51
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McGrath JM, Funk A, Galewski P, Ou S, Townsend B, Davenport K, Daligault H, Johnson S, Lee J, Hastie A, Darracq A, Willems G, Barnes S, Liachko I, Sullivan S, Koren S, Phillippy A, Wang J, Liu T, Pulman J, Childs K, Shu S, Yocum A, Fermin D, Mutasa-Göttgens E, Stevanato P, Taguchi K, Naegele R, Dorn KM. A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.). DNA Res 2022; 30:6748264. [PMID: 36208288 PMCID: PMC9896481 DOI: 10.1093/dnares/dsac033] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/26/2022] [Accepted: 09/12/2022] [Indexed: 02/04/2023] Open
Abstract
A contiguous assembly of the inbred 'EL10' sugar beet (Beta vulgaris ssp. vulgaris) genome was constructed using PacBio long-read sequencing, BioNano optical mapping, Hi-C scaffolding, and Illumina short-read error correction. The EL10.1 assembly was 540 Mb, of which 96.2% was contained in nine chromosome-sized pseudomolecules with lengths from 52 to 65 Mb, and 31 contigs with a median size of 282 kb that remained unassembled. Gene annotation incorporating RNA-seq data and curated sequences via the MAKER annotation pipeline generated 24,255 gene models. Results indicated that the EL10.1 genome assembly is a contiguous genome assembly highly congruent with the published sugar beet reference genome. Gross duplicate gene analyses of EL10.1 revealed little large-scale intra-genome duplication. Reduced gene copy number for well-annotated gene families relative to other core eudicots was observed, especially for transcription factors. Variation in genome size in B. vulgaris was investigated by flow cytometry among 50 individuals producing estimates from 633 to 875 Mb/1C. Read-depth mapping with short-read whole-genome sequences from other sugar beet germplasm suggested that relatively few regions of the sugar beet genome appeared associated with high-copy number variation.
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Affiliation(s)
| | - Andrew Funk
- Plant Breeding, Genetics, and Biotechnology Program, Michigan State University, East Lansing, MI 48824, USA
| | - Paul Galewski
- Plant Breeding, Genetics, and Biotechnology Program, Michigan State University, East Lansing, MI 48824, USA
| | - Shujun Ou
- Plant Breeding, Genetics, and Biotechnology Program, Michigan State University, East Lansing, MI 48824, USA
| | - Belinda Townsend
- Department of Plant Sciences, Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Karen Davenport
- Los Alamos Nat’l Lab, Biosecurity and Public Health, Los Alamos, NM 87545, USA
| | - Hajnalka Daligault
- Los Alamos Nat’l Lab, Biosecurity and Public Health, Los Alamos, NM 87545, USA
| | - Shannon Johnson
- Los Alamos Nat’l Lab, Biosecurity and Public Health, Los Alamos, NM 87545, USA
| | - Joyce Lee
- BioNano Genomics, 9640 Towne Centre Drive, San Diego, CA 92121, USA
| | - Alex Hastie
- BioNano Genomics, 9640 Towne Centre Drive, San Diego, CA 92121, USA
| | - Aude Darracq
- SESVANDERHAVE N.V., Industriepark Soldatenplein Zone 2 Nr 15, 3300 Tienen, Belgium
| | - Glenda Willems
- SESVANDERHAVE N.V., Industriepark Soldatenplein Zone 2 Nr 15, 3300 Tienen, Belgium
| | - Steve Barnes
- SESVANDERHAVE N.V., Industriepark Soldatenplein Zone 2 Nr 15, 3300 Tienen, Belgium
| | - Ivan Liachko
- Phase Genomics, 4000 Mason Road, Suite 225, Seattle, WA 98195, USA
| | - Shawn Sullivan
- Phase Genomics, 4000 Mason Road, Suite 225, Seattle, WA 98195, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Adam Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Jie Wang
- Center for Genomics-Enabled Plant Science, Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA
| | - Tiffany Liu
- Center for Genomics-Enabled Plant Science, Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA
| | - Jane Pulman
- Center for Genomics-Enabled Plant Science, Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA
| | - Kevin Childs
- Center for Genomics-Enabled Plant Science, Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA
| | - Shengqiang Shu
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
| | | | | | - Effie Mutasa-Göttgens
- University of Hertfordshire, Division of Biosciences, Hatfield, Hertfordshire AL10 9AB, UK
| | | | - Kazunori Taguchi
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Shinsei Memuro, Hokkaido 082-0081, Japan
| | - Rachel Naegele
- USDA-ARS Sugarbeet and Bean Research Unit, Michigan State University, 1066 Bogue St., East Lansing, MI 48824, USA
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52
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Cerbin S, Ou S, Li Y, Sun Y, Jiang N. Distinct composition and amplification dynamics of transposable elements in sacred lotus (Nelumbo nucifera Gaertn.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:172-192. [PMID: 35959634 PMCID: PMC9804982 DOI: 10.1111/tpj.15938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/19/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Sacred lotus (Nelumbo nucifera Gaertn.) is a basal eudicot plant with a unique lifestyle, physiological features, and evolutionary characteristics. Here we report the unique profile of transposable elements (TEs) in the genome, using a manually curated repeat library. TEs account for 59% of the genome, and hAT (Ac/Ds) elements alone represent 8%, more than in any other known plant genome. About 18% of the lotus genome is comprised of Copia LTR retrotransposons, and over 25% of them are associated with non-canonical termini (non-TGCA). Such high abundance of non-canonical LTR retrotransposons has not been reported for any other organism. TEs are very abundant in genic regions, with retrotransposons enriched in introns and DNA transposons primarily in flanking regions of genes. The recent insertion of TEs in introns has led to significant intron size expansion, with a total of 200 Mb in the 28 455 genes. This is accompanied by declining TE activity in intergenic regions, suggesting distinct control efficacy of TE amplification in different genomic compartments. Despite the prevalence of TEs in genic regions, some genes are associated with fewer TEs, such as those involved in fruit ripening and stress responses. Other genes are enriched with TEs, and genes in epigenetic pathways are the most associated with TEs in introns, indicating a dynamic interaction between TEs and the host surveillance machinery. The dramatic differential abundance of TEs with genes involved in different biological processes as well as the variation of target preference of different TEs suggests the composition and activity of TEs influence the path of evolution.
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Affiliation(s)
- Stefan Cerbin
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
- Present address:
Department of Ecology & Evolutionary BiologyUniversity of Kansas1200 Sunnyside AvenueLawrenceKS66045USA
| | - Shujun Ou
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
- Present address:
Department of Computer ScienceJohns Hopkins UniversityBaltimoreMD21218USA
| | - Yang Li
- Department of Electrical EngineeringCity University of Hong KongKowloonHong Kong SARChina
| | - Yanni Sun
- Department of Electrical EngineeringCity University of Hong KongKowloonHong Kong SARChina
| | - Ning Jiang
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
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53
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Klein SP, Anderson SN. The evolution and function of transposons in epigenetic regulation in response to the environment. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102277. [PMID: 35961279 DOI: 10.1016/j.pbi.2022.102277] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/21/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Transposable elements (TEs) make up a major proportion of plant genomes. Despite their prevalence genome-wide, TEs are often tossed aside as "junk DNA" since they rarely cause phenotypes, and epigenetic mechanisms silence TEs to prevent them from causing deleterious mutations through movement. While this bleak picture of TEs in genomes is true on average, a growing number of examples across many plant species point to TEs as drivers of phenotypic diversity and novel stress responses. Examples of TE-influenced phenotypes illustrate the many ways that novel transposition events can alter local gene expression and how this relates to potential variation in plant responses to environmental stress. Since TE families and insertions at the locus level lack evolutionary conservation, advancements in the field will require TE experts across diverse species to identify and utilize TE variation in their own systems as a means of crop improvement.
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Affiliation(s)
- Stephanie P Klein
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Sarah N Anderson
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.
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54
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Schley RJ, Pellicer J, Ge X, Barrett C, Bellot S, Guignard MS, Novák P, Suda J, Fraser D, Baker WJ, Dodsworth S, Macas J, Leitch AR, Leitch IJ. The ecology of palm genomes: repeat-associated genome size expansion is constrained by aridity. THE NEW PHYTOLOGIST 2022; 236:433-446. [PMID: 35717562 PMCID: PMC9796251 DOI: 10.1111/nph.18323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Genome size varies 2400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants' environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat 'communities' are analogous to those structuring ecological communities. However, which environmental stressors influence repeat community dynamics has not yet been examined from an ecological perspective. We measured genome size and leveraged climatic data for 91% of genera within the ecologically diverse palm family (Arecaceae). We then generated genomic repeat profiles for 141 palm species, and analysed repeats using phylogenetically informed linear models to explore relationships between repeat dynamics and environmental factors. We show that palm genome size and repeat 'community' composition are best explained by aridity. Specifically, Ty3-gypsy and TIR elements were more abundant in palm species from wetter environments, which generally had larger genomes, suggesting amplification. By contrast, Ty1-copia and LINE elements were more abundant in drier environments. Our results suggest that water stress inhibits repeat expansion through selection on upper genome size limits. However, elements that may associate with stress-response genes (e.g. Ty1-copia) have amplified in arid-adapted palm species. Overall, we provide novel evidence of climate influencing the assembly of repeat 'communities'.
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Affiliation(s)
- Rowan J. Schley
- University of ExeterLaver Building, North Park RoadExeterDevonEX4 4QEUK
- Royal Botanic GardensKewSurreyTW9 3ABUK
| | - Jaume Pellicer
- Royal Botanic GardensKewSurreyTW9 3ABUK
- Institut Botànic de Barcelona (IBB, CSIC‐Ajuntament de Barcelona)Passeig del Migdia sn08038BarcelonaSpain
| | - Xue‐Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhou510650China
| | - Craig Barrett
- Department of BiologyWest Virginia UniversityMorgantownWV26506USA
| | | | | | - Petr Novák
- Biology Centre, Institute of Plant Molecular BiologyCzech Academy of Sciences370 05České BudějoviceCzech Republic
| | | | | | | | - Steven Dodsworth
- School of Biological SciencesUniversity of PortsmouthPortsmouthHampshirePO1 2DYUK
| | - Jiří Macas
- Biology Centre, Institute of Plant Molecular BiologyCzech Academy of Sciences370 05České BudějoviceCzech Republic
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55
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Chumová Z, Belyayev A, Mandáková T, Zeisek V, Hodková E, Šemberová K, Euston-Brown D, Trávníček P. The relationship between transposable elements and ecological niches in the Greater Cape Floristic Region: A study on the genus Pteronia (Asteraceae). FRONTIERS IN PLANT SCIENCE 2022; 13:982852. [PMID: 36247607 PMCID: PMC9559566 DOI: 10.3389/fpls.2022.982852] [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: 06/30/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Non-coding repetitive DNA (repeatome) is an active part of the nuclear genome, involved in its structure, evolution and function. It is dominated by transposable elements (TEs) and satellite DNA and is prone to the most rapid changes over time. The TEs activity presumably causes the global genome reorganization and may play an adaptive or regulatory role in response to environmental challenges. This assumption is applied here for the first time to plants from the Cape Floristic hotspot to determine whether changes in repetitive DNA are related to responses to a harsh, but extremely species-rich environment. The genus Pteronia (Asteraceae) serves as a suitable model group because it shows considerable variation in genome size at the diploid level and has high and nearly equal levels of endemism in the two main Cape biomes, Fynbos and Succulent Karoo. First, we constructed a phylogeny based on multiple low-copy genes that served as a phylogenetic framework for detecting quantitative and qualitative changes in the repeatome. Second, we performed a comparative analysis of the environments of two groups of Pteronia differing in their TEs bursts. Our results suggest that the environmental transition from the Succulent Karoo to the Fynbos is accompanied by TEs burst, which is likely also driving phylogenetic divergence. We thus hypothesize that analysis of rapidly evolving repeatome could serve as an important proxy for determining the molecular basis of lineage divergence in rapidly radiating groups.
