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McEvoy SL, Grady PGS, Pauloski N, O'Neill RJ, Wegrzyn JL. Profiling genome-wide methylation in two maples: Fine-scale approaches to detection with nanopore technology. Evol Appl 2024; 17:e13669. [PMID: 38633133 PMCID: PMC11022628 DOI: 10.1111/eva.13669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 02/04/2024] [Accepted: 02/12/2024] [Indexed: 04/19/2024] Open
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 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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Affiliation(s)
- Susan L. McEvoy
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
- Department of Forest SciencesUniversity of HelsinkiHelsinkiFinland
| | - Patrick G. S. Grady
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - Nicole Pauloski
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsConnecticutUSA
- Institute for Systems GenomicsUniversity of ConnecticutStorrsConnecticutUSA
| | - Rachel J. O'Neill
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsConnecticutUSA
- Institute for Systems GenomicsUniversity of ConnecticutStorrsConnecticutUSA
| | - Jill L. Wegrzyn
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
- Institute for Systems GenomicsUniversity of ConnecticutStorrsConnecticutUSA
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Chromosomal-level genome and multi-omics dataset provides new insights into leaf pigmentation in Acer palmatum. Int J Biol Macromol 2023; 227:93-104. [PMID: 36470439 DOI: 10.1016/j.ijbiomac.2022.11.303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/11/2022]
Abstract
Acer palmatum (A. palmatum), a deciduous shrub or small arbour which belongs to Acer of Aceraceae, is an excellent greening species as well as a beautiful ornamental plant. In this study, a high-quality chromosome-level reference genome for A. palmatum was constructed using Oxford Nanopore sequencing and Hi-C technology. The assembly genome was ∼745.78 Mb long with a contig N50 length of 3.20 Mb, and 95.30 % (710.71 Mb) of the assembly was anchored into 13 pseudochromosomes. A total of 28,559 protein-coding genes were obtained, ∼90.02 % (25,710) of which could be functionally annotated. The genomic evolutionary analysis revealed that A. palmatum is most closely related to A. yangbiense and A. truncatum, and underwent only an ancient gamma whole-genome duplication event. Despite lacking a recent independent WGD, 25,795 (90.32 %) genes of A. palmatum were duplicated, and the unique/expanded gene families were linked with genes involved in plant-pathogen interaction and several metabolic pathways, which might underpin adaptability. A combined genomic, transcriptomic, and metabolomic analysis related to the biosynthesis of anthocyanin in leaves during the different season were characterized. The results indicate that the dark-purple colouration of the leaves in spring was caused by a high amount of anthocyanins, especially delphinidin and its derivatives; and the red colouration of the leaves in autumn by a high amount of cyanidin 3-O-glucoside. In conclusion, these valuable multi-omic resources offer important foundations to explore the molecular regulation mechanism in leaf colouration and also provide a platform for the scientific and efficient utilization of A. palmatum.
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Linscott TM, González-González A, Hirano T, Parent CE. De novo genome assembly and genome skims reveal LTRs dominate the genome of a limestone endemic Mountainsnail (Oreohelix idahoensis). BMC Genomics 2022; 23:796. [PMID: 36460988 PMCID: PMC9719178 DOI: 10.1186/s12864-022-09000-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/10/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Calcareous outcrops, rocky areas composed of calcium carbonate (CaCO3), often host a diverse, specialized, and threatened biomineralizing fauna. Despite the repeated evolution of physiological and morphological adaptations to colonize these mineral rich substrates, there is a lack of genomic resources for calcareous rock endemic species. This has hampered our ability to understand the genomic mechanisms underlying calcareous rock specialization and manage these threatened species. RESULTS Here, we present a new draft genome assembly of the threatened limestone endemic land snail Oreohelix idahoensis and genome skim data for two other Oreohelix species. The O. idahoensis genome assembly (scaffold N50: 404.19 kb; 86.6% BUSCO genes) is the largest (~ 5.4 Gb) and most repetitive mollusc genome assembled to date (85.74% assembly size). The repetitive landscape was unusually dominated by an expansion of long terminal repeat (LTR) transposable elements (57.73% assembly size) which have shaped the evolution genome size, gene composition through retrotransposition of host genes, and ectopic recombination. Genome skims revealed repeat content is more than 2-3 fold higher in limestone endemic O. idahoensis compared to non-calcareous Oreohelix species. Gene family size analysis revealed stress and biomineralization genes have expanded significantly in the O. idahoensis genome. CONCLUSIONS Hundreds of threatened land snail species are endemic to calcareous rock regions but there are very few genomic resources available to guide their conservation or determine the genomic architecture underlying CaCO3 resource specialization. Our study provides one of the first high quality draft genomes of a calcareous rock endemic land snail which will serve as a foundation for the conservation genomics of this threatened species and for other groups. The high proportion and activity of LTRs in the O. idahoensis genome is unprecedented in molluscan genomics and sheds new light how transposable element content can vary across molluscs. The genomic resources reported here will enable further studies of the genomic mechanisms underlying calcareous rock specialization and the evolution of transposable element content across molluscs.
