1
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Goel M, Campoy JA, Krause K, Baus LC, Sahu A, Sun H, Walkemeier B, Marek M, Beaudry R, Ruiz D, Huettel B, Schneeberger K. The vast majority of somatic mutations in plants are layer-specific. Genome Biol 2024; 25:194. [PMID: 39049052 PMCID: PMC11267851 DOI: 10.1186/s13059-024-03337-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Plant meristems are structured organs consisting of distinct layers of stem cells, which differentiate into new plant tissue. Mutations in meristematic layers can propagate into large sectors of the plant. However, the characteristics of meristematic mutations remain unclear, limiting our understanding of the genetic basis of somaclonal phenotypic variation. RESULTS Here, we analyse the frequency and distribution of somatic mutations in an apricot tree. We separately sequence the epidermis (developing from meristem layer 1) and the flesh (developing from meristem layer 2) of several fruits sampled across the entire tree. We find that most somatic mutations (> 90%) are specific to individual layers. Interestingly, layer 1 shows a higher mutation load than layer 2, implying different mutational dynamics between the layers. The distribution of somatic mutations follows the branching of the tree. This suggests that somatic mutations are propagated to developing branches through axillary meristems. In turn, this leads us to the unexpected observation that the genomes of layer 1 of distant branches are more similar to each other than to the genomes of layer 2 of the same branches. Finally, using single-cell RNA sequencing, we demonstrate that layer-specific mutations were only transcribed in the cells of the respective layers and can form the genetic basis of somaclonal phenotypic variation. CONCLUSIONS Here, we analyse the frequency and distribution of somatic mutations with meristematic origin. Our observations on the layer specificity of somatic mutations outline how they are distributed, how they propagate, and how they can impact clonally propagated crops.
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Affiliation(s)
- Manish Goel
- Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - José A Campoy
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Pomology, Estación Experimental de Aula Dei (EEAD), CSIC, Saragossa, 50059, Spain
| | - Kristin Krause
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Present address: Illumina Solutions Center Berlin, Berlin, Germany
| | - Lisa C Baus
- Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Anshupa Sahu
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Hequan Sun
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Present address: Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Birgit Walkemeier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Randy Beaudry
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - David Ruiz
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, Murcia, 30100, Spain
| | | | - Korbinian Schneeberger
- Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
- CEPLAS (Cluster of Excellence On Plant Sciences), Heinrich-Heine University, Düsseldorf, Germany.
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2
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Vo BT, Mas P, Johannes F. Time's up: Epigenetic clocks in plants. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102602. [PMID: 39024859 DOI: 10.1016/j.pbi.2024.102602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/30/2024] [Accepted: 06/26/2024] [Indexed: 07/20/2024]
Abstract
For over a decade, the animal field has led the way in using DNA methylation measurements to construct epigenetic clocks of aging. These clocks can predict organismal age with a level of accuracy that surpasses any other molecular proxy known to date. Evidence is finally emerging that epigenetic clocks also exist in plants. However, these clocks appear to differ from those in animals in some key aspects, including in their ability to measure time beyond the life span of an individual. Clock-like epigenetic changes can be found in plant circadian rhythms (scale: 24 h), during plant aging (scale: weeks/centuries), and across plant lineage evolution (scale: decades/millennia). Here, we provide a first classification of these different types of epigenetic clocks, highlight their main features, and discuss their biological basis.
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Affiliation(s)
- Binh Thanh Vo
- Plant Epigenomics, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Paloma Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain; Consejo Superior de Investigaciones Científicas (CSIC), 08028 Barcelona, Spain
| | - Frank Johannes
- Plant Epigenomics, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany.
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3
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Yu G, Zhang B, Chen Q, Huang Z, Zhang B, Wang K, Han J. Dynamic DNA methylation modifications in the cold stress response of cassava. Genomics 2024; 116:110871. [PMID: 38806102 DOI: 10.1016/j.ygeno.2024.110871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 05/21/2024] [Accepted: 05/25/2024] [Indexed: 05/30/2024]
Abstract
Cassava, a crucial tropical crop, faces challenges from cold stress, necessitating an exploration of its molecular response. Here, we investigated the role of DNA methylation in moderating the response to moderate cold stress (10 °C) in cassava. Using whole-genome bisulfite sequencing, we examined DNA methylation patterns in leaf blades and petioles under control conditions, 5 h, and 48 h of cold stress. Tissue-specific responses were observed, with leaf blades exhibiting subtle changes, while petioles displayed a pronounced decrease in methylation levels under cold stress. We identified cold stress-induced differentially methylated regions (DMRs) that demonstrated both tissue and treatment specificity. Importantly, these DMRs were enriched in genes with altered expression, implying functional relevance. The cold-response transcription factor ERF105 associated with DMRs emerged as a significant and conserved regulator across tissues and treatments. Furthermore, we investigated DNA methylation dynamics in transposable elements, emphasizing the sensitivity of MITEs with bHLH binding motifs to cold stress. These findings provide insights into the epigenetic regulation of response to cold stress in cassava, contributing to an understanding of the molecular mechanisms underlying stress adaptation in this tropical plant.
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Affiliation(s)
- Guangrun Yu
- School of Life Sciences, Nantong University, Nantong 226019, China; Xinglin College, Nantong University, Qidong 226236, China
| | - Baowang Zhang
- Qingdao Smart Rural Development Service Center, Qingdao 266000, China
| | - Qi Chen
- School of Life Sciences, Nantong University, Nantong 226019, China; Xinglin College, Nantong University, Qidong 226236, China
| | - Zequan Huang
- Xinglin College, Nantong University, Qidong 226236, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong 226019, China.
| | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong 226019, China.
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4
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Shao L, Jin S, Chen J, Yang G, Fan R, Zhang Z, Deng Q, Han J, Ma X, Dong Z, Lu H, Hu W, Wang K, Hu L, Shen Z, Huang S, Zhao T, Guan X, Hu Y, Zhang T, Fang L. High-quality genomes of Bombax ceiba and Ceiba pentandra provide insights into the evolution of Malvaceae species and differences in their natural fiber development. PLANT COMMUNICATIONS 2024; 5:100832. [PMID: 38321741 PMCID: PMC11121743 DOI: 10.1016/j.xplc.2024.100832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/15/2023] [Accepted: 02/01/2024] [Indexed: 02/08/2024]
Abstract
Members of the Malvaceae family, including Corchorus spp., Gossypium spp., Bombax spp., and Ceiba spp., are important sources of natural fibers. In the past decade, the genomes of several Malvaceae species have been assembled; however, the evolutionary history of Malvaceae species and the differences in their fiber development remain to be clarified. Here, we report the genome assembly and annotation of two natural fiber plants from the Malvaceae, Bombax ceiba and Ceiba pentandra, whose assembled genome sizes are 783.56 Mb and 1575.47 Mb, respectively. Comparative analysis revealed that whole-genome duplication and Gypsy long terminal repeat retroelements have been the major causes of differences in chromosome number (2n = 14 to 2n = 96) and genome size (234 Mb to 2676 Mb) among Malvaceae species. We also used comparative genomic analyses to reconstruct the ancestral Malvaceae karyotype with 11 proto-chromosomes, providing new insights into the evolutionary trajectories of Malvaceae species. MYB-MIXTA-like 3 is relatively conserved among the Malvaceae and functions in fiber cell-fate determination in the epidermis. It appears to perform this function in any tissue where it is expressed, i.e. in fibers on the endocarp of B. ceiba and in ovule fibers of cotton. We identified a structural variation in a cellulose synthase gene and a higher copy number of cellulose synthase-like genes as possible causes of the finer, less spinnable, weaker fibers of B. ceiba. Our study provides two high-quality genomes of natural fiber plants and offers insights into the evolution of Malvaceae species and differences in their natural fiber formation and development through multi-omics analysis.
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Affiliation(s)
- Lei Shao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Shangkun Jin
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jinwen Chen
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Guangsui Yang
- Tropical Crop Germplasm Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Rui Fan
- Spices and Beverages Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China
| | - Zhiyuan Zhang
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Qian Deng
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jin Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiaowei Ma
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zeyu Dong
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hejun Lu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Wanying Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Lisong Hu
- Spices and Beverages Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China
| | - Zhen Shen
- Tropical Crop Germplasm Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Surong Huang
- Tropical Crop Germplasm Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China.
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5
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Ritter EJ, Cousins P, Quigley M, Kile A, Kenchanmane Raju SK, Chitwood DH, Niederhuth C. From buds to shoots: insights into grapevine development from the Witch's Broom bud sport. BMC PLANT BIOLOGY 2024; 24:283. [PMID: 38627633 PMCID: PMC11020879 DOI: 10.1186/s12870-024-04992-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Bud sports occur spontaneously in plants when new growth exhibits a distinct phenotype from the rest of the parent plant. The Witch's Broom bud sport occurs occasionally in various grapevine (Vitis vinifera) varieties and displays a suite of developmental defects, including dwarf features and reduced fertility. While it is highly detrimental for grapevine growers, it also serves as a useful tool for studying grapevine development. We used the Witch's Broom bud sport in grapevine to understand the developmental trajectories of the bud sports, as well as the potential genetic basis. We analyzed the phenotypes of two independent cases of the Witch's Broom bud sport, in the Dakapo and Merlot varieties of grapevine, alongside wild type counterparts. To do so, we quantified various shoot traits, performed 3D X-ray Computed Tomography on dormant buds, and landmarked leaves from the samples. We also performed Illumina and Oxford Nanopore sequencing on the samples and called genetic variants using these sequencing datasets. RESULTS The Dakapo and Merlot cases of Witch's Broom displayed severe developmental defects, with no fruit/clusters formed and dwarf vegetative features. However, the Dakapo and Merlot cases of Witch's Broom studied were also phenotypically different from one another, with distinct differences in bud and leaf development. We identified 968-974 unique genetic mutations in our two Witch's Broom cases that are potential causal variants of the bud sports. Examining gene function and validating these genetic candidates through PCR and Sanger-sequencing revealed one strong candidate mutation in Merlot Witch's Broom impacting the gene GSVIVG01008260001. CONCLUSIONS The Witch's Broom bud sports in both varieties studied had dwarf phenotypes, but the two instances studied were also vastly different from one another and likely have distinct genetic bases. Future work on Witch's Broom bud sports in grapevine could provide more insight into development and the genetic pathways involved in grapevine.
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Affiliation(s)
- Eleanore J Ritter
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | | | - Michelle Quigley
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
- Center for Quantitative Imaging, Institute of Energy and the Environment, Penn State University, State College, PA, USA
| | - Aidan Kile
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Sunil K Kenchanmane Raju
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Center for Genomics and Systems Biology, New York University, Manhattan, NY, USA
| | - Daniel H Chitwood
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, MI, USA
| | - Chad Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
- Corteva, Inc. Indianapolis, IN, USA.