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Affiliation(s)
- Zuzana Chumová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Alexander Belyayev
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Faculty of Science, Masaryk University, Brno, Czechia
| | - Vojtěch Zeisek
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | - Eva Hodková
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | - Kristýna Šemberová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | | | - Pavel Trávníček
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
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56
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Wang X, Wang M, Dai J, Wang Q, La H. Fine mapping and characterization of RLL6 locus required for anti-silencing of a transgene and DNA demethylation in Arabidopsisthaliana. Front Genet 2022; 13:1008700. [PMID: 36226182 PMCID: PMC9549997 DOI: 10.3389/fgene.2022.1008700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/29/2022] [Indexed: 11/29/2022] Open
Abstract
DNA methylation patterns in plants are dynamically shaped by the antagonistic actions of DNA methylation and demethylation pathways. Although the DNA methylation pathway has been well studied, the DNA demethylation pathway, however, are not fully understood so far. To gain deeper insights into the mechanisms of DNA demethylation pathway, we conducted a genetic screening for proteins that were involved in preventing epigenetic gene silencing, and then the ones, which were also implicated in DNA demethylation pathway, were used for further studies. Eventually, a mutant with low luciferase luminescence (low LUC luminescence) was recovered, and named reduced LUC luminescence 6–1 (rll6-1). Map-based cloning revealed that rll6-1 mutation was located on chromosome 4, and there were a total of 10 candidate genes residing within such a region. Analyses of genome-wide methylation patterns of rll6-1 mutant showed that mutation of RLL6 locus led to 3,863 hyper-DMRs (DMRs for differentially methylated regions) throughout five Arabidopsis chromosomes, and elevated DNA methylation level of 2 × 35S promoter, which was similar to that found in the ros1 (repressor of silencing 1) mutant. Further analysis demonstrated that there were 1,456 common hyper-DMRs shared by rll6-1 and ros1-7 mutants, suggesting that both proteins acted together in a synergistic manner to remove DNA methylation. Further investigations demonstrated that mutation of RLL6 locus did not affect the expression of the four genes of the DNA glycosylase/lyase family. Thus, our results demonstrate that RLL6 locus-encoded protein not only participates in transcriptional anti-silencing of a transgene, but is also involved in DNA demethylation pathway.
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57
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Kuang L, Shen Q, Chen L, Ye L, Yan T, Chen ZH, Waugh R, Li Q, Huang L, Cai S, Fu L, Xing P, Wang K, Shao J, Wu F, Jiang L, Wu D, Zhang G. The genome and gene editing system of sea barleygrass provide a novel platform for cereal domestication and stress tolerance studies. PLANT COMMUNICATIONS 2022; 3:100333. [PMID: 35643085 PMCID: PMC9482977 DOI: 10.1016/j.xplc.2022.100333] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/24/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
The tribe Triticeae provides important staple cereal crops and contains elite wild species with wide genetic diversity and high tolerance to abiotic stresses. Sea barleygrass (Hordeum marinum Huds.), a wild Triticeae species, thrives in saline marshlands and is well known for its high tolerance to salinity and waterlogging. Here, a 3.82-Gb high-quality reference genome of sea barleygrass is assembled de novo, with 3.69 Gb (96.8%) of its sequences anchored onto seven chromosomes. In total, 41 045 high-confidence (HC) genes are annotated by homology, de novo prediction, and transcriptome analysis. Phylogenetics, non-synonymous/synonymous mutation ratios (Ka/Ks), and transcriptomic and functional analyses provide genetic evidence for the divergence in morphology and salt tolerance among sea barleygrass, barley, and wheat. The large variation in post-domestication genes (e.g. IPA1 and MOC1) may cause interspecies differences in plant morphology. The extremely high salt tolerance of sea barleygrass is mainly attributed to low Na+ uptake and root-to-shoot translocation, which are mainly controlled by SOS1, HKT, and NHX transporters. Agrobacterium-mediated transformation and CRISPR/Cas9-mediated gene editing systems were developed for sea barleygrass to promote its utilization for exploration and functional studies of hub genes and for the genetic improvement of cereal crops.
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Affiliation(s)
- Liuhui Kuang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Qiufang Shen
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Liyang Chen
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Lingzhen Ye
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Tao Yan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Zhong-Hua Chen
- School of Science, Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia
| | - Robbie Waugh
- The James Hutton Institute, Dundee DD2 5DA, UK; The Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee DD2 5DA, UK; School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Qi Li
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Lu Huang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Shengguan Cai
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Liangbo Fu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Pengwei Xing
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Kai Wang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Jiari Shao
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Feibo Wu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Lixi Jiang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Dezhi Wu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
| | - Guoping Zhang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China.
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Li SF, She HB, Yang LL, Lan LN, Zhang XY, Wang LY, Zhang YL, Li N, Deng CL, Qian W, Gao WJ. Impact of LTR-Retrotransposons on Genome Structure, Evolution, and Function in Curcurbitaceae Species. Int J Mol Sci 2022; 23:ijms231710158. [PMID: 36077556 PMCID: PMC9456015 DOI: 10.3390/ijms231710158] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Long terminal repeat (LTR)-retrotransposons (LTR-RTs) comprise a major portion of many plant genomes and may exert a profound impact on genome structure, function, and evolution. Although many studies have focused on these elements in an individual species, their dynamics on a family level remains elusive. Here, we investigated the abundance, evolutionary dynamics, and impact on associated genes of LTR-RTs in 16 species in an economically important plant family, Cucurbitaceae. Results showed that full-length LTR-RT numbers and LTR-RT content varied greatly among different species, and they were highly correlated with genome size. Most of the full-length LTR-RTs were amplified after the speciation event, reflecting the ongoing rapid evolution of these genomes. LTR-RTs highly contributed to genome size variation via species-specific distinct proliferations. The Angela and Tekay lineages with a greater evolutionary age were amplified in Trichosanthes anguina, whereas a recent activity burst of Reina and another ancient round of Tekay activity burst were examined in Sechium edule. In addition, Tekay and Retand lineages belonging to the Gypsy superfamily underwent a recent burst in Gynostemma pentaphyllum. Detailed investigation of genes with intronic and promoter LTR-RT insertion showed diverse functions, but the term of metabolism was enriched in most species. Further gene expression analysis in G.pentaphyllum revealed that the LTR-RTs within introns suppress the corresponding gene expression, whereas the LTR-RTs within promoters exert a complex influence on the downstream gene expression, with the main function of promoting gene expression. This study provides novel insights into the organization, evolution, and function of LTR-RTs in Cucurbitaceae genomes.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Hong-Bing She
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Long-Long Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Li-Na Lan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Xin-Yu Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Li-Ying Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Yu-Lan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Wei Qian
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (W.Q.); (W.-J.G.)
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
- Correspondence: (W.Q.); (W.-J.G.)
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Integration of Repeatomic and Cytogenetic Data on Satellite DNA for the Genome Analysis in the Genus Salvia (Lamiaceae). PLANTS 2022; 11:plants11172244. [PMID: 36079625 PMCID: PMC9460151 DOI: 10.3390/plants11172244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/25/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022]
Abstract
Within the complicated and controversial taxonomy of cosmopolitan genus Salvia L. (Lamiaceae) are valuable species Salvia officinalis L. and Salvia sclarea L., which are important for the pharmaceutical, ornamental horticulture, food, and perfume industries. Genome organization and chromosome structure of these essential oil species remain insufficiently studied. For the first time, the comparative repeatome analysis of S. officinalis and S. sclarea was performed using the obtained NGS data, RepeatExplorer/TAREAN pipelines and FISH-based chromosome mapping of the revealed satellite DNA families (satDNAs). In repeatomes of these species, LTR retrotransposons made up the majority of their repetitive DNA. Interspecific variations in genome abundance of Class I and Class II transposable elements, ribosomal DNA, and satellite DNA were revealed. Four (S. sclarea) and twelve (S. officinalis) putative satDNAs were identified. Based on patterns of chromosomal distribution of 45S rDNA; 5S rDNA and the revealed satDNAs, karyograms of S. officinalis and S. sclarea were constructed. Promising satDNAs which can be further used as chromosome markers to assess inter- and intraspecific chromosome variability in Salvia karyotypes were determined. The specific localization of homologous satDNA and 45S rDNA on chromosomes of the studied Salvia species confirmed their common origin, which is consistent with previously reported molecular phylogenetic data.
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Sreeharsha RV, Mudalkar S, Reddy AR. Genome sequencing and analysis uncover the regulatory elements involved in the development and oil biosynthesis of Pongamia pinnata (L.) - A potential biodiesel feedstock. FRONTIERS IN PLANT SCIENCE 2022; 13:747783. [PMID: 36092428 PMCID: PMC9454018 DOI: 10.3389/fpls.2022.747783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Due to rapid industrialization, the consumption of petro-products has increased, while fossil fuel resources have been gradually depleted. There has been a resurgence of interest in plant-derived biofuels as a sustainable alternative to fossil fuels for the purpose of reducing greenhouse gas emissions. Pongamia pinnata L., which is also known as Millettia pinnata is an oil-yielding, leguminous tree with a large and complex genome. Despite its multiple industrial applications, this orphan tree species has inconsistent yields and a limited understanding of its functional genomics. We assessed physiological and morphological characteristics of five high-yielding pongamia accessions and deduced important yield descriptors. Furthermore, we sequenced the genome of this potential biofuel feedstock using Illumina HiSeq, NextSeq, and MiSeq platforms to generate paired-end reads. Around 173 million processed reads amounting to 65.2 Gb were assembled into a 685 Mb genome, with a gap rate of 0.02%. The sequenced scaffolds were used to identify 30,000 gene models, 406,385 Simple-Sequence-Repeat (SSR) markers, and 43.6% of repetitive sequences. We further analyzed the structural information of genes belonging to certain key metabolic pathways, including lipid metabolism, photosynthesis, circadian rhythms, plant-pathogen interactions, and karanjin biosynthesis, all of which are commercially significant for pongamia. A total of 2,219 scaffolds corresponding to 29 transcription factor families provided valuable information about gene regulation in pongamia. Similarity studies and phylogenetic analysis revealed a monophyletic group of Fabaceae members wherein pongamia out-grouped from Glycine max and Cajanus cajan, revealing its unique ability to synthesize oil for biodiesel. This study is the first step toward completing the genome sequence of this imminent biofuel tree species. Further attempts at re-sequencing with different read chemistry will certainly improve the genetic resources at the chromosome level and accelerate the molecular breeding programs.
