Chromosome-Level Genome Assembly for Acer pseudosieboldianum and Highlights to Mechanisms for Leaf Color and Shape Change

Li, Xiang; Cai, Kewei; Han, Zhiming; Zhang, Shikai; Sun, Anran; Xie, Yuning; Han, Rui; Guo, Ruixue; Tigabu, Mulualem; Sederoff, Ronald R.; Pei, Xiaona; Zhao, Chunli; Zhao, Xiyang

doi:10.3389/fpls.2022.850054

Cited by 10 publications

(11 citation statements)

References 103 publications

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“…The Acer species mentioned in our study, A. pseudosieboldianum, A. yangbiense, and A. truncatum, are distributed across different areas of China. Presently, the studies on genome assembly of A. pseudosieboldianum, A. yangbiense, and A. truncatum heve been reported, which provide references for exploring the genome-wide identifications and functions of genes in three species [8,27,28]. CBF transcription factors, also known as DREB1 proteins, belong to the AP2/ERF family.…”

Section: Discussionmentioning

confidence: 99%

Identification and Analysis of the CBF Gene Family in Three Species of Acer under Cold Stress

Zhao

Han

Cai

et al. 2023

IJMS

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The C-Repeat Binding Factor (CBF) gene family has been identified and characterized in multiple plant species, and it plays a crucial role in responding to low temperatures. Presently, only a few studies on tree species demonstrate the mechanisms and potential functions of CBFs associated with cold resistance, while our study is a novel report on the multi-aspect differences of CBFs among three tree species, compared to previous studies. In this study, genome-wide identification and analysis of the CBF gene family in Acer truncatum, Acer pseudosieboldianum, and Acer yangbiense were performed. The results revealed that 16 CBF genes (five ApseCBFs, four AcyanCBFs, and seven AtruCBFs) were unevenly distributed across the chromosomes, and most CBF genes were mapped on chromosome 2 (Chr2) and chromosome 11 (Chr11). The analysis of phylogenetic relationships, gene structure, and conserved motif showed that 16 CBF genes could be clustered into three subgroups; they all contained Motif 1 and Motif 5, and most of them only spanned one exon. The cis-acting elements analysis showed that some CBF genes might be involved in hormone and abiotic stress responsiveness. In addition, CBF genes exhibited tissue expression specificity. High expressions of ApseCBF1, ApseCBF3, AtruCBF1, AtruCBF4, AtruCBF6, AtruCBF7, and ApseCBF3, ApseCBF4, ApseCBF5 were detected on exposure to low temperature for 3 h and 24 h. Low expressions of AtruCBF2, AtruCBF6, AtruCBF7 were detected under cold stress for 24 h, and AtruCBF3 and AtruCBF5 were always down-regulated under cold conditions. Taken together, comprehensive analysis will enhance our understanding of the potential functions of the CBF genes on cold resistance, thereby providing a reference for the introduction of Acer species in our country.

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Section: Discussionmentioning

confidence: 99%

Identification and Analysis of the CBF Gene Family in Three Species of Acer under Cold Stress

Zhao

Han

Cai

et al. 2023

IJMS

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“…Yang et al 2019; Ma et al 2020; Yu et al 2021; X. Li et al 2022). Notable exceptions to the Ty3-gypsy dominance have also been observed in cacao, grape, banana, and Cucumis sativus (Moisy et al 2008; Argout et al 2011; Castanera et al 2019; Pratama, Dwivany, and Nugrahapraja 2021).…”

Section: Resultsmentioning

confidence: 99%

Profiling genome-wide methylation in two maples: fine-scale approaches to detection with nanopore technology

McEvoy

Grady

Pauloski

et al. 2022

Preprint

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DNA methylation is critical to the regulation of transposable elements and gene expression. Traditional methods of methylation quantification rely on bisulfite conversion, which requires treatments to the DNA 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 long-reads. Hybrid and reference-guided assemblies were generated for two new Acer accessions: Acer negundo (65x nanopore and 111X Illumina) and Acer saccharum (93x nanopore and 148X Illumina). The nanopore 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 the new hybrid assemblies to generate four epigenomes. The abundance and distribution of genes (including those previously associated with abiotic stress response), repeats, and methylation contexts were examined and compared with those of recently characterized broadleaf tree species.

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“…To determine which genes these fragments are transcribed from, clean reads from quality control need to be matched to the reference genome. The clean reads are sequenced against the reference genome using HISAT2 ( , accessed on 6 October 2022) [ 64 , 65 ] to obtain information on the position of the reference genome or gene, as well as information on the. sequence characteristics specific to the sequenced sample.…”

Section: Methodsmentioning

confidence: 99%

Transcriptomics Profiling of Acer pseudosieboldianum Molecular Mechanism against Freezing Stress

Han

Zhang

et al. 2022

IJMS

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Low temperature is an important environmental factor that affects the growth and development of trees and leads to the introduction of failure in the genetic improvement of trees. Acer pseudosieboldianum is a tree species that is well-known for its bright red autumn leaf color. These trees are widely used in landscaping in northeast China. However, due to their poor cold resistance, introduced A. pseudosieboldianum trees suffer severe freezing injury in many introduced environments. To elucidate the physiological indicators and molecular mechanisms associated with freezing damage, we analyzed the physiological indicators and transcriptome of A. pseudosieboldianum, using kits and RNA-Seq technology. The mechanism of A. pseudosieboldianum in response to freezing stress is an important scientific question. In this study, we used the shoots of four-year-old A. pseudosieboldianum twig seedlings, and the physiological index and the transcriptome of A. pseudosieboldianum under low temperature stress were investigated. The results showed that more than 20,000 genes were detected in A. pseudosieboldianum under low temperature (4 °C) and freezing temperatures (−10 °C, −20 °C, −30 °C, and −40 °C). There were 2505, 6021, 5125, and 3191 differential genes (DEGs) between −10 °C, −20°C, −30°C, −40 °C, and CK (4 °C), respectively. Among these differential genes, 48 genes are involved in the MAPK pathway and 533 genes are involved in the glucose metabolism pathway. In addition, the important transcription factors (MYB, AP2/ERF, and WRKY) involved in freezing stress were activated under different degrees of freezing stress. A total of 10 sets of physiological indicators of A. pseudosieboldianum were examined, including the activities of five enzymes and the accumulation of five hormones. All of the physiological indicators except SOD and GSH-Px reached their maximum values at −30 °C. The enzyme activity of SOD was highest at −10 °C, and that of GSH-Px was highest at −20 °C. Our study is the first to provide a more comprehensive understanding of the differential genes (DEGs) involved in A. pseudosieboldianum under freezing stress at different temperatures at the transcriptome level. These results may help to clarify the molecular mechanism of cold tolerance of A. pseudosieboldianum and provide new insights and candidate genes for the genetic improvement of the freezing tolerance of A. pseudosieboldianum.

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Chromosome-Level Genome Assembly for Acer pseudosieboldianum and Highlights to Mechanisms for Leaf Color and Shape Change

Cited by 10 publications

References 103 publications

Identification and Analysis of the CBF Gene Family in Three Species of Acer under Cold Stress

Identification and Analysis of the CBF Gene Family in Three Species of Acer under Cold Stress

Profiling genome-wide methylation in two maples: fine-scale approaches to detection with nanopore technology

Transcriptomics Profiling of Acer pseudosieboldianum Molecular Mechanism against Freezing Stress

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