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6
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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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7
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Vanden Broeck A, Meese T, Verschelde P, Cox K, Heinze B, Deforce D, De Meester E, Van Nieuwerburgh F. Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar. BMC Biol 2024; 22:30. [PMID: 38317114 PMCID: PMC10845628 DOI: 10.1186/s12915-024-01816-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Despite the increasing number of epigenomic studies in plants, little is known about the forces that shape the methylome in long-lived woody perennials. The Lombardy poplar offers an ideal opportunity to investigate the impact of the individual environmental history of trees on the methylome. RESULTS We present the results of three interconnected experiments on Lombardy poplar. In the first experiment, we investigated methylome variability during a growing season and across vegetatively reproduced generations. We found that ramets collected over Europe and raised in common conditions have stable methylomes in symmetrical CG-contexts. In contrast, seasonal dynamics occurred in methylation patterns in CHH context. In the second experiment, we investigated whether methylome patterns of plants grown in a non-parental environment correlate with the parental climate. We did not observe a biological relevant pattern that significantly correlates with the parental climate. Finally, we investigated whether the parental environment has persistent carry-over effects on the vegetative offspring's phenotype. We combined new bud set observations of three consecutive growing seasons with former published bud set data. Using a linear mixed effects analysis, we found a statistically significant but weak short-term, parental carry-over effect on the timing of bud set. However, this effect was negligible compared to the direct effects of the offspring environment. CONCLUSIONS Genome-wide cytosine methylation patterns in symmetrical CG-context are stable in Lombardy poplar and appear to be mainly the result of random processes. In this widespread poplar clone, methylation patterns in CG-context can be used as biomarkers to infer a common ancestor and thus to investigate the recent environmental history of a specific Lombardy poplar. The Lombardy poplar shows high phenotypic plasticity in a novel environment which enabled this clonal tree to adapt and survive all over the temperate regions of the world.
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Affiliation(s)
- An Vanden Broeck
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium.
| | - Tim Meese
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Pieter Verschelde
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium
| | - Karen Cox
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium
| | - Berthold Heinze
- Department of Forest Growth, Silviculture and Genetics, Austrian Federal Research Centre for Forests (BFW), Vienna, Austria
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Ellen De Meester
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
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8
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Hernández-Lao T, Tienda-Parrilla M, Labella-Ortega M, Guerrero-Sánchez VM, Rey MD, Jorrín-Novo JV, Castillejo-Sánchez MÁ. Proteomic and Metabolomic Analysis of the Quercus ilex-Phytophthora cinnamomi Pathosystem Reveals a Population-Specific Response, Independent of Co-Occurrence of Drought. Biomolecules 2024; 14:160. [PMID: 38397397 PMCID: PMC10887186 DOI: 10.3390/biom14020160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/18/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Holm oak (Quercus ilex) is considered to be one of the major structural elements of Mediterranean forests and the agrosilvopastoral Spanish "dehesa", making it an outstanding example of ecological and socioeconomic sustainability in forest ecosystems. The exotic Phytophthora cinnamomi is one of the most aggressive pathogens of woody species and, together with drought, is considered to be one of the main drivers of holm oak decline. The effect of and response to P. cinnamomi inoculation were studied in the offspring of mother trees from two Andalusian populations, Cordoba and Huelva. At the two locations, acorns collected from both symptomatic (damaged) and asymptomatic (apparently healthy) trees were sampled. Damage symptoms, mortality, and chlorophyll fluorescence were evaluated in seedlings inoculated under humid and drought conditions. The effect and response depended on the population and were more apparent in Huelva than in Cordoba. An integrated proteomic and metabolomic analysis revealed the involvement of different metabolic pathways in response to the pathogen in both populations, including amino acid metabolism pathways in Huelva, and terpenoid and flavonoid biosynthesis in Cordoba. However, no differential response was observed between seedlings inoculated under humid and drought conditions. A protective mechanism of the photosynthetic apparatus was activated in response to defective photosynthetic activity in inoculated plants, which seemed to be more efficient in the Cordoba population. In addition, enzymes and metabolites of the phenylpropanoid and flavonoid biosynthesis pathways may have conferred higher resistance in the Cordoba population. Some enzymes are proposed as markers of resilience, among which glyoxalase I, glutathione reductase, thioredoxin reductase, and cinnamyl alcohol dehydrogenase are candidates.
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Affiliation(s)
| | | | | | | | | | - Jesús V. Jorrín-Novo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain; (T.H.-L.); (M.T.-P.); (M.L.-O.); (V.M.G.-S.); (M.-D.R.)
| | - María Ángeles Castillejo-Sánchez
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain; (T.H.-L.); (M.T.-P.); (M.L.-O.); (V.M.G.-S.); (M.-D.R.)
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9
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Xiang X, Zhou X, Zi H, Wei H, Cao D, Zhang Y, Zhang L, Hu J. Populus cathayana genome and population resequencing provide insights into its evolution and adaptation. HORTICULTURE RESEARCH 2024; 11:uhad255. [PMID: 38274646 PMCID: PMC10809908 DOI: 10.1093/hr/uhad255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/20/2023] [Indexed: 01/27/2024]
Abstract
Populus cathayana Rehder, an indigenous poplar species of ecological and economic importance, is widely distributed in a high-elevation range from southwest to northeast China. Further development of this species as a sustainable poplar resource has been hindered by a lack of genome information the at the population level. Here, we produced a chromosome-level genome assembly of P. cathayana, covering 406.55 Mb (scaffold N50 = 20.86 Mb) and consisting of 19 chromosomes, with 35 977 protein-coding genes. Subsequently, we made a genomic variation atlas of 438 wild individuals covering 36 representative geographic areas of P. cathayana, which were divided into four geographic groups. It was inferred that the Northwest China regions served as the genetic diversity centers and a population bottleneck happened during the history of P. cathayana. By genotype-environment association analysis, 947 environment-association loci were significantly associated with temperature, solar radiation, precipitation, and altitude variables. We identified local adaptation genes involved in DNA repair and UV radiation response, among which UVR8, HY5, and CUL4 had key roles in high-altitude adaptation of P. cathayana. Predictions of adaptive potential under future climate conditions showed that P. cathayana populations in areas with drastic climate change were anticipated to have greater maladaptation risk. These results provide comprehensive insights for understanding wild poplar evolution and optimizing adaptive potential in molecular breeding.
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Affiliation(s)
- Xiaodong Xiang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Xinglu Zhou
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Hailing Zi
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Hantian Wei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Demei Cao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yahong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
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10
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Zhou R, Jenkins JW, Zeng Y, Shu S, Jang H, Harding SA, Williams M, Plott C, Barry KW, Koriabine M, Amirebrahimi M, Talag J, Rajasekar S, Grimwood J, Schmitz RJ, Dawe RK, Schmutz J, Tsai CJ. Haplotype-resolved genome assembly of Populus tremula × P. alba reveals aspen-specific megabase satellite DNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1003-1017. [PMID: 37675609 DOI: 10.1111/tpj.16454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/08/2023]
Abstract
Populus species play a foundational role in diverse ecosystems and are important renewable feedstocks for bioenergy and bioproducts. Hybrid aspen Populus tremula × P. alba INRA 717-1B4 is a widely used transformation model in tree functional genomics and biotechnology research. As an outcrossing interspecific hybrid, its genome is riddled with sequence polymorphisms which present a challenge for sequence-sensitive analyses. Here we report a telomere-to-telomere genome for this hybrid aspen with two chromosome-scale, haplotype-resolved assemblies. We performed a comprehensive analysis of the repetitive landscape and identified both tandem repeat array-based and array-less centromeres. Unexpectedly, the most abundant satellite repeats in both haplotypes lie outside of the centromeres, consist of a 147 bp monomer PtaM147, frequently span >1 megabases, and form heterochromatic knobs. PtaM147 repeats are detected exclusively in aspens (section Populus) but PtaM147-like sequences occur in LTR-retrotransposons of closely related species, suggesting their origin from the retrotransposons. The genomic resource generated for this transformation model genotype has greatly improved the design and analysis of genome editing experiments that are highly sensitive to sequence polymorphisms. The work should motivate future hypothesis-driven research to probe into the function of the abundant and aspen-specific PtaM147 satellite DNA.
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Affiliation(s)
- Ran Zhou
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Jerry W Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | - Yibing Zeng
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Shengqiang Shu
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Hosung Jang
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Scott A Harding
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Melissa Williams
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | | | - Kerrie W Barry
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Maxim Koriabine
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Mojgan Amirebrahimi
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Shanmugam Rajasekar
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Chung-Jui Tsai
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
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11
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Borkhert EV, Pushkova EN, Nasimovich YA, Kostina MV, Vasilieva NV, Murataev RA, Novakovskiy RO, Dvorianinova EM, Povkhova LV, Zhernova DA, Turba AA, Sigova EA, Snezhkina AV, Kudryavtseva AV, Bolsheva NL, Krasnov GS, Dmitriev AA, Melnikova NV. Sex-determining region complements traditionally used in phylogenetic studies nuclear and chloroplast sequences in investigation of Aigeiros Duby and Tacamahaca Spach poplars (genus Populus L., Salicaceae). FRONTIERS IN PLANT SCIENCE 2023; 14:1204899. [PMID: 37860260 PMCID: PMC10582643 DOI: 10.3389/fpls.2023.1204899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/07/2023] [Indexed: 10/21/2023]
Abstract
Members of the genus Populus L. play an important role in the formation of forests in the northern hemisphere and are used in urban landscaping and timber production. Populus species of closely related sections show extensive hybridization. Therefore, the systematics of the genus is rather complicated, especially for poplars of hybrid origin. We aimed to assess the efficiency of application of the sex-determining region (SDR) in addition to the nuclear and chloroplast genome loci traditionally used in phylogenetic studies of poplars to investigate relationships in sections Aigeiros Duby and Tacamahaca Spach. Targeted deep sequencing of NTS 5S rDNA, ITS, DSH 2, DSH 5, DSH 8, DSH 12, DSH 29, 6, 15, 16, X18, trnG-psbK-psbI, rps2-rpoC2, rpoC2-rpoC1, as well as SDR and ARR17 gene was performed for 379 poplars. The SDR and ARR17 gene together with traditionally used multicopy and single-copy loci of nuclear and chloroplast DNA allowed us to obtain a clustering that is most consistent with poplar systematics based on morphological data and to shed light on several controversial hypotheses about the origin of the studied taxa (for example, the inexpediency of separating P. koreana, P. maximowiczii, and P. suaveolens into different species). We present a scheme of relationships between species and hybrids of sections Aigeiros and Tacamahaca based on molecular genetic, morphological, and geographical data. The geographical proximity of species and, therefore, the possibility of hybridization between them appear to be more important than the affiliation of species to the same section. We speculate that sections Aigeiros and Tacamahaca are distinguished primarily on an ecological principle (plain and mountain poplars) rather than on a genetic basis. Joint analysis of sequencing data for the SDR and chloroplast genome loci allowed us to determine the ancestors of P. × petrovskoe - P. laurifolia (female tree) × P. × canadensis (male tree), and P. × rasumovskoe - P. nigra (female tree) × P. suaveolens (male tree). Thus, the efficiency of using the SDR for the study of poplars of sections Aigeiros and Tacamahaca and the prospects of its use for the investigation of species of the genus Populus were shown.
