plant breeding has adapted the major cereal crops 59 to a wide range of climates and cultivation practices, there is limited genetic diversity within these 60 few plant species for cultivation in the most extreme environments. On the other hand, crop wild 61 relatives and orphan crops are often adapted to extreme environments and their utility to unlock 62 marginal lands for agriculture has recently regained interest 2,6,[11][12][13][14] . Current technological advances 63 in genomics and genome editing provide an opportunity to rapidly domesticate wild relatives and 64 to improve orphan crops 15,16 . De novo domestication of wild species or rapid improvement of semi-65 domesticated crops can be achieved in less than a decade by targeting a few key genes 6 . 66White fonio (Digitaria exilis (Kippist) Stapf) (Fig. 1) is an indigenous African millet species with 67 a great potential for agriculture in marginal environments 17,18 . Fonio is cultivated under a large 68 range of environmental conditions, from a tropical monsoon climate in western Guinea to a hot, 69 arid desert climate (BWh) in the Sahel zone. Some extra-early matur...

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The population genetic structure approach adds new insights into the evolution of plant LTR retrotransposon lineages

Cited by 9 publications

References 77 publications

Profiling genome‐wide methylation in two maples: Fine‐scale approaches to detection with nanopore technology

Profiling genome‐wide methylation in two maples: Fine‐scale approaches to detection with nanopore technology

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

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