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Affiliation(s)
- Rachapudi Venkata Sreeharsha
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
- Department of Life Sciences, Chhatrapati Shahu Ji Maharaj University, Kanpur, India
| | - Shalini Mudalkar
- Department of Tree Breeding and Improvement, Forest College and Research Institute (FCRI), Hyderabad, India
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Characterization of Transposon-Derived Accessible Chromatin Regions in Rice (Oryza Sativa). Int J Mol Sci 2022; 23:ijms23168947. [PMID: 36012213 PMCID: PMC9408979 DOI: 10.3390/ijms23168947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
Growing evidence indicates that transposons or transposable elements (TEs)-derived accessible chromatin regions (ACRs) play essential roles in multiple biological processes by interacting with trans-acting factors. However, the function of TE-derived ACRs in the regulation of gene expression in the rice genome has not been well characterized. In this study, we examined the chromatin dynamics in six types of rice tissues and found that ~8% of ACRs were derived from TEs and exhibited distinct levels of accessibility and conservation as compared to those without TEs. TEs exhibited a TE subtype-dependent impact on ACR formation, which can be mediated by changes in the underlying DNA methylation levels. Moreover, we found that tissue-specific TE-derived ACRs might function in the tissue development through the modulation of nearby gene expression. Interestingly, many genes in domestication sweeps were found to overlap with TE-derived ACRs, suggesting their potential functions in the rice domestication. In addition, we found that the expression divergence of 1070 duplicate gene pairs were associated with TE-derived ACRs and had distinct distributions of TEs and ACRs around the transcription start sites (TSSs), which may experience different selection pressures. Thus, our study provides some insights into the biological implications of TE-derived ACRs in the rice genome. Our results imply that these ACRs are likely involved in the regulation of tissue development, rice domestication and functional divergence of duplicated genes.
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Dobrovolná M, Bohálová N, Peška V, Wang J, Luo Y, Bartas M, Volná A, Mergny JL, Brázda V. The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation. Int J Mol Sci 2022; 23:8482. [PMID: 35955617 PMCID: PMC9369095 DOI: 10.3390/ijms23158482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/20/2022] Open
Abstract
G-quadruplexes (G4s) have been long considered rare and physiologically unimportant in vitro curiosities, but recent methodological advances have proved their presence and functions in vivo. Moreover, in addition to their functional relevance in bacteria and animals, including humans, their importance has been recently demonstrated in evolutionarily distinct plant species. In this study, we analyzed the genome of Pisum sativum (garden pea, or the so-called green pea), a unique member of the Fabaceae family. Our results showed that this genome contained putative G4 sequences (PQSs). Interestingly, these PQSs were located nonrandomly in the nuclear genome. We also found PQSs in mitochondrial (mt) and chloroplast (cp) DNA, and we experimentally confirmed G4 formation for sequences found in these two organelles. The frequency of PQSs for nuclear DNA was 0.42 PQSs per thousand base pairs (kbp), in the same range as for cpDNA (0.53/kbp), but significantly lower than what was found for mitochondrial DNA (1.58/kbp). In the nuclear genome, PQSs were mainly associated with regulatory regions, including 5'UTRs, and upstream of the rRNA region. In contrast to genomic DNA, PQSs were located around RNA genes in cpDNA and mtDNA. Interestingly, PQSs were also associated with specific transposable elements such as TIR and LTR and around them, pointing to their role in their spreading in nuclear DNA. The nonrandom localization of PQSs uncovered their evolutionary and functional significance in the Pisum sativum genome.
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Affiliation(s)
- Michaela Dobrovolná
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Natália Bohálová
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Department of Experimental Biology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Vratislav Peška
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
| | - Jiawei Wang
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
| | - Yu Luo
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, CEDEX, 91405 Orsay, France
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic
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Samoluk SS, Vaio M, Ortíz AM, Chalup LMI, Robledo G, Bertioli DJ, Seijo G. Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species. PLANTA 2022; 256:50. [PMID: 35895167 DOI: 10.1007/s00425-022-03961-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Opposing changes in the abundance of satellite DNA and long terminal repeat (LTR) retroelements are the main contributors to the variation in genome size and heterochromatin amount in Arachis diploids. The South American genus Arachis (Fabaceae) comprises 83 species organized in nine taxonomic sections. Among them, section Arachis is characterized by species with a wide genome and karyotype diversity. Such diversity is determined mainly by the amount and composition of repetitive DNA. Here we performed computational analysis on low coverage genome sequencing to infer the dynamics of changes in major repeat families that led to the differentiation of genomes in diploid species (x = 10) of genus Arachis, focusing on section Arachis. Estimated repeat content ranged from 62.50 to 71.68% of the genomes. Species with different genome composition tended to have different landscapes of repeated sequences. Athila family retrotransposons were the most abundant and variable lineage among Arachis repeatomes, with peaks of transpositional activity inferred at different times in the evolution of the species. Satellite DNAs (satDNAs) were less abundant, but differentially represented among species. High rates of evolution of an AT-rich superfamily of satDNAs led to the differential accumulation of heterochromatin in Arachis genomes. The relationship between genome size variation and the repetitive content is complex. However, largest genomes presented a higher accumulation of LTR elements and lower contents of satDNAs. In contrast, species with lowest genome sizes tended to accumulate satDNAs in detriment of LTR elements. Phylogenetic analysis based on repetitive DNA supported the genome arrangement of section Arachis. Altogether, our results provide the most comprehensive picture on the repeatome dynamics that led to the genome differentiation of Arachis species.
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Affiliation(s)
- Sergio S Samoluk
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina.
| | - Magdalena Vaio
- Laboratory of Plant Genome Evolution and Domestication, Department of Plant Biology, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay
| | - Alejandra M Ortíz
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
| | - Laura M I Chalup
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
| | - Germán Robledo
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - David J Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Guillermo Seijo
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
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Ouadi S, Sierro N, Goepfert S, Bovet L, Glauser G, Vallat A, Peitsch MC, Kessler F, Ivanov NV. The clove (Syzygium aromaticum) genome provides insights into the eugenol biosynthesis pathway. Commun Biol 2022; 5:684. [PMID: 35810198 PMCID: PMC9271057 DOI: 10.1038/s42003-022-03618-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 06/22/2022] [Indexed: 11/09/2022] Open
Abstract
The clove (Syzygium aromaticum) is an important tropical spice crop in global trade. Evolving environmental pressures necessitate modern characterization and selection techniques that are currently inaccessible to clove growers owing to the scarcity of genomic and genetic information. Here, we present a 370-Mb high-quality chromosome-scale genome assembly for clove. Comparative genomic analysis between S. aromaticum and Eucalyptus grandis—both species of the Myrtaceae family—reveals good genome structure conservation and intrachromosomal rearrangements on seven of the eleven chromosomes. We report genes that belong to families involved in the biosynthesis of eugenol, the major bioactive component of clove products. On the basis of our transcriptomic and metabolomic findings, we propose a hypothetical scenario in which eugenol acetate plays a key role in high eugenol accumulation in clove leaves and buds. The clove genome is a new contribution to omics resources for the Myrtaceae family and an important tool for clove research. A newly assembled clove genome is compared with E. grandis to investigate genome evolution between the two genera of the Myrtaceae family, and putative genes involved in the biosynthesis of eugenol are identified through transcriptomics and metabolomics.
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Affiliation(s)
- Sonia Ouadi
- Faculty of Sciences, Laboratory of Plant Physiology, University of Neuchâtel, 2000, Neuchâtel, Switzerland.,PMI R&D, Philip Morris Products S. A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Nicolas Sierro
- PMI R&D, Philip Morris Products S. A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Simon Goepfert
- PMI R&D, Philip Morris Products S. A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Lucien Bovet
- PMI R&D, Philip Morris Products S. A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Gaetan Glauser
- Faculty of Sciences, Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, 2000, Neuchâtel, Switzerland
| | - Armelle Vallat
- Faculty of Sciences, Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, 2000, Neuchâtel, Switzerland
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S. A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Felix Kessler
- Faculty of Sciences, Laboratory of Plant Physiology, University of Neuchâtel, 2000, Neuchâtel, Switzerland
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S. A, Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland.
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Taheri S, Teo CH, Heslop-Harrison JS, Schwarzacher T, Tan YS, Wee WY, Khalid N, Biswas MK, Mutha NVR, Mohd-Yusuf Y, Gan HM, Harikrishna JA. Genome Assembly and Analysis of the Flavonoid and Phenylpropanoid Biosynthetic Pathways in Fingerroot Ginger ( Boesenbergia rotunda). Int J Mol Sci 2022; 23:7269. [PMID: 35806276 PMCID: PMC9266397 DOI: 10.3390/ijms23137269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 01/27/2023] Open
Abstract
Boesenbergia rotunda (Zingiberaceae), is a high-value culinary and ethno-medicinal plant of Southeast Asia. The rhizomes of this herb have a high flavanone and chalcone content. Here we report the genome analysis of B. rotunda together with a complete genome sequence as a hybrid assembly. B. rotunda has an estimated genome size of 2.4 Gb which is assembled as 27,491 contigs with an N50 size of 12.386 Mb. The highly heterozygous genome encodes 71,072 protein-coding genes and has a 72% repeat content, with class I TEs occupying ~67% of the assembled genome. Fluorescence in situ hybridization of the 18 chromosome pairs at the metaphase showed six sites of 45S rDNA and two sites of 5S rDNA. An SSR analysis identified 238,441 gSSRs and 4604 EST-SSRs with 49 SSR markers common among related species. Genome-wide methylation percentages ranged from 73% CpG, 36% CHG and 34% CHH in the leaf to 53% CpG, 18% CHG and 25% CHH in the embryogenic callus. Panduratin A biosynthetic unigenes were most highly expressed in the watery callus. B rotunda has a relatively large genome with a high heterozygosity and TE content. This assembly and data (PRJNA71294) comprise a source for further research on the functional genomics of B. rotunda, the evolution of the ginger plant family and the potential genetic selection or improvement of gingers.
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Affiliation(s)
- Sima Taheri
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur 50603, Malaysia; (S.T.); (C.H.T.); (Y.M.-Y.)
| | - Chee How Teo
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur 50603, Malaysia; (S.T.); (C.H.T.); (Y.M.-Y.)
| | - John S. Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (T.S.); (M.K.B.)
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (T.S.); (M.K.B.)
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yew Seong Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Wei Yee Wee
- School of Science, Monash University Malaysia, Subang Jaya 47500, Malaysia;
| | - Norzulaani Khalid
- Department of Biology, International University of Malaya-Wales, Kuala Lumpur 50603, Malaysia;
| | - Manosh Kumar Biswas
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (T.S.); (M.K.B.)
| | - Naresh V. R. Mutha
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37203, USA;
| | - Yusmin Mohd-Yusuf
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur 50603, Malaysia; (S.T.); (C.H.T.); (Y.M.-Y.)
- Biology Division, Centre for Foundation Studies in Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Han Ming Gan
- Department of Biological Sciences, Sunway University, Bandar Sunway, Petaling Jaya 47500, Malaysia;
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur 50603, Malaysia; (S.T.); (C.H.T.); (Y.M.-Y.)
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia;
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Interspecific hybridization in tomato influences endogenous viral sRNAs and alters gene expression. Genome Biol 2022; 23:120. [PMID: 35597968 PMCID: PMC9124383 DOI: 10.1186/s13059-022-02685-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/09/2022] [Indexed: 11/23/2022] Open
Abstract
Background Hybridization is associated with the activation of transposable elements and changes in the patterns of gene expression leading to phenotypic changes. However, the underlying mechanisms are not well understood. Results Here, we describe the changes to the gene expression in interspecific Solanum hybrids that are associated with small RNAs derived from endogenous (para)retroviruses (EPRV). There were prominent changes to sRNA profiles in these hybrids involving 22-nt species produced in the DCL2 biogenesis pathway, and the hybridization-induced changes to the gene expression were similar to those in a dcl2 mutant. Conclusions These findings indicate that hybridization leads to activation of EPRV, perturbation of small RNA profiles, and, consequently, changes in the gene expression. Such hybridization-induced variation in the gene expression could increase the natural phenotypic variation in natural evolution or in breeding for agriculture. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02685-z.
