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SUMMARY Maples (the genusAcer) represent important and beloved forest, urban, and ornamental trees distributed throughout the Northern hemisphere. They exist in a diverse array of native ranges and distributions, across spectrums of tolerance or decline, and have varying levels of susceptibility to biotic and abiotic stress. AmongAcerspecies, several stand out in their importance to economic interest. Here we report the first two chromosome‐scale genomes for North American species,Acer negundoandAcer saccharum. Both assembled genomes contain scaffolds corresponding to 13 chromosomes, withA. negundoat a length of 442 Mb, an N50 of 32 Mb, and 30 491 genes, andA. saccharumat a length of 626 Mb, an N50 of 46 Mb, and 40 074 genes. No recent whole genome duplications were detected, thoughA. saccharumhas local gene duplication and more recent bursts of transposable elements, as well as a large‐scale translocation between two chromosomes. Genomic comparison revealed thatA. negundohas a smaller genome with recent gene family evolution that is predominantly contracted and expansions that are potentially related to invasive tendencies and tolerance to abiotic stress. Examination of RNA sequencing data obtained fromA. saccharumgiven long‐term aluminum and calcium soil treatments at the Hubbard Brook Experimental Forest provided insights into genes involved in the aluminum stress response at the systemic level, as well as signs of compromised processes upon calcium deficiency, a condition contributing to maple decline.
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Profiling genome‐wide methylation in two maples: Fine‐scale approaches to detection with nanopore technology
Abstract 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 newAceraccessions:Acer negundo(box elder; 65x ONT and 111X Illumina) andAcer 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 publishedAcerreferences (PacBio assemblies) and hybrid assemblies reported herein to generate four epigenomes. Examination of the transposable element landscape revealed the dominance ofLTR Copiaelements 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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- Award ID(s):
- 1943371
- PAR ID:
- 10502747
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Evolutionary Applications
- Volume:
- 17
- Issue:
- 4
- ISSN:
- 1752-4571
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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