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Affiliation(s)
- Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yuri A. Nasimovich
- State Environmental Protection Budgetary Institution of Moscow “Mospriroda”, Moscow, Russia
| | - Marina V. Kostina
- Institute of Biology and Chemistry, Moscow Pedagogical State University, Moscow, Russia
| | | | - Ramil A. Murataev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Daiana A. Zhernova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anastasia A. Turba
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | | | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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12
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Mérai Z, Xu F, Musilek A, Ackerl F, Khalil S, Soto-Jiménez LM, Lalatović K, Klose C, Tarkowská D, Turečková V, Strnad M, Mittelsten Scheid O. Phytochromes mediate germination inhibition under red, far-red, and white light in Aethionema arabicum. PLANT PHYSIOLOGY 2023; 192:1584-1602. [PMID: 36861637 PMCID: PMC10231562 DOI: 10.1093/plphys/kiad138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 11/22/2022] [Accepted: 12/19/2022] [Indexed: 06/01/2023]
Abstract
The view on the role of light during seed germination stems mainly from studies with Arabidopsis (Arabidopsis thaliana), where light is required to initiate this process. In contrast, white light is a strong inhibitor of germination in other plants, exemplified by accessions of Aethionema arabicum, another member of Brassicaceae. Their seeds respond to light with gene expression changes of key regulators converse to that of Arabidopsis, resulting in opposite hormone regulation and prevention of germination. However, the photoreceptors involved in this process in A. arabicum remain unknown. Here, we screened a mutant collection of A. arabicum and identified koy-1, a mutant that lost light inhibition of germination due to a deletion in the promoter of HEME OXYGENASE 1, the gene for a key enzyme in the biosynthesis of the phytochrome chromophore. koy-1 seeds were unresponsive to red- and far-red light and hyposensitive under white light. Comparison of hormone and gene expression between wild type and koy-1 revealed that very low light fluence stimulates germination, while high irradiance of red and far-red light is inhibitory, indicating a dual role of phytochromes in light-regulated seed germination. The mutation also affects the ratio between the 2 fruit morphs of A. arabicum, suggesting that light reception via phytochromes can fine-tune several parameters of propagation in adaptation to conditions in the habitat.
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Affiliation(s)
- Zsuzsanna Mérai
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Fei Xu
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Andreas Musilek
- Technical University of Vienna, TRIGA Center Atominstitut, Vienna 1020, Austria
| | - Florian Ackerl
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Sarhan Khalil
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Luz Mayela Soto-Jiménez
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Katarina Lalatović
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Cornelia Klose
- Institute of Biology II, University of Freiburg, Freiburg D-79104, Germany
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Palacký University & Institute of Experimental Botany, Czech Academy of Sciences, Olomouc CZ-78371, Czech Republic
| | - Veronika Turečková
- Laboratory of Growth Regulators, Palacký University & Institute of Experimental Botany, Czech Academy of Sciences, Olomouc CZ-78371, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Palacký University & Institute of Experimental Botany, Czech Academy of Sciences, Olomouc CZ-78371, Czech Republic
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
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13
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Li J, Han F, Yuan T, Li W, Li Y, Wu HX, Wei H, Niu S. The methylation landscape of giga-genome and the epigenetic timer of age in Chinese pine. Nat Commun 2023; 14:1947. [PMID: 37029142 PMCID: PMC10082083 DOI: 10.1038/s41467-023-37684-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 03/27/2023] [Indexed: 04/09/2023] Open
Abstract
Epigenetics has been revealed to play a crucial role in the long-term memory in plants. However, little is known about whether the epigenetic modifications occur with age progressively in conifers. Here, we present the single-base resolution DNA methylation landscapes of the 25-gigabase Chinese pine (Pinus tabuliformis) genome at different ages. The result shows that DNA methylation is closely coupled with the regulation of gene transcription. The age-dependent methylation profile with a linearly increasing trend is the most significant pattern of DMRs between ages. Two segments at the five-prime end of the first ultra-long intron in DAL1, a conservative age biomarker in conifers, shows a gradual decline of CHG methylation as the age increased, which is highly correlated with its expression profile. Similar high correlation is also observed in nine other age marker genes. Our results suggest that DNA methylation serves as an important epigenetic signature of developmental age in conifers.
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Affiliation(s)
- Jiang Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, PR China
| | - Fangxu Han
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, PR China
| | - Tongqi Yuan
- College of Material Science and Technology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Wei Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, PR China
| | - Yue Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, PR China
| | - Harry X Wu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Linnaeus väg 6, SE-901 83, Umeå, Sweden
- CSIRO National Research Collection Australia, Black Mountain Laboratory, Canberra, ACT, 2601, Australia
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Shihui Niu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, PR China.
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14
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Tomimoto S, Satake A. Modelling somatic mutation accumulation and expansion in a long-lived tree with hierarchical modular architecture. J Theor Biol 2023; 565:111465. [PMID: 36931388 DOI: 10.1016/j.jtbi.2023.111465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023]
Abstract
In a long-lived organism with a modular architecture, such as trees, somatic mutations accumulate throughout the long lifespan and result in genetic mosaicism in each module within the same individual. In recent years, next-generation sequencing technology has provided a snapshot of such intra-organismal genetic variability. However, the dynamic processes underlying the accumulation and expansion of somatic mutations during the growth remain poorly understood. In this study, we constructed a model to describe these processes in a form that can be applied to a real tree. Given that the proliferation dynamics of meristematic cells vary across plant species, multiple possible processes for elongation and branching were comprehensively expressed in our model. Using published data from a poplar tree, we compared the prediction of the models with the observation and explained the cell lineage dynamics underlying somatic mutations accumulation that were not evident from the snapshot of the sequenced data. We showed that the somatic genetic drift during growth increases inter-meristem mosaicism, resulting in genetically distinct branches and less integrity within an individual tree. We also showed that the somatic genetic drift during branching leads to the mutation accumulation pattern that does not reflect the tree topology. Our modelling framework can help interpret and provide further insights into the empirical findings of genetic mosaicism in long-lived trees.
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Affiliation(s)
- Sou Tomimoto
- Graduate School of Systems Life Science, Kyushu University, Fukuoka 819-0395, Japan.
| | - Akiko Satake
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
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15
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Liu J, Zhao G, Geng J, Geng Z, Dou H, Liu X, An Z, Zhang H, Wang Y. Genome-wide analysis of mutations induced by carbon ion beam irradiation in cotton. FRONTIERS IN PLANT SCIENCE 2023; 14:1056662. [PMID: 36875607 PMCID: PMC9978701 DOI: 10.3389/fpls.2023.1056662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Carbon ion beam (CIB) irradiation is a powerful way to create mutations in animals, plants, and microbes. Research on the mutagenic effects and molecular mechanisms of radiation is an important and multidisciplinary issue. However, the effect of carbon ion radiation on cotton is uncertain. In this study, five different upland cotton varieties and five CIB doses were used to identify the suitable irradiation dose for cotton. Three mutagenized progeny cotton lines from the wild-type Ji172 were re-sequenced. The effect of half-lethal dose on mutation induction indicated that 200 Gy with LETmax of 226.9 KeV/μm was the most effective heavy-ion dose for upland cotton and a total of 2,959-4,049 single-base substitutions (SBSs) and 610-947 insertion-deletion polymorphisms (InDels) were identified among the three mutants by resequencing. The ratio of transition to transversion in the three mutants ranged from 2.16 to 2.24. Among transversion events, G:C>C:G was significantly less common than three other types of mutations (A:T>C:G, A:T>T:A, and G:C>T:A). The proportions of six types of mutations were very similar in each mutant. The distributions of identified SBSs and InDels were similar with unevenly distributed across the genome and chromosomes. Some chromosomes had significantly more SBSs than others, and there were "hotspot" mutation regions at the ends of chromosomes. Overall, our study revealed a profile of cotton mutations caused by CIB irradiation, and these data could provide valuable information for cotton mutation breeding.
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Affiliation(s)
- Jianguang Liu
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Guiyuan Zhao
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Jinpeng Geng
- School of Science, Hebei University of Technology, Tianjin, China
| | - Zhao Geng
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Haikuan Dou
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Xu Liu
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Zetong An
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Hanshuang Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Yongqiang Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
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16
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Zhou J, Xiao L, Huang R, Song F, Li L, Li P, Fang Y, Lu W, Lv C, Quan M, Zhang D, Du Q. Local diversity of drought resistance and resilience in Populus tomentosa correlates with the variation of DNA methylation. PLANT, CELL & ENVIRONMENT 2023; 46:479-497. [PMID: 36385613 DOI: 10.1111/pce.14490] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/25/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Little information is known about DNA methylation variation in shaping environment-specific drought resistance and resilience for tree adaptation. In this study, we leveraged RNA sequencing and whole-genome bisulfite sequencing data to dissect the distinction of epigenetic regulation under drought stress and rewater condition of Populus tomentosa accessions from three geographical regions. We demonstrated low resistance and high resilience for accessions from South. Non-CG methylation levels in promoter regions of Southern accessions were lower than accessions from higher latitudes and negatively regulated gene expression. CHH context methylation was more sensitive to drought stress, and the geographical-specific differentially methylated regions were scarcely changed by environmental fluctuation. We identified 60 conserved hub genes within the co-expression networks that correlate with photosynthetic and stomatal morphological traits. Epigenome-wide association studies and genome-wide association studies of these 60 hub genes revealed the interdependency between genetic and epigenetic variation in GATA9 and LECRK-VIII.2, which was associated with stomatal morphology and chlorophyll content. The natural epigenetic variation in GATA9 was also faithfully transmitted to progenies in two family-based F1 populations. This study indicates a functional relationship of DNA methylation diversity with drought resistance and resilience which offers new insights into plants' local adaptation to a stressful environment.
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Affiliation(s)
- Jiaxuan Zhou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Liang Xiao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Rui Huang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Fangyuan Song
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Lianzheng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Peng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Yuanyuan Fang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Wenjie Lu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Chenfei Lv
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Mingyang Quan
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Deqiang Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Qingzhang Du
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
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17
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Abeyratne CR, Macaya-Sanz D, Zhou R, Barry KW, Daum C, Haiby K, Lipzen A, Stanton B, Yoshinaga Y, Zane M, Tuskan GA, DiFazio SP. High-resolution mapping reveals hotspots and sex-biased recombination in Populus trichocarpa. G3 (BETHESDA, MD.) 2023; 13:jkac269. [PMID: 36250890 PMCID: PMC9836356 DOI: 10.1093/g3journal/jkac269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/28/2022] [Indexed: 12/14/2022]
Abstract
Fine-scale meiotic recombination is fundamental to the outcome of natural and artificial selection. Here, dense genetic mapping and haplotype reconstruction were used to estimate recombination for a full factorial Populus trichocarpa cross of 7 males and 7 females. Genomes of the resulting 49 full-sib families (N = 829 offspring) were resequenced, and high-fidelity biallelic SNP/INDELs and pedigree information were used to ascertain allelic phase and impute progeny genotypes to recover gametic haplotypes. The 14 parental genetic maps contained 1,820 SNP/INDELs on average that covered 376.7 Mb of physical length across 19 chromosomes. Comparison of parental and progeny haplotypes allowed fine-scale demarcation of cross-over regions, where 38,846 cross-over events in 1,658 gametes were observed. Cross-over events were positively associated with gene density and negatively associated with GC content and long-terminal repeats. One of the most striking findings was higher rates of cross-overs in males in 8 out of 19 chromosomes. Regions with elevated male cross-over rates had lower gene density and GC content than windows showing no sex bias. High-resolution analysis identified 67 candidate cross-over hotspots spread throughout the genome. DNA sequence motifs enriched in these regions showed striking similarity to those of maize, Arabidopsis, and wheat. These findings, and recombination estimates, will be useful for ongoing efforts to accelerate domestication of this and other biomass feedstocks, as well as future studies investigating broader questions related to evolutionary history, perennial development, phenology, wood formation, vegetative propagation, and dioecy that cannot be studied using annual plant model systems.