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Zhu Y, Chen L, Hong X, Shi H, Li X. Revealing the novel complexity of plant long non-coding RNA by strand-specific and whole transcriptome sequencing for evolutionarily representative plant species. BMC Genomics 2022; 23:381. [PMID: 35590257 PMCID: PMC9118565 DOI: 10.1186/s12864-022-08602-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 12/02/2022] Open
Abstract
Background Previous studies on plant long noncoding RNAs (lncRNAs) lacked consistency and suffered from many factors like heterogeneous data sources and experimental protocols, different plant tissues, inconsistent bioinformatics pipelines, etc. For example, the sequencing of RNAs with poly(A) tails excluded a large portion of lncRNAs without poly(A), and use of regular RNA-sequencing technique did not distinguish transcripts’ direction for lncRNAs. The current study was designed to systematically discover and analyze lncRNAs across eight evolutionarily representative plant species, using strand-specific (directional) and whole transcriptome sequencing (RiboMinus) technique. Results A total of 39,945 lncRNAs (25,350 lincRNAs and 14,595 lncNATs) were identified, which showed molecular features of lncRNAs that are consistent across divergent plant species but different from those of mRNA. Further, transposable elements (TEs) were found to play key roles in the origination of lncRNA, as significantly large number of lncRNAs were found to contain TEs in gene body and promoter region, and transcription of many lncRNAs was driven by TE promoters. The lncRNA sequences were divergent even in closely related species, and most plant lncRNAs were genus/species-specific, amid rapid turnover in evolution. Evaluated with PhastCons scores, plant lncRNAs showed similar conservation level to that of intergenic sequences, suggesting that most lincRNAs were young and with short evolutionary age. INDUCED BY PHOSPHATE STARVATION (IPS) was found so far to be the only plant lncRNA group with conserved motifs, which may play important roles in the adaptation of terrestrial life during migration from aquatic to terrestrial. Most highly and specially expressed lncRNAs formed co-expression network with coding genes, and their functions were believed to be closely related to their co-expression genes. Conclusion The study revealed novel features and complexity of lncRNAs in plants through systematic analysis, providing important insights into the origination and evolution of plant lncRNAs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08602-9.
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Affiliation(s)
- Yan Zhu
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Longxian Chen
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiangna Hong
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,Henan University, Kaifeng, China
| | - Han Shi
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China. .,University of Chinese Academy of Sciences, Beijing, China.
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Gu X, Su Y, Wang T. 转座元件对植物基因组进化、表观遗传和适应性的作用. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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69
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Fernández P, Hidalgo O, Juan A, Leitch IJ, Leitch AR, Palazzesi L, Pegoraro L, Viruel J, Pellicer J. Genome Insights into Autopolyploid Evolution: A Case Study in Senecio doronicum (Asteraceae) from the Southern Alps. PLANTS 2022; 11:plants11091235. [PMID: 35567236 PMCID: PMC9099586 DOI: 10.3390/plants11091235] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022]
Abstract
Polyploidy is a widespread phenomenon across angiosperms, and one of the main drivers of diversification. Whilst it frequently involves hybridisation, autopolyploidy is also an important feature of plant evolution. Minority cytotypes are frequently overlooked due to their lower frequency in populations, but the development of techniques such as flow cytometry, which enable the rapid screening of cytotype diversity across large numbers of individuals, is now providing a more comprehensive understanding of cytotype diversity within species. Senecio doronicum is a relatively common daisy found throughout European mountain grasslands from subalpine to almost nival elevations. We have carried out a population-level cytotype screening of 500 individuals from Tête Grosse (Alpes-de-Haute-Provence, France), confirming the coexistence of tetraploid (28.2%) and octoploid cytotypes (71.2%), but also uncovering a small number of hexaploid individuals (0.6%). The analysis of repetitive elements from short-read genome-skimming data combined with nuclear (ITS) and whole plastid DNA sequences support an autopolyploid origin of the polyploid S. doronicum individuals and provide molecular evidence regarding the sole contribution of tetraploids in the formation of hexaploid individuals. The evolutionary impact and resilience of the new cytotype have yet to be determined, although the coexistence of different cytotypes may indicate nascent speciation.
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Affiliation(s)
- Pol Fernández
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain;
- Correspondence: (P.F.); (J.P.); Tel.: +34-932890611 (P.F. & J.P.)
| | - Oriane Hidalgo
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain;
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK; (I.J.L.); (J.V.)
| | - Ana Juan
- Departamento de Ciencias Ambientales y Recursos Naturales, Universidad de Alicante, 03080 Alicante, Spain;
| | - Ilia J. Leitch
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK; (I.J.L.); (J.V.)
| | - Andrew R. Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK;
| | - Luis Palazzesi
- Museo Argentino de Ciencias Naturales, CONICET, División Paleobotánica, Buenos Aires C1405DJR, Argentina;
| | - Luca Pegoraro
- Biodiversity and Conservation Biology Research Unit, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Bimensdorf, Switzerland;
| | - Juan Viruel
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK; (I.J.L.); (J.V.)
| | - Jaume Pellicer
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain;
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK; (I.J.L.); (J.V.)
- Correspondence: (P.F.); (J.P.); Tel.: +34-932890611 (P.F. & J.P.)
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Gong W, Xiao S, Wang L, Liao Z, Chang Y, Mo W, Hu G, Li W, Zhao G, Zhu H, Hu X, Ji K, Xiang X, Song Q, Yuan D, Jin S, Zhang L. Chromosome-level genome of Camellia lanceoleosa provides a valuable resource for understanding genome evolution and self-incompatibility. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:881-898. [PMID: 35306701 DOI: 10.1111/tpj.15739] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 03/12/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
The section Oleifera (Theaceae) has attracted attention for the high levels of unsaturated fatty acids found in its seeds. Here, we report the chromosome-scale genome of the sect. Oleifera using diploid wild Camellia lanceoleosa with a final size of 3.00 Gb and an N50 scaffold size of 186.43 Mb. Repetitive sequences accounted for 80.63% and were distributed unevenly across the genome. Camellia lanceoleosa underwent a whole-genome duplication event approximately 65 million years ago (65 Mya), prior to the divergence of C. lanceoleosa and Camellia sinensis (approx. 6-7 Mya). Syntenic comparisons of these two species elucidated the genomic rearrangement, appearing to be driven in part by the activity of transposable elements. The expanded and positively selected genes in C. lanceoleosa were significantly enriched in oil biosynthesis, and the expansion of homomeric acetyl-coenzyme A carboxylase (ACCase) genes and the seed-biased expression of genes encoding heteromeric ACCase, diacylglycerol acyltransferase, glyceraldehyde-3-phosphate dehydrogenase and stearoyl-ACP desaturase could be of primary importance for the high oil and oleic acid content found in C. lanceoleosa. Theanine and catechins were present in the leaves of C. lanceoleosa. However, caffeine can not be dectected in the leaves but was abundant in the seeds and roots. The functional and transcriptional divergence of genes encoding SAM-dependent N-methyltransferases may be associated with caffeine accumulation and distribution. Gene expression profiles, structural composition and chromosomal location suggest that the late-acting self-incompatibility of C. lanceoleosa is likely to have favoured a novel mechanism co-occurring with gametophytic self-incompatibility. This study provides valuable resources for quantitative and qualitative improvements and genome assembly of polyploid plants in sect. Oleifera.
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Affiliation(s)
- Wenfang Gong
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Shixin Xiao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Linkai Wang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Zhenyang Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yihong Chang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Wenjuan Mo
- Experiment Center of Forestry in North China, Chinese Academy of Forestry, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiu Long Mountain in Beijing, Beijing, 102300, China
- College of Agriculture and Life Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Guanxing Hu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Wenying Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Guang Zhao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Huaguo Zhu
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, Hubei, 438000, China
| | - Xiaoming Hu
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, Hubei, 438000, China
| | - Ke Ji
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Xiaofeng Xiang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Qiling Song
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Deyi Yuan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
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Yurkevich OY, Samatadze TE, Selyutina IY, Suprun NA, Suslina SN, Zoshchuk SA, Amosova AV, Muravenko OV. Integration of Genomic and Cytogenetic Data on Tandem DNAs for Analyzing the Genome Diversity Within the Genus Hedysarum L. (Fabaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:865958. [PMID: 35574118 PMCID: PMC9101955 DOI: 10.3389/fpls.2022.865958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
The section Multicaulia is the largest clade in the genus Hedysarum L. (Fabaceae). Representatives of the sect. Multicaulia are valuable plants used for medicinal and fodder purposes. The taxonomy and phylogeny of the sect. Multicaulia are still ambiguous. To clarify the species relationships within sect. Multicaulia, we, for the first time, explored repeatomes of H. grandiflorum Pall., H. zundukii Peschkova, and H. dahuricum Turcz. using next-generation sequencing technologies and a subsequent bioinformatic analysis by RepeatExplorer/TAREAN pipelines. The comparative repeatome analysis showed that mobile elements made up 20-24% (Class I) and about 2-2.5% (Class II) of their repetitive DNAs. The amount of ribosomal DNA varied from 1 to 2.6%, and the content of satellite DNA ranged from 2.7 to 5.1%. For each species, five high confident putative tandem DNA repeats and 5-10 low confident putative DNA repeats were identified. According to BLAST, these repeats demonstrated high sequence similarity within the studied species. FISH-based mapping of 35S rDNA, 5S rDNA, and satDNAs made it possible to detect new effective molecular chromosome markers for Hedysarum species and construct the species karyograms. Comparison of the patterns of satDNA localization on chromosomes of the studied species allowed us to assess genome diversity within the sect. Multicaulia. In all studied species, we revealed intra- and interspecific variabilities in patterns of the chromosomal distribution of molecular chromosome markers. In H. gmelinii Ledeb. and H. setigerum Turcz. ex Fisch. et Meyer, similar subgenomes were detected, which confirmed the polyploid status of their genomes. Our findings demonstrated a close genomic relationship among six studied species indicating their common origin and confirmed the taxonomic status of H. setigerum as a subspecies of H. gmelinii as well as the validity of combining the sect. Multicaulia and Subacaulia into one sect. Multicaulia.
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Affiliation(s)
- Olga Yu. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Peoples’ Friendship University of Russia, Moscow, Russia
| | - Inessa Yu. Selyutina
- Central Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | | | | | - Alexandra V. Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Amosova AV, Yurkevich OY, Bolsheva NL, Samatadze TE, Zoshchuk SA, Muravenko OV. Repeatome Analyses and Satellite DNA Chromosome Patterns in Deschampsia sukatschewii, D. cespitosa, and D. antarctica (Poaceae). Genes (Basel) 2022; 13:genes13050762. [PMID: 35627148 PMCID: PMC9141916 DOI: 10.3390/genes13050762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 02/05/2023] Open
Abstract
Subpolar and polar ecotypes of Deschampsia sukatschewii (Popl.) Roshev, D. cespitosa (L.) P. Beauv, and D. antarctica E. Desv. are well adapted to stressful environmental conditions, which make them useful model plants for genetic research and breeding. For the first time, the comparative repeatome analyses of subpolar and polar D. sukatschewii, D. cespitosa, and D. antarctica was performed using RepeatExplorer/TAREAN pipelines and FISH-based chromosomal mapping of the identified satellite DNA families (satDNAs). In the studied species, mobile genetic elements of class 1 made up the majority of their repetitive DNA; interspecific variations in the total amount of Ty3/Gypsy and Ty1/Copia retroelements, DNA transposons, ribosomal, and satellite DNA were revealed; 12–18 high confident and 7–9 low confident putative satDNAs were identified. According to BLAST, most D. sukatschewii satDNAs demonstrated sequence similarity with satDNAs of D. antarctica and D. cespitosa indicating their common origin. Chromosomal mapping of 45S rDNA, 5S rDNA, and satDNAs of D. sukatschewii allowed us to construct the species karyograms and detect new molecular chromosome markers important for Deschampsia species. Our findings confirmed that genomes of D. sukatschewii and D. cespitosa were more closely related compared to D. antarctica according to repeatome composition and patterns of satDNA chromosomal distribution.