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Affiliation(s)
- T. Mason Linscott
- grid.266456.50000 0001 2284 9900Department of Biological Sciences, University of Idaho, Moscow, ID USA ,grid.266456.50000 0001 2284 9900Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID USA
| | - Andrea González-González
- grid.15276.370000 0004 1936 8091Department of Biology, University of Florida, Gainesville, Florida USA
| | - Takahiro Hirano
- grid.69566.3a0000 0001 2248 6943Center for Northeast Asian Studies, Tohoku University, Sendai, Miyagi Japan
| | - Christine E. Parent
- grid.266456.50000 0001 2284 9900Department of Biological Sciences, University of Idaho, Moscow, ID USA ,grid.266456.50000 0001 2284 9900Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID USA
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Bhowmick S, Jing T, Wang W, Zhang EY, Zhang F, Yang Y. In Silico Protein Folding Prediction of COVID-19 Mutations and Variants. Biomolecules 2022; 12:1665. [PMID: 36359015 PMCID: PMC9688002 DOI: 10.3390/biom12111665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 08/27/2023] Open
Abstract
With its fast-paced mutagenesis, the SARS-CoV-2 Omicron variant has threatened many societies worldwide. Strategies for predicting mutagenesis such as the computational prediction of SARS-CoV-2 structural diversity and its interaction with the human receptor will greatly benefit our understanding of the virus and help develop therapeutics against it. We aim to use protein structure prediction algorithms along with molecular docking to study the effects of various mutations in the Receptor Binding Domain (RBD) of the SARS-CoV-2 and its key interactions with the angiotensin-converting enzyme 2 (ACE-2) receptor. The RBD structures of the naturally occurring variants of SARS-CoV-2 were generated from the WUHAN-Hu-1 using the trRosetta algorithm. Docking (HADDOCK) and binding analysis (PRODIGY) between the predicted RBD sequences and ACE-2 highlighted key interactions at the Receptor-Binding Motif (RBM). Further mutagenesis at conserved residues in the Original, Delta, and Omicron variants (P499S and T500R) demonstrated stronger binding and interactions with the ACE-2 receptor. The predicted T500R mutation underwent some preliminary tests in vitro for its binding and transmissibility in cells; the results correlate with the in-silico analysis. In summary, we suggest conserved residues P499 and T500 as potential mutation sites that could increase the binding affinity and yet do not exist in nature. This work demonstrates the use of the trRosetta algorithm to predict protein structure and future mutations at the RBM of SARS-CoV-2, followed by experimental testing for further efficacy verification. It is important to understand the protein structure and folding to help develop potential therapeutics.
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Affiliation(s)
| | | | | | | | | | - Yanmin Yang
- Department of Neurology and Neurological Sciences, School of Medicine, Stanford University, 1201 Welch Road, MSLS, P259, Stanford, CA 94305, USA
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Li X, Cai K, Han Z, Zhang S, Sun A, Xie Y, Han R, Guo R, Tigabu M, Sederoff R, Pei X, Zhao C, Zhao X. Chromosome-Level Genome Assembly for Acer pseudosieboldianum and Highlights to Mechanisms for Leaf Color and Shape Change. FRONTIERS IN PLANT SCIENCE 2022; 13:850054. [PMID: 35310631 PMCID: PMC8927880 DOI: 10.3389/fpls.2022.850054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Acer pseudosieboldianum (Pax) Komarov is an ornamental plant with prominent potential and is naturally distributed in Northeast China. Here, we obtained a chromosome-scale genome assembly of A. pseudosieboldianum combining HiFi and Hi-C data, and the final assembled genome size was 690.24 Mb and consisted of 287 contigs, with a contig N50 value of 5.7 Mb and a BUSCO complete gene percentage of 98.4%. Genome evolution analysis showed that an ancient duplication occurred in A. pseudosieboldianum. Phylogenetic analyses revealed that Aceraceae family could be incorporated into Sapindaceae, consistent with the present Angiosperm Phylogeny Group system. We further construct a gene-to-metabolite correlation network and identified key genes and metabolites that might be involved in anthocyanin biosynthesis pathways during leaf color change. Additionally, we identified crucial teosinte branched1, cycloidea, and proliferating cell factors (TCP) transcription factors that might be involved in leaf morphology regulation of A. pseudosieboldianum, Acer yangbiense and Acer truncatum. Overall, this reference genome is a valuable resource for evolutionary history studies of A. pseudosieboldianum and lays a fundamental foundation for its molecular breeding.
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Affiliation(s)
- Xiang Li
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
| | - Kewei Cai
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
| | - Zhiming Han
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
| | - Shikai Zhang
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
| | - Anran Sun
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
| | - Ying Xie
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
| | - Rui Han
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
| | - Ruixue Guo
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
| | - Mulualem Tigabu
- Southern Swedish Forest Research Centre, Faculty of Forest Science, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Ronald Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Xiaona Pei
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
| | - Chunli Zhao
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
| | - Xiyang Zhao
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
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McEvoy SL, Sezen UU, Trouern‐Trend A, McMahon SM, Schaberg PG, Yang J, Wegrzyn JL, Swenson NG. Strategies of tolerance reflected in two North American maple genomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1591-1613. [PMID: 34967059 PMCID: PMC9304320 DOI: 10.1111/tpj.15657] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/22/2021] [Indexed: 05/24/2023]
Abstract
The first chromosome‐scale assemblies for North American members of the Acer genus, sugar maple (Acer saccharum) and boxelder (Acer negundo), as well as transcriptomic evaluation of the abiotic stress response in A. saccharum are reported. This integrated study describes in‐depth aspects contributing to each species' approach to tolerance and applies current knowledge in many areas of plant genome biology with Acer physiology to help convey the genomic complexities underlying tolerance in broadleaf tree species.
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Affiliation(s)
- Susan L. McEvoy
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
| | - U. Uzay Sezen
- Smithsonian Environmental Research CenterEdgewaterMaryland21037USA
| | - Alexander Trouern‐Trend
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
| | - Sean M. McMahon
- Smithsonian Environmental Research CenterEdgewaterMaryland21037USA
| | - Paul G. Schaberg
- Forest ServiceU.S. Department of Agriculture, Northern Research StationBurlingtonVermont05405USA
| | - Jie Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMengla666303YunnanChina
| | - Jill L. Wegrzyn
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
| | - Nathan G. Swenson
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana46556USA
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