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Affiliation(s)
| | - David Macaya-Sanz
- Department of Forest Ecology & Genetics, CIFOR-INIA, CSIC, Madrid 28040, Spain
| | - Ran Zhou
- Warnell School of Forestry and Natural Resources, Department of Genetics, and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Kerrie W Barry
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Christopher Daum
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | | | - Anna Lipzen
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | | | - Yuko Yoshinaga
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Matthew Zane
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Gerald A Tuskan
- Biosciences Division, Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA
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18
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Ji Y, Chen X, Lin S, Traw MB, Tian D, Yang S, Wang L, Huang J. High level of somatic mutations detected in a diploid banana wild relative Musa basjoo. Mol Genet Genomics 2023; 298:67-77. [PMID: 36283995 DOI: 10.1007/s00438-022-01959-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 09/27/2022] [Indexed: 01/10/2023]
Abstract
Plants are thought to lack an early segregating germline and often retain both asexual and sexual reproduction, both of which may allow somatic mutations to enter the gametes or clonal progeny, and thereby impact plant evolution. It is yet unclear how often these somatic mutations occur during plant development and what proportion is transmitted to their sexual or cloned offspring. Asexual "seedless" propagation has contributed greatly to the breeding in many fruit crops, such as citrus, grapes and bananas. Whether plants in these lineages experience substantial somatic mutation accumulation is unknown. To estimate the somatic mutation accumulation and inheritance among a clonal population of plant, here we assess somatic mutation accumulation in Musa basjoo, a diploid banana wild relative, using 30 whole-genome resequenced samples collected from five structures, including leaves, sheaths, panicle, roots and underground rhizome connecting three clonal individuals. We observed 18.5 high proportion de novo somatic mutations on average between each two adjacent clonal suckers, equivalent to ~ 2.48 × 10-8 per site per asexual generation, higher than the per site per sexual generation rates (< 1 × 10-8) reported in Arabidopsis and peach. Interestingly, most of these inter-ramet somatic mutations were shared simultaneously in different tissues of the same individual with a high level of variant allele fractions, suggesting that these somatic mutations arise early in ramet development and that each individual may develop only from a few apical stem cells. These results thus suggest substantial mutation accumulation in a wild relative of banana. Our work reveals the significance of somatic mutation in Musa basjoo genetics variations and contribute to the trait improvement breeding of bananas and other asexual clonal crops.
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Affiliation(s)
- Yilun Ji
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xiaonan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Shengqiu Lin
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Milton Brian Traw
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.
| | - Ju Huang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
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19
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Evo-devo perspectives on cancer. Essays Biochem 2022; 66:797-815. [PMID: 36250956 DOI: 10.1042/ebc20220041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 12/13/2022]
Abstract
The integration of evolutionary and developmental approaches into the field of evolutionary developmental biology has opened new areas of inquiry- from understanding the evolution of development and its underlying genetic and molecular mechanisms to addressing the role of development in evolution. For the last several decades, the terms 'evolution' and 'development' have been increasingly linked to cancer, in many different frameworks and contexts. This mini-review, as part of a special issue on Evolutionary Developmental Biology, discusses the main areas in cancer research that have been addressed through the lenses of both evolutionary and developmental biology, though not always fully or explicitly integrated in an evo-devo framework. First, it briefly introduces the current views on carcinogenesis that invoke evolutionary and/or developmental perspectives. Then, it discusses the main mechanisms proposed to have specifically evolved to suppress cancer during the evolution of multicellularity. Lastly, it considers whether the evolution of multicellularity and development was shaped by the threat of cancer (a cancer-evo-devo perspective), and/or whether the evolution of developmental programs and life history traits can shape cancer resistance/risk in various lineages (an evo-devo-cancer perspective). A proper evolutionary developmental framework for cancer, both as a disease and in terms of its natural history (in the context of the evolution of multicellularity and development as well as life history traits), could bridge the currently disparate evolutionary and developmental perspectives and uncover aspects that will provide new insights for cancer prevention and treatment.
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20
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Balimponya EG, Dwiyanti MS, Ito T, Sakaguchi S, Yamamori K, Kanaoka Y, Koide Y, Nagayoshi Y, Kishima Y. Seed management using NGS technology to rapidly eliminate a deleterious allele from rice breeder seeds. BREEDING SCIENCE 2022; 72:362-371. [PMID: 36776441 PMCID: PMC9895803 DOI: 10.1270/jsbbs.22058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/26/2022] [Indexed: 06/18/2023]
Abstract
Spontaneous mutations are stochastic phenomena that occur in every population. However, deleterious mutated allele present in seeds distributed to farmers must be detected and removed. Here, we eliminated undesirable mutations from the parent population in one generation through a strategy based on next-generation sequencing (NGS). This study dealt with a spontaneous albino mutant in the 'Hinohikari' rice variety grown at the Miyazaki Comprehensive Agricultural Experiment Station, Japan. The incidence of albinism in the population was 1.36%. NGS analysis revealed the genomic basis for differences between green and albino phenotypes. Every albino plant had a C insertion in the Snow-White Leaf1 (SWL1) gene on chromosome 4 causing a frameshift mutation. Selfing plants heterozygous for the mutant allele, swl1-R332P, resulted in a 3:1 green/albino ratio, confirming that a single recessive gene controls albinism. Ultrastructural leaf features in the swl1-R332P mutants displayed deformed chlorophyll-associated organelles in albino plants that were similar to those of previously described swl1 mutants. Detection of the causative gene and its confirmation using heterozygous progenies were completed within a year. The NGS technique outlined here facilitates rapid identification of spontaneous mutations that can occur in breeder seeds.
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Affiliation(s)
- Elias G. Balimponya
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Maria S. Dwiyanti
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Toshiaki Ito
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Shuntaro Sakaguchi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Koichi Yamamori
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Yoshitaka Kanaoka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Yohei Koide
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Yoshifumi Nagayoshi
- Miyazaki Comprehensive Agricultural Experiment Station, Miyazaki 880-0212, Japan
| | - Yuji Kishima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
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21
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da Cunha NL, Xue H, Wright SI, Barrett SCH. Genetic variation and clonal diversity in floating aquatic plants: Comparative genomic analysis of water hyacinth species in their native range. Mol Ecol 2022; 31:5307-5325. [PMID: 35984729 DOI: 10.1111/mec.16664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 07/24/2022] [Accepted: 08/10/2022] [Indexed: 12/15/2022]
Abstract
Many eukaryotic organisms reproduce by sexual and asexual reproduction. Genetic diversity in populations can be strongly dependent on the relative importance of these two reproductive modes. Here, we compare the amounts and patterns of genetic diversity in related water hyacinths that differ in their propensity for clonal propagation - highly clonal Eichhornia crassipes and moderately clonal E. azurea (Pontederiaceae). Our comparisons involved genotype-by-sequencing (GBS) of 137 E. crassipes ramets from 60 locations (193,495 nucleotide sites) and 118 E. azurea ramets from 53 locations (198,343 nucleotide sites) among six hydrological basins in central South America, the native range of both species. We predicted that because of more prolific clonal propagation, E. crassipes would exhibit lower clonal diversity than E. azurea. This prediction was supported by all measures of clonal diversity that we examined. Eichhornia crassipes also had a larger excess of heterozygotes at variant sites, another signature of clonality. However, genome-wide heterozygosity was not significantly different between the species. Eichhornia crassipes had weaker spatial genetic structure and lower levels of differentiation among hydrological basins than E. azurea, probably because of higher clonality and more extensive dispersal of its free-floating life form. Our findings for E. crassipes contrast with earlier studies from the invasive range which have reported very low levels of clonal diversity and extensive geographic areas of genetic uniformity.
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Affiliation(s)
- Nicolay Leme da Cunha
- Grupo de Ecología de la Polinización, INIBIOMA, CONICET-Universidad Nacional del Comahue, San Carlos de Bariloche, Rio Negro, Argentina.,Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Haoran Xue
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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22
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Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons. Proc Natl Acad Sci U S A 2022; 119:e2208496119. [PMID: 36122204 PMCID: PMC9522333 DOI: 10.1073/pnas.2208496119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Wild relatives of domesticated plants provide a rich resource for crop improvement and a valuable comparative perspective for understanding genomic, physiological, and agricultural traits. Here, we provide high-quality reference genomes of one early domesticated form of the economically most important cotton species, Gossypium hirsutum, and two other wild species, to clarify evolutionary relationships and understand the genomic changes that characterize these species and their close relatives. We document abundant gene resources involved in adaptation to environmental challenges, highlighting the potential for introgression of favorable genes into domesticated cotton and for increasing resilience to climate variability. Our study complements other recent genomic analyses in the cotton genus and provides a valuable foundation for breeding improved cotton varieties. Allotetraploid cotton (Gossypium) species represents a model system for the study of plant polyploidy, molecular evolution, and domestication. Here, chromosome-scale genome sequences were obtained and assembled for two recently described wild species of tetraploid cotton, Gossypium ekmanianum [(AD)6, Ge] and Gossypium stephensii [(AD)7, Gs], and one early form of domesticated Gossypium hirsutum, race punctatum [(AD)1, Ghp]. Based on phylogenomic analysis, we provide a dated whole-genome level perspective for the evolution of the tetraploid Gossypium clade and resolved the evolutionary relationships of Gs, Ge, and domesticated G. hirsutum. We describe genomic structural variation that arose during Gossypium evolution and describe its correlates—including phenotypic differentiation, genetic isolation, and genetic convergence—that contributed to cotton biodiversity and cotton domestication. Presence/absence variation is prominent in causing cotton genomic structural variations. A presence/absence variation-derived gene encoding a phosphopeptide-binding protein is implicated in increasing fiber length during cotton domestication. The relatively unimproved Ghp offers the potential for gene discovery related to adaptation to environmental challenges. Expanded gene families enoyl-CoA δ isomerase 3 and RAP2-7 may have contributed to abiotic stress tolerance, possibly by targeting plant hormone-associated biochemical pathways. Our results generate a genomic context for a better understanding of cotton evolution and for agriculture.