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Sicat JPA, Visendi P, Sewe SO, Bouvaine S, Seal SE. Characterization of transposable elements within the Bemisia tabaci species complex. Mob DNA 2022; 13:12. [PMID: 35440097 PMCID: PMC9017028 DOI: 10.1186/s13100-022-00270-6] [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: 01/30/2022] [Accepted: 03/30/2022] [Indexed: 12/24/2022] Open
Abstract
Background Whiteflies are agricultural pests that cause negative impacts globally to crop yields resulting at times in severe economic losses and food insecurity. The Bemisia tabaci whitefly species complex is the most damaging in terms of its broad crop host range and its ability to serve as vector for over 400 plant viruses. Genomes of whiteflies belonging to this species complex have provided valuable genomic data; however, transposable elements (TEs) within these genomes remain unexplored. This study provides the first accurate characterization of TE content within the B. tabaci species complex. Results This study identified that an average of 40.61% of the genomes of three whitefly species (MEAM1, MEDQ, and SSA-ECA) consists of TEs. The majority of the TEs identified were DNA transposons (22.85% average) while SINEs (0.14% average) were the least represented. This study also compared the TE content of the three whitefly genomes with three other hemipteran genomes and found significantly more DNA transposons and less LINEs in the whitefly genomes. A total of 63 TE superfamilies were identified to be present across the three whitefly species (39 DNA transposons, six LTR, 16 LINE, and two SINE). The sequences of the identified TEs were clustered which generated 5766 TE clusters. A total of 2707 clusters were identified as uniquely found within the whitefly genomes while none of the generated clusters were from both whitefly and non-whitefly TE sequences. This study is the first to characterize TEs found within different B. tabaci species and has created a standardized annotation workflow that could be used to analyze future whitefly genomes. Conclusion This study is the first to characterize the landscape of TEs within the B. tabaci whitefly species complex. The characterization of these elements within the three whitefly genomes shows that TEs occupy significant portions of B. tabaci genomes, with DNA transposons representing the vast majority. This study also identified TE superfamilies and clusters of TE sequences of potential interest, providing essential information, and a framework for future TE studies within this species complex. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-022-00270-6.
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Affiliation(s)
- Juan Paolo A Sicat
- Natural Resources Institute, University of Greenwich, Central Avenue, Gillingham, Chatham, ME4 4TB, UK.
| | - Paul Visendi
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Steven O Sewe
- Natural Resources Institute, University of Greenwich, Central Avenue, Gillingham, Chatham, ME4 4TB, UK
| | - Sophie Bouvaine
- Natural Resources Institute, University of Greenwich, Central Avenue, Gillingham, Chatham, ME4 4TB, UK
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Gillingham, Chatham, ME4 4TB, UK
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Sharbrough J, Conover JL, Fernandes Gyorfy M, Grover CE, Miller ER, Wendel JF, Sloan DB. Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms. Mol Biol Evol 2022; 39:msac074. [PMID: 35383845 PMCID: PMC9040051 DOI: 10.1093/molbev/msac074] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Whole-genome duplications (WGDs) are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes on cytoplasmic genomes are not well understood, despite the central role that cytonuclear interactions play in eukaryotic function and fitness. Cellular respiration and photosynthesis depend on successful interaction between the 3,000+ nuclear-encoded proteins destined for the mitochondria or plastids and the gene products of cytoplasmic genomes in multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I and II, and Rubisco. Allopolyploids are thus faced with the critical task of coordinating interactions between the nuclear and cytoplasmic genes that were inherited from different species. Because the cytoplasmic genomes share a more recent history of common descent with the maternal nuclear subgenome than the paternal subgenome, evolutionary "mismatches" between the paternal subgenome and the cytoplasmic genomes in allopolyploids might lead to the accelerated rates of evolution in the paternal homoeologs of allopolyploids, either through relaxed purifying selection or strong directional selection to rectify these mismatches. We report evidence from six independently formed allotetraploids that the subgenomes exhibit unequal rates of protein-sequence evolution, but we found no evidence that cytonuclear incompatibilities result in altered evolutionary trajectories of the paternal homoeologs of organelle-targeted genes. The analyses of gene content revealed mixed evidence for whether the organelle-targeted genes are lost more rapidly than the non-organelle-targeted genes. Together, these global analyses provide insights into the complex evolutionary dynamics of allopolyploids, showing that the allopolyploid subgenomes have separate evolutionary trajectories despite sharing the same nucleus, generation time, and ecological context.
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Affiliation(s)
- Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, CO, USA
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Justin L. Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | | | - Corrinne E. Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Emma R. Miller
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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Comparative Analysis of Transposable Elements and the Identification of Candidate Centromeric Elements in the Prunus Subgenus Cerasus and Its Relatives. Genes (Basel) 2022; 13:genes13040641. [PMID: 35456447 PMCID: PMC9028240 DOI: 10.3390/genes13040641] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 12/04/2022] Open
Abstract
The subgenus Cerasus and its relatives include many crucial economic drupe fruits and ornamental plants. Repetitive elements make up a large part of complex genomes, and some of them play an important role in gene regulation that can affect phenotypic variation. However, the variation in their genomes remains poorly understood. This work conducted a comprehensive repetitive sequence identification across the draft genomes of eight taxa of the genus Prunus, including four of the Prunus subgenus Cerasus (Prunus pseudocerasus, P. avium, P. yedoensis and P. × yedoensis) as well as congeneric species (Prunus salicina, P. armeniaca, P. dulcis and P. persica). Annotation results showed high proportions of transposable elements in their genomes, ranging from 52.28% (P. armeniaca) to 61.86% (P. pseudocerasus). The most notable differences in the contents of long terminal repeat retrotransposons (LTR-RTs) and tandem repeats (TRs) were confirmed with de novo identification based on the structure of each genome, which significantly contributed to their genome size variation, especially in P. avium and P.salicina. Sequence comparisons showed many similar LTR-RTs closely related to their phylogenetic relationships, and a highly similar monomer unit of the TR sequence was conserved among species. Additionally, the predicted centromere-associated sequence was located in centromeric regions with FISH in the 12 taxa of Prunus. It presented significantly different signal intensities, even within the diverse interindividual phenotypes for Prunus tomentosa. This study provides insight into the LTR-RT and TR variation within Prunus and increases our knowledge about its role in genome evolution.
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Specificities and Dynamics of Transposable Elements in Land Plants. BIOLOGY 2022; 11:biology11040488. [PMID: 35453688 PMCID: PMC9033089 DOI: 10.3390/biology11040488] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/10/2022] [Accepted: 03/18/2022] [Indexed: 01/27/2023]
Abstract
Simple Summary Transposable elements are dynamic components of plant genomes, and display a high diversity of lineages and distribution as the result of evolutionary driving forces and overlapping mechanisms of genetic and epigenetic regulation. They are now regarded as main contributors for genome evolution and function, and important regulators of endogenous gene expression. In this review, we survey recent progress and current challenges in the identification and classification of transposon lineages in complex plant genomes, highlighting the molecular specificities that may explain the expansion and diversification of mobile genetic elements in land plants. Abstract Transposable elements (TEs) are important components of most plant genomes. These mobile repetitive sequences are highly diverse in terms of abundance, structure, transposition mechanisms, activity and insertion specificities across plant species. This review will survey the different mechanisms that may explain the variability of TE patterns in land plants, highlighting the tight connection between TE dynamics and host genome specificities, and their co-evolution to face and adapt to a changing environment. We present the current TE classification in land plants, and describe the different levels of genetic and epigenetic controls originating from the plant, the TE itself, or external environmental factors. Such overlapping mechanisms of TE regulation might be responsible for the high diversity and dynamics of plant TEs observed in nature.
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Dolatabadian A, Fernando WGD. Genomic Variations and Mutational Events Associated with Plant-Pathogen Interactions. BIOLOGY 2022; 11:421. [PMID: 35336795 PMCID: PMC8945218 DOI: 10.3390/biology11030421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/23/2022]
Abstract
Phytopathologists are actively researching the molecular basis of plant-pathogen interactions. The mechanisms of responses to pathogens have been studied extensively in model crop plant species and natural populations. Today, with the rapid expansion of genomic technologies such as DNA sequencing, transcriptomics, proteomics, and metabolomics, as well as the development of new methods and protocols, data analysis, and bioinformatics, it is now possible to assess the role of genetic variation in plant-microbe interactions and to understand the underlying molecular mechanisms of plant defense and microbe pathogenicity with ever-greater resolution and accuracy. Genetic variation is an important force in evolution that enables organisms to survive in stressful environments. Moreover, understanding the role of genetic variation and mutational events is essential for crop breeders to produce improved cultivars. This review focuses on genetic variations and mutational events associated with plant-pathogen interactions and discusses how these genome compartments enhance plants' and pathogens' evolutionary processes.
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Affiliation(s)
- Aria Dolatabadian
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada;
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Ma J, Li C, Zong M, Qiu Y, Liu Y, Huang Y, Xie Y, Zhang H, Wang J. CmFSI8/CmOFP13 encoding an OVATE family protein controls fruit shape in melon. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1370-1384. [PMID: 34849737 DOI: 10.1093/jxb/erab510] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/20/2021] [Indexed: 06/13/2023]
Abstract
Fruit shape is an important quality and yield trait in melon (Cucumis melo). Although some quantitative trait loci for fruit shape have been reported in in this species, the genes responsible and the underlying mechanisms remain poorly understood. Here, we identified and characterized a gene controlling fruit shape from two melon inbred lines, B8 with long-horn fruit and HP22 with flat-round fruit. Genetic analysis suggested that the shape was controlled by a single and incompletely dominant locus, which we designate as CmFSI8/CmOFP13. This gene was finely mapped to a 53.7-kb interval on chromosome 8 based on bulked-segregant analysis sequencing and map-based cloning strategies. CmFSI8/CmOFP13 encodes an OVATE family protein (OFP) and is orthologous to AtOFP1 and SlOFP20. The transcription level of CmFSI8/CmOFP13 in the ovary of HP22 was significantly higher than that in B8, and sequence analysis showed that a 12.5-kb genomic variation with a retrotransposon insertion identified in the promoter was responsible for elevating the expression, and this ultimately caused the differences in fruit shape. Ectopic overexpression of CmFSI8/CmOFP13 in Arabidopsis led to multiple phenotypic changes, including kidney-shaped leaves and shortened siliques. Taken together, our results demonstrate the involvement of an OFP in regulating fruit shape in melon, and our improved understanding of the molecular mechanisms will enable us to better manipulate fruit shape in breeding.