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23
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Zhao Y, Guo Q, Cao S, Tian Y, Han K, Sun Y, Li J, Yang Q, Ji Q, Sederoff R, Li Y. Genome-wide identification of the AlkB homologs gene family, PagALKBH9B and PagALKBH10B regulated salt stress response in Populus. FRONTIERS IN PLANT SCIENCE 2022; 13:994154. [PMID: 36204058 PMCID: PMC9530910 DOI: 10.3389/fpls.2022.994154] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
The AlkB homologs (ALKBH) gene family regulates N6-methyladenosine (m6A) RNA methylation and is involved in plant growth and the abiotic stress response. Poplar is an important model plant for studying perennial woody plants. Poplars typically have a long juvenile period of 7-10 years, requiring long periods of time for studies of flowering or mature wood properties. Consequently, functional studies of the ALKBH genes in Populus species have been limited. Based on AtALKBHs sequence similarity with Arabidopsis thaliana, 23 PagALKBHs were identified in the genome of the poplar 84K hybrid genotype (P. alba × P. tremula var. glandulosa), and gene structures and conserved domains were confirmed between homologs. The PagALKBH proteins were classified into six groups based on conserved sequence compared with human, Arabidopsis, maize, rice, wheat, tomato, barley, and grape. All homologs of PagALKBHs were tissue-specific; most were highly expressed in leaves. ALKBH9B and ALKBH10B are m6A demethylases and overexpression of their homologs PagALKBH9B and PagALKBH10B reduced m6A RNA methylation in transgenic lines. The number of adventitious roots and the biomass accumulation of transgenic lines decreased compared with WT. Therefore, PagALKBH9B and PagALKBH10B mediate m6A RNA demethylation and play a regulatory role in poplar growth and development. Overexpression of PagALKBH9B and PagALKBH10B can reduce the accumulation of H2O2 and oxidative damage by increasing the activities of SOD, POD, and CAT, and enhancing protection for Chl a/b, thereby increasing the salt tolerance of transgenic lines. However, overexpression lines were more sensitive to drought stress due to reduced proline content. This research revealed comprehensive information about the PagALKBH gene family and their roles in growth and development and responsing to salt stress of poplar.
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Affiliation(s)
- Ye Zhao
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Qi Guo
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Sen Cao
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Yanting Tian
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Kunjin Han
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Yuhan Sun
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Juan Li
- Natural Resources and Planning Bureau of Yanshan County, Cangzhou, Hebei, China
| | - Qingshan Yang
- Shandong Academy of Forestry, Jinan, Shandong, China
| | - Qingju Ji
- Cangzhou Municipal Forestry Seeding and Cutting Management Center, Cangzhou, China
| | - Ronald Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Yun Li
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
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24
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Sork VL, Cokus SJ, Fitz-Gibbon ST, Zimin AV, Puiu D, Garcia JA, Gugger PF, Henriquez CL, Zhen Y, Lohmueller KE, Pellegrini M, Salzberg SL. High-quality genome and methylomes illustrate features underlying evolutionary success of oaks. Nat Commun 2022; 13:2047. [PMID: 35440538 PMCID: PMC9018854 DOI: 10.1038/s41467-022-29584-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 03/11/2022] [Indexed: 02/01/2023] Open
Abstract
The genus Quercus, which emerged ∼55 million years ago during globally warm temperatures, diversified into ∼450 extant species. We present a high-quality de novo genome assembly of a California endemic oak, Quercus lobata, revealing features consistent with oak evolutionary success. Effective population size remained large throughout history despite declining since early Miocene. Analysis of 39,373 mapped protein-coding genes outlined copious duplications consistent with genetic and phenotypic diversity, both by retention of genes created during the ancient γ whole genome hexaploid duplication event and by tandem duplication within families, including numerous resistance genes and a very large block of duplicated DUF247 genes, which have been found to be associated with self-incompatibility in grasses. An additional surprising finding is that subcontext-specific patterns of DNA methylation associated with transposable elements reveal broadly-distributed heterochromatin in intergenic regions, similar to grasses. Collectively, these features promote genetic and phenotypic variation that would facilitate adaptability to changing environments.
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Affiliation(s)
- Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA.
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095, USA.
| | - Shawn J Cokus
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095-7239, USA
| | - Sorel T Fitz-Gibbon
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Aleksey V Zimin
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Daniela Puiu
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jesse A Garcia
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Paul F Gugger
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, 21532, USA
| | - Claudia L Henriquez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Ying Zhen
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095-7239, USA
| | - Steven L Salzberg
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, 21218, USA
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25
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Wang Z, Xue JY, Hu SY, Zhang F, Yu R, Chen D, Van de Peer Y, Jiang J, Song A, Ni L, Hua J, Lu Z, Yu C, Yin Y, Gu C. The genome of hibiscus hamabo reveals its adaptation to saline and waterlogged habitat. HORTICULTURE RESEARCH 2022; 9:uhac067. [PMID: 35480957 PMCID: PMC9039499 DOI: 10.1093/hr/uhac067] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Hibiscus hamabo is a semi-mangrove species with strong tolerance to salt and waterlogging stress. However, the molecular basis and mechanisms that underlie this strong adaptability to harsh environments remain poorly understood. Here, we assembled a high-quality, chromosome-level genome of this semi-mangrove plant and analyzed its transcriptome under different stress treatments to reveal regulatory responses and mechanisms. Our analyses suggested that H. hamabo has undergone two recent successive polyploidy events, a whole-genome duplication followed by a whole-genome triplication, resulting in an unusually large gene number (107 309 genes). Comparison of the H. hamabo genome with that of its close relative Hibiscus cannabinus, which has not experienced a recent WGT, indicated that genes associated with high stress resistance have been preferentially preserved in the H. hamabo genome, suggesting an underlying association between polyploidy and stronger stress resistance. Transcriptomic data indicated that genes in the roots and leaves responded differently to stress. In roots, genes that regulate ion channels involved in biosynthetic and metabolic processes responded quickly to adjust the ion concentration and provide metabolic products to protect root cells, whereas no such rapid response was observed from genes in leaves. Using co-expression networks, potential stress resistance genes were identified for use in future functional investigations. The genome sequence, along with several transcriptome datasets, provide insights into genome evolution and the mechanism of salt and waterlogging tolerance in H. hamabo, suggesting the importance of polyploidization for environmental adaptation.
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Affiliation(s)
- Zhiquan Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai-Ya Hu
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Fengjiao Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Ranran Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yves Van de Peer
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-UGent Center for Plant Systems Biology, B-9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Longjie Ni
- College of Forest Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Jianfeng Hua
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Zhiguo Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Chaoguang Yu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Yunlong Yin
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Chunsun Gu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
- College of Forest Sciences, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Utilization of Agricultural Germplasm, Nanjing, 210014, China
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26
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Wang S, Liang H, Wang H, Li L, Xu Y, Liu Y, Liu M, Wei J, Ma T, Le C, Yang J, He C, Liu J, Zhao J, Zhao Y, Lisby M, Sahu SK, Liu H. The chromosome-scale genomes of Dipterocarpus turbinatus and Hopea hainanensis (Dipterocarpaceae) provide insights into fragrant oleoresin biosynthesis and hardwood formation. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:538-553. [PMID: 34687252 PMCID: PMC8882806 DOI: 10.1111/pbi.13735] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/01/2021] [Accepted: 10/12/2021] [Indexed: 05/30/2023]
Abstract
Dipterocarpaceae are typical tropical plants (dipterocarp forests) that are famous for their high economic value because of their production of fragrant oleoresins, top-quality timber and usage in traditional Chinese medicine. Currently, the lack of Dipterocarpaceae genomes has been a limiting factor to decipher the fragrant oleoresin biosynthesis and gain evolutionary insights into high-quality wood formation in Dipterocarpaceae. We generated chromosome-level genome assemblies for two representative Dipterocarpaceae species viz. Dipterocarpus turbinatus Gaertn. f. and Hopea hainanensis Merr. et Chun. Our whole-genome duplication (WGD) analysis revealed that Dipterocarpaceae underwent a shared WGD event, which showed significant impacts on increased copy numbers of genes related to the biosynthesis of terpene, BAHD acyltransferases, fatty acid and benzenoid/phenylpropanoid, which probably confer to the formation of their characteristic fragrant oleoresin. Additionally, compared with common soft wood plants, the expansion of gene families was also found to be associated with wood formation, such as in CESA (cellulose synthase), CSLE (cellulose synthase-like protein E), laccase and peroxidase in Dipterocarpaceae genomes, which might also contribute to the formation of harder, stronger and high-density timbers. Finally, an integrative analysis on a combination of genomic, transcriptomic and metabolic data from different tissues provided further insights into the molecular basis of fragrant oleoresins biosynthesis and high-quality wood formation of Dipterocarpaceae. Our study contributes the first two representative genomes for Dipterocarpaceae, which are valuable genetic resources for further researches on the fragrant oleoresins and superior-quality timber, genome-assisted breeding and improvement, and conservation biology of this family.
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Affiliation(s)
- Sibo Wang
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
| | - Hongping Liang
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Hongli Wang
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Linzhou Li
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Yan Xu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Yang Liu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
| | - Min Liu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
| | - Jinpu Wei
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
| | - Tao Ma
- Key Laboratory of Bio‐resource and Eco‐Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduChina
| | - Cheng Le
- BGI‐Yunnan, BGI‐ShenzhenYunnanChina
| | - Jinlong Yang
- BGI‐Yunnan, BGI‐ShenzhenYunnanChina
- College of Forensic ScienceXi'an Jiaotong UniversityXi'anChina
| | | | - Jie Liu
- Forestry Bureau of RuiliYunnan Dehong, RuiliChina
| | | | | | - Michael Lisby
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
| | - Huan Liu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
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27
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Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits. Biochem Soc Trans 2022; 50:583-596. [PMID: 35212360 PMCID: PMC9022969 DOI: 10.1042/bst20210908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/01/2022] [Accepted: 02/14/2022] [Indexed: 12/18/2022]
Abstract
DNA methylation is a chromatin modification that plays an essential role in regulating gene expression and genome stability and it is typically associated with gene silencing and heterochromatin. Owing to its heritability, alterations in the patterns of DNA methylation have the potential to provide for epigenetic inheritance of traits. Contemporary epigenomic technologies provide information beyond sequence variation and could supply alternative sources of trait variation for improvement in crops such as sorghum. Yet, compared with other species such as maize and rice, the sorghum DNA methylome is far less well understood. The distribution of CG, CHG, and CHH methylation in the genome is different compared with other species. CG and CHG methylation levels peak around centromeric segments in the sorghum genome and are far more depleted in the gene dense chromosome arms. The genes regulating DNA methylation in sorghum are also yet to be functionally characterised; better understanding of their identity and functional analysis of DNA methylation machinery mutants in diverse genotypes will be important to better characterise the sorghum methylome. Here, we catalogue homologous genes encoding methylation regulatory enzymes in sorghum based on genes in Arabidopsis, maize, and rice. Discovering variation in the methylome may uncover epialleles that provide extra information to explain trait variation and has the potential to be applied in epigenome-wide association studies or genomic prediction. DNA methylation can also improve genome annotations and discover regulatory elements underlying traits. Thus, improving our knowledge of the sorghum methylome can enhance our understanding of the molecular basis of traits and may be useful to improve sorghum performance.
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28
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Hazarika RR, Serra M, Zhang Z, Zhang Y, Schmitz RJ, Johannes F. Molecular properties of epimutation hotspots. NATURE PLANTS 2022; 8:146-156. [PMID: 35087209 PMCID: PMC8866225 DOI: 10.1038/s41477-021-01086-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Mistakes in the maintenance of CG methylation are a source of heritable epimutations in plants. Multigenerational surveys indicate that the rate of these stochastic events varies substantially across the genome, with some regions harbouring localized 'epimutation hotspots'. Using Arabidopsis as a model, we show that epimutation hotspots are indexed by a specific set of chromatin states that map to subregions of gene body methylation genes. Although these regions comprise only ~12% of all CGs in the genome, they account for ~63% of all epimutation events per unit time. Molecular profiling revealed that these regions contain unique sequence features, harbour steady-state intermediate methylation levels and act as putative targets of antagonistic DNA methylation pathways. We further demonstrate that experimentally induced shifts in steady-state methylation in these hotspot regions are sufficient to significantly alter local epimutation intensities. Our work lays the foundation for dissecting the molecular mechanisms and evolutionary consequences of epimutation hotspots in plants.
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Affiliation(s)
- Rashmi R Hazarika
- Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany
- TUM Institute for Advanced Study, Garching, Germany
| | - Michele Serra
- Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany
| | - Zhilin Zhang
- Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany
| | - Yinwen Zhang
- Department of Genetics, The University of Georgia, Athens, GA, USA
| | - Robert J Schmitz
- TUM Institute for Advanced Study, Garching, Germany.
- Department of Genetics, The University of Georgia, Athens, GA, USA.
| | - Frank Johannes
- Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany.
- TUM Institute for Advanced Study, Garching, Germany.
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29
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Hou Q, Wan X. Epigenome and Epitranscriptome: Potential Resources for Crop Improvement. Int J Mol Sci 2021; 22:12912. [PMID: 34884725 PMCID: PMC8658206 DOI: 10.3390/ijms222312912] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 12/26/2022] Open
Abstract
Crop breeding faces the challenge of increasing food demand, especially under climatic changes. Conventional breeding has relied on genetic diversity by combining alleles to obtain desired traits. In recent years, research on epigenetics and epitranscriptomics has shown that epigenetic and epitranscriptomic diversity provides additional sources for crop breeding and harnessing epigenetic and epitranscriptomic regulation through biotechnologies has great potential for crop improvement. Here, we review epigenome and epitranscriptome variations during plant development and in response to environmental stress as well as the available sources for epiallele formation. We also discuss the possible strategies for applying epialleles and epitranscriptome engineering in crop breeding.
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Affiliation(s)
- Quancan Hou
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100024, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100024, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
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30
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Neinavaie F, Ibrahim-Hashim A, Kramer AM, Brown JS, Richards CL. The Genomic Processes of Biological Invasions: From Invasive Species to Cancer Metastases and Back Again. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.681100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The concept of invasion is useful across a broad range of contexts, spanning from the fine scale landscape of cancer tumors up to the broader landscape of ecosystems. Invasion biology provides extraordinary opportunities for studying the mechanistic basis of contemporary evolution at the molecular level. Although the field of invasion genetics was established in ecology and evolution more than 50 years ago, there is still a limited understanding of how genomic level processes translate into invasive phenotypes across different taxa in response to complex environmental conditions. This is largely because the study of most invasive species is limited by information about complex genome level processes. We lack good reference genomes for most species. Rigorous studies to examine genomic processes are generally too costly. On the contrary, cancer studies are fortified with extensive resources for studying genome level dynamics and the interactions among genetic and non-genetic mechanisms. Extensive analysis of primary tumors and metastatic samples have revealed the importance of several genomic mechanisms including higher mutation rates, specific types of mutations, aneuploidy or whole genome doubling and non-genetic effects. Metastatic sites can be directly compared to primary tumor cell counterparts. At the same time, clonal dynamics shape the genomics and evolution of metastatic cancers. Clonal diversity varies by cancer type, and the tumors’ donor and recipient tissues. Still, the cancer research community has been unable to identify any common events that provide a universal predictor of “metastatic potential” which parallels findings in evolutionary ecology. Instead, invasion in cancer studies depends strongly on context, including order of events and clonal composition. The detailed studies of the behavior of a variety of human cancers promises to inform our understanding of genome level dynamics in the diversity of invasive species and provide novel insights for management.
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31
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Abstract
Plant intra-individual and inter-individual variation can be determined by the epigenome, a set of covalent modifications of DNA and chromatin that can alter genome structure and activity without changes to the genome sequence. The epigenome of plant cells is plastic, that is, it can change in response to internal or external cues, such as during development or due to environmental changes, to create a memory of such events. Ongoing advances in technologies to read and write epigenomic patterns with increasing resolution, scale and precision are enabling the extent of plant epigenome variation to be more extensively characterized and functionally interrogated. In this Review, we discuss epigenome dynamics and variation within plants during development and in response to environmental changes, including stress, as well as between plants. We review known or potential functions of such plasticity and emphasize the importance of investigating the causality of epigenomic changes. Finally, we discuss emerging technologies that may underpin future research into plant epigenome plasticity.
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Affiliation(s)
- James P B Lloyd
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
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32
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Melnikova NV, Pushkova EN, Dvorianinova EM, Beniaminov AD, Novakovskiy RO, Povkhova LV, Bolsheva NL, Snezhkina AV, Kudryavtseva AV, Krasnov GS, Dmitriev AA. Genome Assembly and Sex-Determining Region of Male and Female Populus × sibirica. FRONTIERS IN PLANT SCIENCE 2021; 12:625416. [PMID: 34567016 PMCID: PMC8455832 DOI: 10.3389/fpls.2021.625416] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
The genus Populus is presented by dioecious species, and it became a promising object to study the genetics of sex in plants. In this work, genomes of male and female Populus × sibirica individuals were sequenced for the first time. To achieve high-quality genome assemblies, we used Oxford Nanopore Technologies and Illumina platforms. A protocol for the isolation of long and pure DNA from young poplar leaves was developed, which enabled us to obtain 31 Gb (N50 = 21 kb) for the male poplar and 23 Gb (N50 = 24 kb) for the female one using the MinION sequencer. Genome assembly was performed with different tools, and Canu provided the most complete and accurate assemblies with a length of 818 Mb (N50 = 1.5 Mb) for the male poplar and 816 Mb (N50 = 0.5 Mb) for the female one. After polishing with Racon and Medaka (Nanopore reads) and then with POLCA (Illumina reads), assembly completeness was 98.45% (87.48% duplicated) for the male and 98.20% (76.77% duplicated) for the female according to BUSCO (benchmarking universal single-copy orthologs). A high proportion of duplicated BUSCO and the increased genome size (about 300 Mb above the expected) pointed at the separation of haplotypes in a large part of male and female genomes of P. × sibirica. Due to this, we were able to identify two haplotypes of the sex-determining region (SDR) in both assemblies; and one of these four SDR haplotypes, in the male genome, contained partial repeats of the ARR17 gene (Y haplotype), while the rest three did not (X haplotypes). The analysis of the male P. × sibirica SDR suggested that the Y haplotype originated from P. nigra, while the X haplotype is close to P. trichocarpa and P. balsamifera species. Moreover, we revealed a Populus-specific repeat that could be involved in translocation of the ARR17 gene or its part to the SDR of P. × sibirica and other Populus species. The obtained results expand our knowledge on SDR features in the genus Populus and poplar phylogeny.
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Affiliation(s)
- Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Artemy D. Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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33
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Herrera CM, Bazaga P, Pérez R, Alonso C. Lifetime genealogical divergence within plants leads to epigenetic mosaicism in the shrub Lavandula latifolia (Lamiaceae). THE NEW PHYTOLOGIST 2021; 231:2065-2076. [PMID: 33634863 DOI: 10.1111/nph.17257] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Epigenetic mosaicism is a possible source of within-plant phenotypic heterogeneity, yet its frequency and developmental origin remain unexplored. This study examines whether extant epigenetic heterogeneity within Lavandula latifolia (Lamiaceae) shrubs reflects recent epigenetic modifications experienced independently by different plant parts or, alternatively, it is the cumulative outcome of a steady lifetime process. Leaf samples from different architectural modules (branch tips) were collected from three L. latifolia plants and characterized epigenetically by global DNA cytosine methylation and methylation state of methylation-sensitive amplified fragment-length polymorphism (MS-AFLP) markers. Epigenetic characteristics of modules were then assembled with information on the branching history of plants. Methods borrowed from phylogenetic research were used to assess genealogical signal of extant epigenetic variation and reconstruct within-plant genealogical trajectory of epigenetic traits. Plants were epigenetically heterogeneous, as shown by differences among modules in global DNA methylation and variation in the methylation states of 6 to 8% of MS-AFLP markers. All epigenetic features exhibited significant genealogical signal within plants. Events of epigenetic divergence occurred throughout the lifespan of individuals and were subsequently propagated by branch divisions. Internal epigenetic diversification of L. latifolia individuals took place steadily during their development, a process which eventually led to persistent epigenetic mosaicism.
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Affiliation(s)
- Carlos M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 26, Sevilla, E-41092, Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 26, Sevilla, E-41092, Spain
| | - Ricardo Pérez
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de La Cartuja, CSIC-US, Avda. Américo Vespucio 49, Sevilla, E-41092, Spain
| | - Conchita Alonso
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 26, Sevilla, E-41092, Spain
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34
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Pushkova EN, Krasnov GS, Lakunina VA, Novakovskiy RO, Povkhova LV, Dvorianinova EM, Beniaminov AD, Fedorova MS, Snezhkina AV, Kudryavtseva AV, Dmitriev AA, Melnikova NV. Genome and Transcriptome Sequencing of Populus × sibirica Identified Sex-Associated Allele-Specific Expression of the CLC Gene. Front Genet 2021; 12:676935. [PMID: 34456967 PMCID: PMC8385651 DOI: 10.3389/fgene.2021.676935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/28/2021] [Indexed: 12/04/2022] Open
Abstract
Transcriptome sequencing of leaves, catkin axes, and flowers from male and female trees of Populus × sibirica and genome sequencing of the same plants were performed for the first time. The availability of both genome and transcriptome sequencing data enabled the identification of allele-specific expression. Such an analysis was performed for genes from the sex-determining region (SDR). P. × sibirica is an intersectional hybrid between species from sections Aigeiros (Populus nigra) and Tacamahaca (Populus laurifolia, Populus suaveolens, or Populus × moskoviensis); therefore, a significant number of heterozygous polymorphisms were identified in the SDR that allowed us to distinguish between alleles. In the SDR, both allelic variants of the TCP (T-complex protein 1 subunit gamma), CLC (Chloride channel protein CLC-c), and MET1 (DNA-methyltransferase 1) genes were expressed in females, while in males, two allelic variants were expressed for TCP and MET1 but only one allelic variant prevailed for CLC. Targeted sequencing of TCP, CLC, and MET1 regions on a representative set of trees confirmed the sex-associated allele-specific expression of the CLC gene in generative and vegetative tissues of P. × sibirica. Our study brings new knowledge on sex-associated differences in Populus species.
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Affiliation(s)
- Elena N Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Valentina A Lakunina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Liubov V Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Ekaterina M Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Artemy D Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria S Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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35
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Kakoulidou I, Avramidou EV, Baránek M, Brunel-Muguet S, Farrona S, Johannes F, Kaiserli E, Lieberman-Lazarovich M, Martinelli F, Mladenov V, Testillano PS, Vassileva V, Maury S. Epigenetics for Crop Improvement in Times of Global Change. BIOLOGY 2021; 10:766. [PMID: 34439998 PMCID: PMC8389687 DOI: 10.3390/biology10080766] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022]
Abstract
Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity-naturally, genetically, chemically, or environmentally induced-can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.