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Affiliation(s)
- Jian Ma
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Congcong Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mei Zong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yanhong Qiu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yuemin Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yating Huang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yuli Xie
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Huijun Zhang
- School of Life Science, Huaibei Normal University, Huaibei, Anhui, 235000, China
| | - Jianshe Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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Miryeganeh M, Marlétaz F, Gavriouchkina D, Saze H. De novo genome assembly and in natura epigenomics reveal salinity-induced DNA methylation in the mangrove tree Bruguiera gymnorhiza. THE NEW PHYTOLOGIST 2022; 233:2094-2110. [PMID: 34532854 PMCID: PMC9293310 DOI: 10.1111/nph.17738] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 09/02/2021] [Indexed: 05/27/2023]
Abstract
Mangroves are adapted to harsh environments, such as high ultraviolet (UV) light, low nutrition, and fluctuating salinity in coastal zones. However, little is known about the transcriptomic and epigenomic basis of the resilience of mangroves due to limited available genome resources. We performed a de novo genome assembly and in natura epigenome analyses of the mangrove Bruguiera gymnorhiza, one of the dominant mangrove species. We also performed the first genome-guided transcriptome assembly for mangrove species. The 309 Mb of the genome is predicted to encode 34 403 genes and has a repeat content of 48%. Depending on its growing environment, the natural B. gymnorhiza population showed drastic morphological changes associated with expression changes in thousands of genes. Moreover, high-salinity environments induced genome-wide DNA hypermethylation of transposable elements (TEs) in the B. gymnorhiza. DNA hypermethylation was concurrent with the transcriptional regulation of chromatin modifier genes, suggesting robust epigenome regulation of TEs in the B. gymnorhiza genome under high-salinity environments. The genome and epigenome data in this study provide novel insights into the epigenome regulation of mangroves and a better understanding of the adaptation of plants to fluctuating, harsh natural environments.
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Affiliation(s)
- Matin Miryeganeh
- Plant Epigenetics UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawa904‐0495Japan
| | - Ferdinand Marlétaz
- Department of Genetics, Evolution and Environment (GEE)University College LondonDarwin Building, Gower StreetLondonWC1E 6BTUK
| | - Daria Gavriouchkina
- Molecular Genetics UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawa904‐0495Japan
| | - Hidetoshi Saze
- Plant Epigenetics UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawa904‐0495Japan
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Constitutive Heterochromatin in Eukaryotic Genomes: A Mine of Transposable Elements. Cells 2022; 11:cells11050761. [PMID: 35269383 PMCID: PMC8909793 DOI: 10.3390/cells11050761] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/10/2022] [Accepted: 02/18/2022] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are abundant components of constitutive heterochromatin of the most diverse evolutionarily distant organisms. TEs enrichment in constitutive heterochromatin was originally described in the model organism Drosophila melanogaster, but it is now considered as a general feature of this peculiar portion of the genomes. The phenomenon of TE enrichment in constitutive heterochromatin has been proposed to be the consequence of a progressive accumulation of transposable elements caused by both reduced recombination and lack of functional genes in constitutive heterochromatin. However, this view does not take into account classical genetics studies and most recent evidence derived by genomic analyses of heterochromatin in Drosophila and other species. In particular, the lack of functional genes does not seem to be any more a general feature of heterochromatin. Sequencing and annotation of Drosophila melanogaster constitutive heterochromatin have shown that this peculiar genomic compartment contains hundreds of transcriptionally active genes, generally larger in size than that of euchromatic ones. Together, these genes occupy a significant fraction of the genomic territory of heterochromatin. Moreover, transposable elements have been suggested to drive the formation of heterochromatin by recruiting HP1 and repressive chromatin marks. In addition, there are several pieces of evidence that transposable elements accumulation in the heterochromatin might be important for centromere and telomere structure. Thus, there may be more complexity to the relationship between transposable elements and constitutive heterochromatin, in that different forces could drive the dynamic of this phenomenon. Among those forces, preferential transposition may be an important factor. In this article, we present an overview of experimental findings showing cases of transposon enrichment into the heterochromatin and their positive evolutionary interactions with an impact to host genomes.
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81
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Ma X, Feng Y, Yang Y, Li X, Shi Y, Tao S, Cheng X, Huang J, Wang XE, Chen C, Monchaud D, Zhang W. Genome-wide characterization of i-motifs and their potential roles in the stability and evolution of transposable elements in rice. Nucleic Acids Res 2022; 50:3226-3238. [PMID: 35188565 PMCID: PMC8989525 DOI: 10.1093/nar/gkac121] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/13/2022] [Accepted: 02/07/2022] [Indexed: 12/15/2022] Open
Abstract
I-motifs (iMs) are non-canonical DNA secondary structures that fold from cytosine (C)-rich genomic DNA regions termed putative i-motif forming sequences (PiMFSs). The structure of iMs is stabilized by hemiprotonated C-C base pairs, and their functions are now suspected in key cellular processes in human cells such as genome stability and regulation of gene transcription. In plants, their biological relevance is still largely unknown. Here, we characterized PiMFSs with high potential for i-motif formation in the rice genome by developing and applying a protocol hinging on an iMab antibody-based immunoprecipitation (IP) coupled with high-throughput sequencing (seq), consequently termed iM-IP-seq. We found that PiMFSs had intrinsic subgenomic distributions, cis-regulatory functions and an intricate relationship with DNA methylation. We indeed found that the coordination of PiMFSs with DNA methylation may affect dynamics of transposable elements (TEs) among different cultivated Oryza subpopulations or during evolution of wild rice species. Collectively, our study provides first and unique insights into the biology of iMs in plants, with potential applications in plant biotechnology for improving important agronomic rice traits.
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Affiliation(s)
- Xing Ma
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Yilong Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Ying Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Xin Li
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan410125, P.R. China
| | - Yining Shi
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Shentong Tao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Jian Huang
- School of Biology & Basic Medical Science, Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Xiu-e Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Caiyan Chen
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan410125, P.R. China
| | - David Monchaud
- Institut de Chimie Moleculaire, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
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82
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Catlin NS, Josephs EB. The important contribution of transposable elements to phenotypic variation and evolution. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102140. [PMID: 34883307 DOI: 10.1016/j.pbi.2021.102140] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/04/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
Transposable elements (TEs) are responsible for significant genomic variation in plants. Our understanding of the evolutionary forces shaping TE polymorphism has lagged behind other mutations because of the difficulty of accurately identifying TE polymorphism in short-read population genomic data. However, new approaches allow us to quantify TE polymorphisms in population datasets and address fundamental questions about the evolution of these polymorphisms. Here, we discuss how insertional biases shape where, when, and how often TEs insert throughout the genome. Next, we examine mechanisms by which TEs can affect phenotype. Finally, we evaluate current evidence for selection on TE polymorphisms. All together, it is clear that TEs are important, but underappreciated, contributors to intraspecific phenotypic variation, and that understanding the dynamics governing TE polymorphism is crucial for evolutionary biologists interested in the maintenance of variation.
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Affiliation(s)
- Nathan S Catlin
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA.
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA
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83
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Lambert P, Confolent C, Heurtevin L, Dlalah N, Signoret V, Quilot-Turion B, Pascal T. Insertion of a mMoshan transposable element in PpLMI1, is associated with the absence or globose phenotype of extrafloral nectaries in peach [Prunus persica (L.) Batsch]. HORTICULTURE RESEARCH 2022; 9:uhab044. [PMID: 35039854 PMCID: PMC8829895 DOI: 10.1093/hr/uhab044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 08/14/2021] [Accepted: 09/17/2021] [Indexed: 06/14/2023]
Abstract
Most commercial peach [Prunus persica (L.) Batsch] cultivars have leaves with extrafloral nectaries (EFNs). Breeders have selected this character over time, as they observed that the eglandular phenotype resulted in high susceptibility to peach powdery mildew, a major disease of peach trees. EFNs are controlled by a Mendelian locus (E), mapped on chromosome 7. However, the genetic factor underlying E was unknown. In order to address this point, we developed a mapping population of 833 individuals derived from the selfing of "Malo Konare", a Bulgarian peach cultivar, heterozygous for the trait. This progeny was used to investigate the E-locus region, along with additional resources including peach genomic resequencing data, and 271 individuals from various origins used for validation. High-resolution mapping delimited a 40.6 kbp interval including the E-locus and four genes. Moreover, three double-recombinants allowed identifying Prupe.7G121100, a LMI1-like homeodomain leucine zipper (HD-Zip) transcription factor, as a likely candidate for the trait. By comparing peach genomic resequencing data from individuals with contrasted phenotypes, a MITE-like transposable element of the hAT superfamily (mMoshan) was identified in the third exon of Prupe.7G121100. It was associated with the absence or globose phenotype of EFNs. The insertion of the transposon was positively correlated with enhanced expression of Prupe.7G121100. Furthermore, a PCR marker designed from the sequence-variants, allowed to properly assign the phenotypes of all the individuals studied. These findings provide valuable information on the genetic control of a trait poorly known so far although selected for a long time in peach.
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Affiliation(s)
| | - Carole Confolent
- INRAE, GAFL, Montfavet, F-84143, FRANCE
- INRAE, UMR GDEC, Clermont-Ferrand, F-63100, FRANCE
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84
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Pellicer J, Balant M, Fernández P, Rodríguez González R, Hidalgo O. Morphological and Genome-Wide Evidence of Homoploid Hybridisation in Urospermum (Asteraceae). PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11020182. [PMID: 35050070 PMCID: PMC8779322 DOI: 10.3390/plants11020182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 05/11/2023]
Abstract
The genus Urospermum is distributed in the Mediterranean region and Macaronesia, and has been introduced to other extra-Mediterranean regions. Although the two species constituting the genus, U. dalechampii and U. picroides, are frequently found together, hybrids have so far only been reported once, from Morocco. However, we found certain individuals in Catalonia, whose intermediate morphology suggested a potential hybrid origin. In this study, we applied morphological and molecular methods to investigate the origin of those individuals. Intermediate features at phenotype, karyological, cytogenetic, and genomic levels were identified in morphologically intermediate individuals, supporting their homoploid hybrid origin. Chloroplast sequence data suggest that U. dalechampii is the maternal progenitor of the hybrid. Together with the intermediate traits displayed, the lack of fertile seeds suggests that hybrids are probably F1. Future monitoring studies will be, nonetheless, needed to evaluate the extent of hybridisation and its potential impact on the biology of the genus.
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Affiliation(s)
- Jaume Pellicer
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain; (M.B.); (P.F.); (R.R.G.)
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK
- Correspondence: (J.P.); (O.H.); Tel.: +34-932890611 (J.P. & O.H.)
| | - Manica Balant
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain; (M.B.); (P.F.); (R.R.G.)
| | - Pol Fernández
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain; (M.B.); (P.F.); (R.R.G.)
| | - Roi Rodríguez González
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain; (M.B.); (P.F.); (R.R.G.)
| | - Oriane Hidalgo
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain; (M.B.); (P.F.); (R.R.G.)
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK
- Correspondence: (J.P.); (O.H.); Tel.: +34-932890611 (J.P. & O.H.)