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Affiliation(s)
- Ioanna Kakoulidou
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
| | - Evangelia V. Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-Dimitra (ELGO-DIMITRA), 11528 Athens, Greece;
| | - Miroslav Baránek
- Faculty of Horticulture, Mendeleum—Institute of Genetics, Mendel University in Brno, Valtická 334, 69144 Lednice, Czech Republic;
| | - Sophie Brunel-Muguet
- UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, UNICAEN, INRAE, Normandie Université, CEDEX, F-14032 Caen, France;
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, National University of Ireland (NUI) Galway, H91 TK33 Galway, Ireland;
| | - Frank Johannes
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
- Institute for Advanced Study, Technical University of Munich, Lichtenberg Str. 2a, 85748 Garching, Germany
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Michal Lieberman-Lazarovich
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel;
| | - Federico Martinelli
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Sq. Dositeja Obradovića 8, 21000 Novi Sad, Serbia;
| | - Pilar S. Testillano
- Pollen Biotechnology of Crop Plants Group, Centro de Investigaciones Biológicas Margarita Salas-(CIB-CSIC), Ramiro Maeztu 9, 28040 Madrid, Spain;
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bldg. 21, 1113 Sofia, Bulgaria;
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE, EA1207 USC1328, Université d’Orléans, F-45067 Orléans, France
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36
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Denkena J, Johannes F, Colomé-Tatché M. Region-level epimutation rates in Arabidopsis thaliana. Heredity (Edinb) 2021; 127:190-202. [PMID: 33966050 PMCID: PMC8322157 DOI: 10.1038/s41437-021-00441-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 02/03/2023] Open
Abstract
Failure to maintain DNA methylation patterns during plant development can occasionally give rise to so-called "spontaneous epimutations". These stochastic methylation changes are sometimes heritable across generations and thus accumulate in plant genomes over time. Recent evidence indicates that spontaneous epimutations have a major role in shaping patterns of methylation diversity in plant populations. Using single CG dinucleotides as units of analysis, previous work has shown that the epimutation rate is several orders of magnitude higher than the genetic mutation rate. While these large rate differences have obvious implications for understanding genome-methylome co-evolution, the functional relevance of single CG methylation changes remains questionable. In contrast to single CG, solid experimental evidence has linked methylation gains and losses in larger genomic regions with transcriptional variation and heritable phenotypic effects. Here we show that such region-level changes arise stochastically at about the same rate as those at individual CG sites, are only marginal dependent on region size and cytosine density, but strongly dependent on chromosomal location. We also find consistent evidence that region-level epimutations are not restricted to CG contexts but also frequently occur in non-CG regions at the genome-wide scale. Taken together, our results support the view that many differentially methylated regions (DMRs) in natural populations originate from epimutation events and may not be effectively tagged by proximal SNPs. This possibility reinforces the need for epigenome-wide association studies (EWAS) in plants as a way to identify the epigenetic basis of complex traits.
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Affiliation(s)
- Johanna Denkena
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Frank Johannes
- grid.6936.a0000000123222966Department of Molecular Life Sciences, Hans Eisenmann-Zentrum for Agricultural Sciences, Technical University Munich, Freising, Germany
| | - Maria Colomé-Tatché
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany ,grid.5252.00000 0004 1936 973XBiomedical Center, Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
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37
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Yao N, Schmitz RJ, Johannes F. Epimutations Define a Fast-Ticking Molecular Clock in Plants. Trends Genet 2021; 37:699-710. [PMID: 34016450 PMCID: PMC8282728 DOI: 10.1016/j.tig.2021.04.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/16/2022]
Abstract
Stochastic gains and losses of DNA methylation at CG dinucleotides are a frequent occurrence in plants. These spontaneous 'epimutations' occur at a rate that is 100 000 times higher than the genetic mutation rate, are effectively neutral at the genome-wide scale, and are stably inherited across mitotic and meiotic cell divisions. Mathematical models have been extraordinarily successful at describing how epimutations accumulate in plant genomes over time, making this process one of the most predictable epigenetic phenomena to date. Here, we propose that their high rate and effective neutrality make epimutations a powerful new molecular clock for timing evolutionary events of the recent past and for age dating of long-lived perennials such as trees.
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Affiliation(s)
- Nan Yao
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA, USA; Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Frank Johannes
- Institute for Advanced Study, Technical University of Munich, Garching, Germany; Population Epigenetics and Epigenomics, Technical University of Munich, Freising, Germany.
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38
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Lovell JT, Bentley NB, Bhattarai G, Jenkins JW, Sreedasyam A, Alarcon Y, Bock C, Boston LB, Carlson J, Cervantes K, Clermont K, Duke S, Krom N, Kubenka K, Mamidi S, Mattison CP, Monteros MJ, Pisani C, Plott C, Rajasekar S, Rhein HS, Rohla C, Song M, Hilaire RS, Shu S, Wells L, Webber J, Heerema RJ, Klein PE, Conner P, Wang X, Grauke LJ, Grimwood J, Schmutz J, Randall JJ. Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding. Nat Commun 2021; 12:4125. [PMID: 34226565 PMCID: PMC8257795 DOI: 10.1038/s41467-021-24328-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
Genome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence-absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the 'Pawnee' cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence-absence and functional annotation database among genomes and within the two outbred haplotypes of the 'Lakota' genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops.
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Affiliation(s)
- John T. Lovell
- grid.417691.c0000 0004 0408 3720Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Nolan B. Bentley
- grid.264756.40000 0004 4687 2082Department of Horticultural Science, Texas A&M University, College Station, TX USA
| | - Gaurab Bhattarai
- grid.213876.90000 0004 1936 738XInstitute of Plant Breeding, Genetics & Genomics, University of Georgia, Athens, GA USA
| | - Jerry W. Jenkins
- grid.417691.c0000 0004 0408 3720Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Avinash Sreedasyam
- grid.417691.c0000 0004 0408 3720Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Yanina Alarcon
- grid.419447.b0000 0004 0370 5663Noble Research Institute, Ardmore, OK USA
| | - Clive Bock
- USDA Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA USA
| | - Lori Beth Boston
- grid.417691.c0000 0004 0408 3720Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Joseph Carlson
- grid.451309.a0000 0004 0449 479XDOE Joint Genome Institute, Berkeley, CA USA
| | - Kimberly Cervantes
- grid.24805.3b0000 0001 0687 2182Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM USA
| | - Kristen Clermont
- grid.507314.4USDA-ARS Food Processing and Sensory Quality Research, New Orleans, LA USA
| | - Sara Duke
- USDA-ARS Plains Area Administrative Office, College Station, TX USA
| | - Nick Krom
- grid.419447.b0000 0004 0370 5663Noble Research Institute, Ardmore, OK USA
| | - Keith Kubenka
- USDA Pecan Breeding and Genetics, College Station, TX USA
| | - Sujan Mamidi
- grid.417691.c0000 0004 0408 3720Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | | | - Maria J. Monteros
- grid.419447.b0000 0004 0370 5663Noble Research Institute, Ardmore, OK USA
| | - Cristina Pisani
- USDA Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA USA
| | - Christopher Plott
- grid.417691.c0000 0004 0408 3720Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Shanmugam Rajasekar
- grid.134563.60000 0001 2168 186XArizona Genomics Institute, University of Arizona, Tucson, AZ USA
| | - Hormat Shadgou Rhein
- grid.24805.3b0000 0001 0687 2182Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM USA
| | - Charles Rohla
- grid.419447.b0000 0004 0370 5663Noble Research Institute, Ardmore, OK USA
| | - Mingzhou Song
- grid.24805.3b0000 0001 0687 2182Department of Computer Science, New Mexico State University, Las Cruces, NM USA
| | - Rolston St. Hilaire
- grid.24805.3b0000 0001 0687 2182Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM USA
| | - Shengqiang Shu
- grid.451309.a0000 0004 0449 479XDOE Joint Genome Institute, Berkeley, CA USA
| | - Lenny Wells
- grid.213876.90000 0004 1936 738XDepartment of Horticulture, University of Georgia-Tifton Campus, Tifton, GA USA
| | - Jenell Webber
- grid.417691.c0000 0004 0408 3720Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Richard J. Heerema
- grid.24805.3b0000 0001 0687 2182Department of Computer Science, New Mexico State University, Las Cruces, NM USA
| | - Patricia E. Klein
- grid.264756.40000 0004 4687 2082Department of Horticultural Science, Texas A&M University, College Station, TX USA
| | - Patrick Conner
- grid.213876.90000 0004 1936 738XDepartment of Horticulture, University of Georgia-Tifton Campus, Tifton, GA USA
| | - Xinwang Wang
- USDA Pecan Breeding and Genetics, College Station, TX USA
| | - L. J. Grauke
- USDA Pecan Breeding and Genetics, College Station, TX USA
| | - Jane Grimwood
- grid.417691.c0000 0004 0408 3720Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Jeremy Schmutz
- grid.417691.c0000 0004 0408 3720Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL USA ,grid.451309.a0000 0004 0449 479XDOE Joint Genome Institute, Berkeley, CA USA
| | - Jennifer J. Randall
- grid.24805.3b0000 0001 0687 2182Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM USA
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Noshay JM, Springer NM. Stories that can't be told by SNPs; DNA methylation variation in plant populations. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:101989. [PMID: 33445144 DOI: 10.1016/j.pbi.2020.101989] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/18/2020] [Accepted: 12/11/2020] [Indexed: 05/23/2023]
Abstract
Epigenetic variation has been observed in many plant populations. This variation can influence qualitative and quantitative traits. A key question is whether there is novel information in the epigenome that is not captured by SNP-based genetic markers. The answer likely varies depending on the sources and stability of epigenetic variation as well as the type of population being studied. We consider the epigenetic variation in several plant systems and how this relates to potential for hidden information that could increase our understanding of phenotypic variation.
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Affiliation(s)
- Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA.
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40
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Ritter EJ, Niederhuth CE. Intertwined evolution of plant epigenomes and genomes. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:101990. [PMID: 33445143 DOI: 10.1016/j.pbi.2020.101990] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/08/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
DNA methylation is found across eukaryotes; however, plants have evolved patterns and pathways of DNA methylation that are distinct from animals and fungi. DNA methylation shapes the evolution of genomes through its direct roles in transposon silencing, gene expression, genome stability, and its impact on mutation rates. In return the diversity of DNA methylation across species is shaped by genome sequence evolution. Extensive diversification of key DNA methylation pathways has continued in plants through gene duplication and loss. Meanwhile, frequent movement of transposons has altered local DNA methylation patterns and the genes affected. Only recently has the diversity and evolutionary history of plant DNA methylation become evident with the availability of increasing genomic and epigenomic data. However, much remains unresolved regarding the evolutionary forces that have shaped the dynamics of the complex and intertwined history of plant genome and epigenome evolution.
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Affiliation(s)
- Eleanore J Ritter
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; AgBioResearch, Michigan State University, East Lansing, MI 48824, USA.
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41
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Lu Z, Cui J, Wang L, Teng N, Zhang S, Lam HM, Zhu Y, Xiao S, Ke W, Lin J, Xu C, Jin B. Genome-wide DNA mutations in Arabidopsis plants after multigenerational exposure to high temperatures. Genome Biol 2021; 22:160. [PMID: 34034794 PMCID: PMC8145854 DOI: 10.1186/s13059-021-02381-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 05/13/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Elevated temperatures can cause physiological, biochemical, and molecular responses in plants that can greatly affect their growth and development. Mutations are the most fundamental force driving biological evolution. However, how long-term elevations in temperature influence the accumulation of mutations in plants remains unknown. RESULTS Multigenerational exposure of Arabidopsis MA (mutation accumulation) lines and MA populations to extreme heat and moderate warming results in significantly increased mutation rates in single-nucleotide variants (SNVs) and small indels. We observe distinctive mutational spectra under extreme and moderately elevated temperatures, with significant increases in transition and transversion frequencies. Mutation occurs more frequently in intergenic regions, coding regions, and transposable elements in plants grown under elevated temperatures. At elevated temperatures, more mutations accumulate in genes associated with defense responses, DNA repair, and signaling. Notably, the distribution patterns of mutations among all progeny differ between MA populations and MA lines, suggesting that stronger selection effects occurred in populations. Methylation is observed more frequently at mutation sites, indicating its contribution to the mutation process at elevated temperatures. Mutations occurring within the same genome under elevated temperatures are significantly biased toward low gene density regions, special trinucleotides, tandem repeats, and adjacent simple repeats. Additionally, mutations found in all progeny overlap significantly with genetic variations reported in 1001 Genomes, suggesting non-uniform distribution of de novo mutations through the genome. CONCLUSION Collectively, our results suggest that elevated temperatures can accelerate the accumulation, and alter the molecular profiles, of DNA mutations in plants, thus providing significant insight into how environmental temperatures fuel plant evolution.
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Affiliation(s)
- Zhaogeng Lu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
| | - Jiawen Cui
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Li Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Nianjun Teng
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Shoudong Zhang
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region China
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region China
| | - Yingfang Zhu
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
| | - Siwei Xiao
- Wuhan Frasergen Bioinformatics Co, Wuhan, China
| | - Wensi Ke
- Wuhan Frasergen Bioinformatics Co, Wuhan, China
| | - Jinxing Lin
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Chenwu Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
| | - Biao Jin
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
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Stability across the Whole Nuclear Genome in the Presence and Absence of DNA Mismatch Repair. Cells 2021; 10:cells10051224. [PMID: 34067668 PMCID: PMC8156620 DOI: 10.3390/cells10051224] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 01/06/2023] Open
Abstract
We describe the contribution of DNA mismatch repair (MMR) to the stability of the eukaryotic nuclear genome as determined by whole-genome sequencing. To date, wild-type nuclear genome mutation rates are known for over 40 eukaryotic species, while measurements in mismatch repair-defective organisms are fewer in number and are concentrated on Saccharomyces cerevisiae and human tumors. Well-studied organisms include Drosophila melanogaster and Mus musculus, while less genetically tractable species include great apes and long-lived trees. A variety of techniques have been developed to gather mutation rates, either per generation or per cell division. Generational rates are described through whole-organism mutation accumulation experiments and through offspring–parent sequencing, or they have been identified by descent. Rates per somatic cell division have been estimated from cell line mutation accumulation experiments, from systemic variant allele frequencies, and from widely spaced samples with known cell divisions per unit of tissue growth. The latter methods are also used to estimate generational mutation rates for large organisms that lack dedicated germlines, such as trees and hyphal fungi. Mechanistic studies involving genetic manipulation of MMR genes prior to mutation rate determination are thus far confined to yeast, Arabidopsis thaliana, Caenorhabditis elegans, and one chicken cell line. A great deal of work in wild-type organisms has begun to establish a sound baseline, but far more work is needed to uncover the variety of MMR across eukaryotes. Nonetheless, the few MMR studies reported to date indicate that MMR contributes 100-fold or more to genome stability, and they have uncovered insights that would have been impossible to obtain using reporter gene assays.
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Carey S, Yu Q, Harkess A. The Diversity of Plant Sex Chromosomes Highlighted through Advances in Genome Sequencing. Genes (Basel) 2021; 12:381. [PMID: 33800038 PMCID: PMC8000587 DOI: 10.3390/genes12030381] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 01/21/2023] Open
Abstract
For centuries, scientists have been intrigued by the origin of dioecy in plants, characterizing sex-specific development, uncovering cytological differences between the sexes, and developing theoretical models. Through the invention and continued improvements in genomic technologies, we have truly begun to unlock the genetic basis of dioecy in many species. Here we broadly review the advances in research on dioecy and sex chromosomes. We start by first discussing the early works that built the foundation for current studies and the advances in genome sequencing that have facilitated more-recent findings. We next discuss the analyses of sex chromosomes and sex-determination genes uncovered by genome sequencing. We synthesize these results to find some patterns are emerging, such as the role of duplications, the involvement of hormones in sex-determination, and support for the two-locus model for the origin of dioecy. Though across systems, there are also many novel insights into how sex chromosomes evolve, including different sex-determining genes and routes to suppressed recombination. We propose the future of research in plant sex chromosomes should involve interdisciplinary approaches, combining cutting-edge technologies with the classics to unravel the patterns that can be found across the hundreds of independent origins.
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Affiliation(s)
- Sarah Carey
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA;
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX 75252, USA
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA;
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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44
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Burian A. Does Shoot Apical Meristem Function as the Germline in Safeguarding Against Excess of Mutations? FRONTIERS IN PLANT SCIENCE 2021; 12:707740. [PMID: 34421954 PMCID: PMC8374955 DOI: 10.3389/fpls.2021.707740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/19/2021] [Indexed: 05/04/2023]
Abstract
A genetic continuity of living organisms relies on the germline which is a specialized cell lineage producing gametes. Essential in the germline functioning is the protection of genetic information that is subjected to spontaneous mutations. Due to indeterminate growth, late specification of the germline, and unique longevity, plants are expected to accumulate somatic mutations during their lifetime that leads to decrease in individual and population fitness. However, protective mechanisms, similar to those in animals, exist in plant shoot apical meristem (SAM) allowing plants to reduce the accumulation and transmission of mutations. This review describes cellular- and tissue-level mechanisms related to spatio-temporal distribution of cell divisions, organization of stem cell lineages, and cell fate specification to argue that the SAM functions analogous to animal germline.
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45
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Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. Nature 2021; 590:438-444. [PMID: 33505029 PMCID: PMC7886653 DOI: 10.1038/s41586-020-03127-1] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/16/2020] [Indexed: 01/30/2023]
Abstract
Long-term climate change and periodic environmental extremes threaten food and fuel security1 and global crop productivity2-4. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience5, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation6-knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate-gene-biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene-trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.
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46
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Yang X, Medford JI, Markel K, Shih PM, De Paoli HC, Trinh CT, McCormick AJ, Ployet R, Hussey SG, Myburg AA, Jensen PE, Hassan MM, Zhang J, Muchero W, Kalluri UC, Yin H, Zhuo R, Abraham PE, Chen JG, Weston DJ, Yang Y, Liu D, Li Y, Labbe J, Yang B, Lee JH, Cottingham RW, Martin S, Lu M, Tschaplinski TJ, Yuan G, Lu H, Ranjan P, Mitchell JC, Wullschleger SD, Tuskan GA. Plant Biosystems Design Research Roadmap 1.0. BIODESIGN RESEARCH 2020; 2020:8051764. [PMID: 37849899 PMCID: PMC10521729 DOI: 10.34133/2020/8051764] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 10/30/2020] [Indexed: 10/19/2023] Open
Abstract
Human life intimately depends on plants for food, biomaterials, health, energy, and a sustainable environment. Various plants have been genetically improved mostly through breeding, along with limited modification via genetic engineering, yet they are still not able to meet the ever-increasing needs, in terms of both quantity and quality, resulting from the rapid increase in world population and expected standards of living. A step change that may address these challenges would be to expand the potential of plants using biosystems design approaches. This represents a shift in plant science research from relatively simple trial-and-error approaches to innovative strategies based on predictive models of biological systems. Plant biosystems design seeks to accelerate plant genetic improvement using genome editing and genetic circuit engineering or create novel plant systems through de novo synthesis of plant genomes. From this perspective, we present a comprehensive roadmap of plant biosystems design covering theories, principles, and technical methods, along with potential applications in basic and applied plant biology research. We highlight current challenges, future opportunities, and research priorities, along with a framework for international collaboration, towards rapid advancement of this emerging interdisciplinary area of research. Finally, we discuss the importance of social responsibility in utilizing plant biosystems design and suggest strategies for improving public perception, trust, and acceptance.
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Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - June I. Medford
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kasey Markel
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Patrick M. Shih
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
| | - Henrique C. De Paoli
- Department of Biodesign, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cong T. Trinh
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Alistair J. McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Raphael Ployet
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Steven G. Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Poul Erik Jensen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1858, Frederiksberg, Copenhagen, Denmark
| | - Md Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Udaya C. Kalluri
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - David J. Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yinong Yang
- Department of Plant Pathology and Environmental Microbiology and the Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Degao Liu
- Department of Genetics, Cell Biology and Development, Center for Precision Plant Genomics and Center for Genome Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269, USA
| | - Jessy Labbe
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Jun Hyung Lee
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | | | - Stanton Martin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Mengzhu Lu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Julie C. Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Stan D. Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Shahryary Y, Symeonidi A, Hazarika RR, Denkena J, Mubeen T, Hofmeister B, van Gurp T, Colomé-Tatché M, Verhoeven KJ, Tuskan G, Schmitz RJ, Johannes F. AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants. Genome Biol 2020; 21:260. [PMID: 33023650 PMCID: PMC7539454 DOI: 10.1186/s13059-020-02161-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 09/02/2020] [Indexed: 01/28/2023] Open
Abstract
Stochastic changes in DNA methylation (i.e., spontaneous epimutations) contribute to methylome diversity in plants. Here, we describe AlphaBeta, a computational method for estimating the precise rate of such stochastic events using pedigree-based DNA methylation data as input. We demonstrate how AlphaBeta can be employed to study transgenerationally heritable epimutations in clonal or sexually derived mutation accumulation lines, as well as somatic epimutations in long-lived perennials. Application of our method to published and new data reveals that spontaneous epimutations accumulate neutrally at the genome-wide scale, originate mainly during somatic development and that they can be used as a molecular clock for age-dating trees.
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Affiliation(s)
- Yadollah Shahryary
- Technical University of Munich, Department of Plant Sciences, Liesel-Beckmann-Str. 2, Freising, 85354 Germany
- Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 2a, Garching, 85748 Germany
| | - Aikaterini Symeonidi
- Technical University of Munich, Department of Plant Sciences, Liesel-Beckmann-Str. 2, Freising, 85354 Germany
| | - Rashmi R. Hazarika
- Technical University of Munich, Department of Plant Sciences, Liesel-Beckmann-Str. 2, Freising, 85354 Germany
- Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 2a, Garching, 85748 Germany
| | - Johanna Denkena
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg, 85764 Germany
| | - Talha Mubeen
- Technical University of Munich, Department of Plant Sciences, Liesel-Beckmann-Str. 2, Freising, 85354 Germany
- Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 2a, Garching, 85748 Germany
| | | | - Thomas van Gurp
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Wageningen, Wageningen, The Netherlands
| | - Maria Colomé-Tatché
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg, 85764 Germany
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, Groningen, 9713 AV Netherlands
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Erlenmeyer-Forum 2, Freising, 85354 Germany
| | - Koen J.F. Verhoeven
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Wageningen, Wageningen, The Netherlands
| | - Gerald Tuskan
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, USA
| | - Robert J. Schmitz
- Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 2a, Garching, 85748 Germany
- Department of Genetics, The University of Georgia, 120 East Green Street, Athens, 30602 USA
| | - Frank Johannes
- Technical University of Munich, Department of Plant Sciences, Liesel-Beckmann-Str. 2, Freising, 85354 Germany
- Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 2a, Garching, 85748 Germany
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