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85
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Galli M, Martiny E, Imani J, Kumar N, Koch A, Steinbrenner J, Kogel K. CRISPR/SpCas9-mediated double knockout of barley Microrchidia MORC1 and MORC6a reveals their strong involvement in plant immunity, transcriptional gene silencing and plant growth. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:89-102. [PMID: 34487614 PMCID: PMC8710901 DOI: 10.1111/pbi.13697] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
The Microrchidia (MORC) family proteins are important nuclear regulators in both animals and plants with critical roles in epigenetic gene silencing and genome stabilization. In the crop plant barley (Hordeum vulgare), seven MORC gene family members have been described. While barley HvMORC1 has been functionally characterized, very little information is available about other HvMORC paralogs. In this study, we elucidate the role of HvMORC6a and its potential interactors in regulating plant immunity via analysis of CRISPR/SpCas9-mediated single and double knockout (dKO) mutants, hvmorc1 (previously generated and characterized by our group), hvmorc6a, and hvmorc1/6a. For generation of hvmorc1/6a, we utilized two different strategies: (i) successive Agrobacterium-mediated transformation of homozygous single mutants, hvmorc1 and hvmorc6a, with the respective second construct, and (ii) simultaneous transformation with both hvmorc1 and hvmorc6a CRISPR/SpCas9 constructs. Total mutation efficiency in transformed homozygous single mutants ranged from 80 to 90%, while upon simultaneous transformation, SpCas9-induced mutation in both HvMORC1 and HvMORC6a genes was observed in 58% of T0 plants. Subsequent infection assays showed that HvMORC6a covers a key role in resistance to biotrophic (Blumeria graminis) and necrotrophic (Fusarium graminearum) plant pathogenic fungi, where the dKO hvmorc1/6a showed the strongest resistant phenotype. Consistent with this, the dKO showed highest levels of basal PR gene expression and derepression of TEs. Finally, we demonstrate that HvMORC1 and HvMORC6a form distinct nucleocytoplasmic homo-/heteromers with other HvMORCs and interact with components of the RNA-directed DNA methylation (RdDM) pathway, further substantiating that MORC proteins are involved in the regulation of TEs in barley.
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Affiliation(s)
- Matteo Galli
- Institute of PhytopathologyResearch Centre for BioSystems, Land Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Engie Martiny
- Institute of PhytopathologyResearch Centre for BioSystems, Land Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Jafargholi Imani
- Institute of PhytopathologyResearch Centre for BioSystems, Land Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Neelendra Kumar
- Institute of PhytopathologyResearch Centre for BioSystems, Land Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Aline Koch
- Institute for PhytomedicineUniversity of HohenheimStuttgartGermany
| | - Jens Steinbrenner
- Institute of PhytopathologyResearch Centre for BioSystems, Land Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Karl‐Heinz Kogel
- Institute of PhytopathologyResearch Centre for BioSystems, Land Use and NutritionJustus Liebig University GiessenGiessenGermany
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86
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Zhang Y, Li Z, Zhang Y, Lin K, Peng Y, Ye L, Zhuang Y, Wang M, Xie Y, Guo J, Teng W, Tong Y, Zhang W, Xue Y, Lang Z, Zhang Y. Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements. Genome Res 2021; 31:2276-2289. [PMID: 34503979 PMCID: PMC8647832 DOI: 10.1101/gr.275658.121] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023]
Abstract
More than 80% of the wheat genome consists of transposable elements (TEs), which act as major drivers of wheat genome evolution. However, their contributions to the regulatory evolution of wheat adaptations remain largely unclear. Here, we created genome-binding maps for 53 transcription factors (TFs) underlying environmental responses by leveraging DAP-seq in Triticum urartu, together with epigenomic profiles. Most TF binding sites (TFBSs) located distally from genes are embedded in TEs, whose functional relevance is supported by purifying selection and active epigenomic features. About 24% of the non-TE TFBSs share significantly high sequence similarity with TE-embedded TFBSs. These non-TE TFBSs have almost no homologous sequences in non-Triticeae species and are potentially derived from Triticeae-specific TEs. The expansion of TE-derived TFBS linked to wheat-specific gene responses, suggesting TEs are an important driving force for regulatory innovations. Altogether, TEs have been significantly and continuously shaping regulatory networks related to wheat genome evolution and adaptation.
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Affiliation(s)
- Yuyun Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zijuan Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu'e Zhang
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Kande Lin
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yuan Peng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Luhuan Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yili Zhuang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Meiyue Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yilin Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingyu Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Henan University, School of Life Science, Kaifeng, Henan 457000, China
| | - Wan Teng
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yiping Tong
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yongbiao Xue
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, and National Centre for Bioinformation, Beijing 100101 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Zhaobo Lang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
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87
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Haider S, Iqbal J, Naseer S, Yaseen T, Shaukat M, Bibi H, Ahmad Y, Daud H, Abbasi NL, Mahmood T. Molecular mechanisms of plant tolerance to heat stress: current landscape and future perspectives. PLANT CELL REPORTS 2021; 40:2247-2271. [PMID: 33890138 DOI: 10.1007/s00299-021-02696-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
We summarize recent studies focusing on the molecular basis of plant heat stress response (HSR), how HSR leads to thermotolerance, and promote plant adaptation to recurring heat stress events. The global crop productivity is facing unprecedented threats due to climate change as high temperature negatively influences plant growth and metabolism. Owing to their sessile nature, plants have developed complex signaling networks which enable them to perceive changes in ambient temperature. This in turn activates a suite of molecular changes that promote plant survival and reproduction under adverse conditions. Deciphering these mechanisms is an important task, as this could facilitate development of molecular markers, which could be ultimately used to breed thermotolerant crop cultivars. In current article, we summarize mechanisms involve in plant heat stress acclimation with special emphasis on advances related to heat stress perception, heat-induced signaling, heat stress-responsive gene expression and thermomemory that promote plant adaptation to short- and long-term-recurring heat-stress events. In the end, we will discuss impact of emerging technologies that could facilitate the development of heat stress-tolerant crop cultivars.
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Affiliation(s)
- Saqlain Haider
- Plant Biochemistry and Molecular Biology Laboratory, Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Javed Iqbal
- Plant Biochemistry and Molecular Biology Laboratory, Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
- Center for Plant Sciences and Biodiversity, University of Swat, Kanju, 19201, Pakistan.
| | - Sana Naseer
- Plant Biochemistry and Molecular Biology Laboratory, Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Tabassum Yaseen
- Department of Botany, Bacha Khan University, Charsadda, Khyber Pakhtunkhwa, Pakistan
| | - Muzaffar Shaukat
- Plant Biochemistry and Molecular Biology Laboratory, Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Haleema Bibi
- Plant Biochemistry and Molecular Biology Laboratory, Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Yumna Ahmad
- Plant Biochemistry and Molecular Biology Laboratory, Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Hina Daud
- Plant Biochemistry and Molecular Biology Laboratory, Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Nayyab Laiba Abbasi
- Plant Biochemistry and Molecular Biology Laboratory, Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Tariq Mahmood
- Plant Biochemistry and Molecular Biology Laboratory, Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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88
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Young Chae G, Hong WJ, Jeong Jang M, Jung KH, Kim S. Recurrent mutations promote widespread structural and functional divergence of MULE-derived genes in plants. Nucleic Acids Res 2021; 49:11765-11777. [PMID: 34725701 PMCID: PMC8599713 DOI: 10.1093/nar/gkab932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/08/2021] [Accepted: 09/29/2021] [Indexed: 11/23/2022] Open
Abstract
Transposable element (TE)-derived genes are increasingly recognized as major sources conferring essential traits in agriculturally important crops but underlying evolutionary mechanisms remain obscure. We updated previous annotations and constructed 18,744 FAR-RED IMPAIRED RESPONSE1 (FAR1) genes, a transcription factor family derived from Mutator-like elements (MULEs), from 80 plant species, including 15,546 genes omitted in previous annotations. In-depth sequence comparison of the updated gene repertoire revealed that FAR1 genes underwent continuous structural divergence via frameshift and nonsense mutations that caused premature translation termination or specific domain truncations. CRISPR/Cas9-based genome editing and transcriptome analysis determined a novel gene involved in fertility-regulating transcription of rice pollen, denoting the functional capacity of our re-annotated gene models especially in monocots which had the highest copy numbers. Genomic evidence showed that the functional gene adapted by obtaining a shortened form through a frameshift mutation caused by a tandem duplication of a 79-bp sequence resulting in premature translation termination. Our findings provide improved resources for comprehensive studies of FAR1 genes with beneficial agricultural traits and unveil novel evolutionary mechanisms generating structural divergence and subsequent adaptation of TE-derived genes in plants.
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Affiliation(s)
- Geun Young Chae
- Department of Environmental Horticulture, University of Seoul, Seoul 02504, Republic of Korea
| | - Woo-Jong Hong
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Min Jeong Jang
- Department of Environmental Horticulture, University of Seoul, Seoul 02504, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Seungill Kim
- Department of Environmental Horticulture, University of Seoul, Seoul 02504, Republic of Korea
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Mokhtar MM, Alsamman AM, Abd-Elhalim HM, El Allali A. CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species. PLoS One 2021; 16:e0259540. [PMID: 34762703 PMCID: PMC8584679 DOI: 10.1371/journal.pone.0259540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/20/2021] [Indexed: 11/19/2022] Open
Abstract
Recently, Cicer species have experienced increased research interest due to their economic importance, especially in genetics, genomics, and crop improvement. The Cicer arietinum, Cicer reticulatum, and Cicer echinospermum genomes have been sequenced and provide valuable resources for trait improvement. Since the publication of the chickpea draft genome, progress has been made in genome assembly, functional annotation, and identification of polymorphic markers. However, work is still needed to identify transposable elements (TEs) and make them available for researchers. In this paper, we present CicerSpTEdb, a comprehensive TE database for Cicer species that aims to improve our understanding of the organization and structural variations of the chickpea genome. Using structure and homology-based methods, 3942 C. echinospermum, 3579 C. reticulatum, and 2240 C. arietinum TEs were identified. Comparisons between Cicer species indicate that C. echinospermum has the highest number of LTR-RT and hAT TEs. C. reticulatum has more Mutator, PIF Harbinger, Tc1 Mariner, and CACTA TEs, while C. arietinum has the highest number of Helitron. CicerSpTEdb enables users to search and visualize TEs by location and download their results. The database will provide a powerful resource that can assist in developing TE target markers for molecular breeding and answer related biological questions. Database URL: http://cicersptedb.easyomics.org/index.php.
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Affiliation(s)
- Morad M. Mokhtar
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- * E-mail: (AEA); (MMM)
| | | | - Haytham M. Abd-Elhalim
- Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza, Egypt
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- * E-mail: (AEA); (MMM)
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90
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Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement. J Adv Res 2021; 42:315-329. [PMID: 36513421 PMCID: PMC9788938 DOI: 10.1016/j.jare.2021.10.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/20/2021] [Accepted: 10/24/2021] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Legume crops are an important source of protein and oil for human health and in fixing atmospheric N2 for soil enrichment. With an objective to accelerate much-needed genetic analyses and breeding applications, draft genome assemblies were generated in several legume crops; many of them are not high quality because they are mainly based on short reads. However, the superior quality of genome assembly is crucial for a detailed understanding of genomic architecture, genome evolution, and crop improvement. OBJECTIVES Present study was undertaken with an objective of developing improved chromosome-length genome assemblies in six different legumes followed by their systematic investigation to unravel different aspects of genome organization and legume evolution. METHODS We employed in situ Hi-C data to improve the existing draft genomes and performed different evolutionary and comparative analyses using improved genome assemblies. RESULTS We have developed chromosome-length genome assemblies in chickpea, pigeonpea, soybean, subterranean clover, and two wild progenitor species of cultivated groundnut (A. duranensis and A. ipaensis). A comprehensive comparative analysis of these genome assemblies offered improved insights into various evolutionary events that shaped the present-day legume species. We highlighted the expansion of gene families contributing to unique traits such as nodulation in legumes, gravitropism in groundnut, and oil biosynthesis in oilseed legume crops such as groundnut and soybean. As examples, we have demonstrated the utility of improved genome assemblies for enhancing the resolution of "QTL-hotspot" identification for drought tolerance in chickpea and marker-trait associations for agronomic traits in pigeonpea through genome-wide association study. Genomic resources developed in this study are publicly available through an online repository, 'Legumepedia'. CONCLUSION This study reports chromosome-length genome assemblies of six legume species and demonstrates the utility of these assemblies in crop improvement. The genomic resources developed here will have significant role in accelerating genetic improvement applications of legume crops.
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91
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Viviani A, Ventimiglia M, Fambrini M, Vangelisti A, Mascagni F, Pugliesi C, Usai G. Impact of transposable elements on the evolution of complex living systems and their epigenetic control. Biosystems 2021; 210:104566. [PMID: 34718084 DOI: 10.1016/j.biosystems.2021.104566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 10/20/2022]
Abstract
Transposable elements (TEs) contribute to genomic innovations, as well as genome instability, across a wide variety of species. Popular designations such as 'selfish DNA' and 'junk DNA,' common in the 1980s, may be either inaccurate or misleading, while a more enlightened view of the TE-host relationship covers a range from parasitism to mutualism. Both plant and animal hosts have evolved epigenetic mechanisms to reduce the impact of TEs, both by directly silencing them and by reducing their ability to transpose in the genome. However, TEs have also been co-opted by both plant and animal genomes to perform a variety of physiological functions, ranging from TE-derived proteins acting directly in normal biological functions to innovations in transcription factor activity and also influencing gene expression. Their presence, in fact, can affect a range of features at genome, phenotype, and population levels. The impact TEs have had on evolution is multifaceted, and many aspects still remain unexplored. In this review, the epigenetic control of TEs is contextualized according to the evolution of complex living systems.
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Affiliation(s)
- Ambra Viviani
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Maria Ventimiglia
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Alberto Vangelisti
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Flavia Mascagni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy.
| | - Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
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92
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Ho EKH, Bellis ES, Calkins J, Adrion JR, Latta IV LC, Schaack S. Engines of change: Transposable element mutation rates are high and variable within Daphnia magna. PLoS Genet 2021; 17:e1009827. [PMID: 34723969 PMCID: PMC8594854 DOI: 10.1371/journal.pgen.1009827] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/16/2021] [Accepted: 09/16/2021] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) represent a major portion of most eukaryotic genomes, yet little is known about their mutation rates or how their activity is shaped by other evolutionary forces. Here, we compare short- and long-term patterns of genome-wide mutation accumulation (MA) of TEs among 9 genotypes from three populations of Daphnia magna from across a latitudinal gradient. While the overall proportion of the genome comprised of TEs is highly similar among genotypes from Finland, Germany, and Israel, populations are distinguishable based on patterns of insertion site polymorphism. Our direct rate estimates indicate TE movement is highly variable (net rates ranging from -11.98 to 12.79 x 10-5 per copy per generation among genotypes), differing both among populations and TE families. Although gains outnumber losses when selection is minimized, both types of events appear to be highly deleterious based on their low frequency in control lines where propagation is not limited to random, single-progeny descent. With rate estimates 4 orders of magnitude higher than base substitutions, TEs clearly represent a highly mutagenic force in the genome. Quantifying patterns of intra- and interspecific variation in TE mobility with and without selection provides insight into a powerful mechanism generating genetic variation in the genome.
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Affiliation(s)
- Eddie K. H. Ho
- Department of Biology, Reed College, Portland, Oregon, United States of America
| | - Emily S. Bellis
- Department of Biology, Reed College, Portland, Oregon, United States of America
- Department of Computer Science, Arkansas State University, Jonesboro, Arkansas, United States of America
| | - Jaclyn Calkins
- Department of Biology, Reed College, Portland, Oregon, United States of America
- College of Human Medicine, Michigan State University, East Lansing, Michigan, United States of America
| | - Jeffrey R. Adrion
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Leigh C. Latta IV
- Department of Biology, Reed College, Portland, Oregon, United States of America
- Lewis-Clark State College, Lewiston, Idaho, United States of America
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, Oregon, United States of America
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93
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The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation. Int J Mol Sci 2021; 22:ijms222111387. [PMID: 34768817 PMCID: PMC8583499 DOI: 10.3390/ijms222111387] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 02/06/2023] Open
Abstract
Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can provide the plant with protection from environmental stresses. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. These epigenetic alterations are mainly regulated by transposable elements (TEs) whose abundance in plant genomes results in their interaction with genomes. Thus, TEs are the main source of epigenetic changes and form a substantial part of the plant genome. Furthermore, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability. This introduces novel gene functions and structural variation in the insertion sites and primarily contributes to epigenetic modifications. Altogether, these modifications indirectly or directly provide the ability to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major role in the evolution of the plant genome through epigenetic process that regulate gene imprinting, thereby upholding genome stability. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, leading to genomic stress. These TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Thus, TE methylation is essential for plant evolution and stress adaptation, and TEs hold a relevant military position in the plant genome. High-throughput techniques have greatly advanced the understanding of TE-mediated gene expression and its associations with genome methylation and suggest that controlled mobilization of TEs could be used for crop breeding. However, development application in this area has been limited, and an integrated view of TE function and subsequent processes is lacking. In this review, we explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and discuss some recent examples of how TEs impact gene expression in plant development and stress adaptation.
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94
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Roquis D, Robertson M, Yu L, Thieme M, Julkowska M, Bucher E. Genomic impact of stress-induced transposable element mobility in Arabidopsis. Nucleic Acids Res 2021; 49:10431-10447. [PMID: 34551439 PMCID: PMC8501995 DOI: 10.1093/nar/gkab828] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 12/11/2022] Open
Abstract
Transposable elements (TEs) have long been known to be major contributors to plant evolution, adaptation and crop domestication. Stress-induced TE mobilization is of particular interest because it may result in novel gene regulatory pathways responding to stresses and thereby contribute to stress adaptation. Here, we investigated the genomic impacts of stress induced TE mobilization in wild type Arabidopsis plants. We find that the heat-stress responsive ONSEN TE displays an insertion site preference that is associated with specific chromatin states, especially those rich in H2A.Z histone variant and H3K27me3 histone mark. In order to better understand how novel ONSEN insertions affect the plant's response to heat stress, we carried out an in-depth transcriptomic analysis. We find that in addition to simple gene knockouts, ONSEN can produce a plethora of gene expression changes such as: constitutive activation of gene expression, alternative splicing, acquisition of heat-responsiveness, exonisation and genesis of novel non-coding and antisense RNAs. This report shows how the mobilization of a single TE-family can lead to a rapid rise of its copy number increasing the host's genome size and contribute to a broad range of transcriptomic novelty on which natural selection can then act.
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Affiliation(s)
- David Roquis
- Plant Breeding and Genetic Resources, Agroscope, 1260 Nyon, Switzerland
| | - Marta Robertson
- Plant Breeding and Genetic Resources, Agroscope, 1260 Nyon, Switzerland
| | - Liang Yu
- Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY 14853, USA
| | - Michael Thieme
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
| | | | - Etienne Bucher
- Plant Breeding and Genetic Resources, Agroscope, 1260 Nyon, Switzerland
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95
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Faizullah L, Morton JA, Hersch-Green EI, Walczyk AM, Leitch AR, Leitch IJ. Exploring environmental selection on genome size in angiosperms. TRENDS IN PLANT SCIENCE 2021; 26:1039-1049. [PMID: 34219022 DOI: 10.1016/j.tplants.2021.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 05/22/2023]
Abstract
Angiosperms show a remarkable range in genome size (GS), yet most species have small genomes, despite the frequency of polyploidy and repeat amplification in the ancestries of most lineages. It has been suggested that larger genomes incur costs that have driven selection for GS reduction, although the nature of these costs and how they might impact selection remain unclear. We explore potential costs of increased GS encompassing impacts on minimum cell size with consequences for photosynthesis and water-use efficiency and effects of greater nitrogen and phosphorus demands of the nucleus leading to more severe trade-offs with photosynthesis. We suggest that nutrient-, water-, and/or CO2-stressed conditions might favour species with smaller genomes, with implications for species' ecological and evolutionary dynamics.
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Affiliation(s)
- Lubna Faizullah
- Character Evolution Team, Royal Botanic Gardens, Kew, Richmond, Surrey, UK; School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, UK
| | - Joseph A Morton
- Character Evolution Team, Royal Botanic Gardens, Kew, Richmond, Surrey, UK; School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, UK
| | - Erika I Hersch-Green
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Angela M Walczyk
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, UK.
| | - Ilia J Leitch
- Character Evolution Team, Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
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96
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Liu Z, Zhao H, Yan Y, Wei MX, Zheng YC, Yue EK, Alam MS, Smartt KO, Duan MH, Xu JH. Extensively Current Activity of Transposable Elements in Natural Rice Accessions Revealed by Singleton Insertions. FRONTIERS IN PLANT SCIENCE 2021; 12:745526. [PMID: 34650583 PMCID: PMC8505701 DOI: 10.3389/fpls.2021.745526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/08/2021] [Indexed: 06/01/2023]
Abstract
Active transposable elements (TEs) have drawn more attention as they continue to create new insertions and contribute to genetic diversity of the genome. However, only a few have been discovered in rice up to now, and their activities are mostly induced by artificial treatments (e.g., tissue culture, hybridization etc.) rather than under normal growth conditions. To systematically survey the current activity of TEs in natural rice accessions and identify rice accessions carrying highly active TEs, the transposon insertion polymorphisms (TIPs) profile was used to identify singleton insertions, which were unique to a single accession and represented the new insertion of TEs in the genome. As a result, 10,924 high-confidence singletons from 251 TE families were obtained, covering all investigated TE types. The number of singletons varied substantially among different superfamilies/families, perhaps reflecting distinct current activity. Particularly, eight TE families maintained potentially higher activity in 3,000 natural rice accessions. Sixty percent of rice accessions were detected to contain singletons, indicating the extensive activity of TEs in natural rice accessions. Thirty-five TE families exhibited potentially high activity in at least one rice accession, and the majority of them showed variable activity among different rice groups/subgroups. These naturally active TEs would be ideal candidates for elucidating the molecular mechanisms underlying the transposition and activation of TEs, as well as investigating the interactions between TEs and the host genome.
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Affiliation(s)
- Zhen Liu
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Han Zhao
- Jiangsu Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yan Yan
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Ming-Xiao Wei
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Yun-Chao Zheng
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Er-Kui Yue
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Mohammad Shah Alam
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Kwesi Odel Smartt
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Ming-Hua Duan
- Zhejiang Zhengjingyuan Pharmacy Chain Co., Ltd., Hangzhou, China
- Hangzhou Zhengcaiyuan Pharmaceutical Co., Ltd., Hangzhou, China
| | - Jian-Hong Xu
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou, China
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97
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Kalendar R, Sabot F, Rodriguez F, Karlov GI, Natali L, Alix K. Editorial: Mobile Elements and Plant Genome Evolution, Comparative Analyzes and Computational Tools. FRONTIERS IN PLANT SCIENCE 2021; 12:735134. [PMID: 34630484 PMCID: PMC8500305 DOI: 10.3389/fpls.2021.735134] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/30/2021] [Indexed: 05/28/2023]
Affiliation(s)
- Ruslan Kalendar
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Francois Sabot
- DIADE, University of Montpellier, CIRAD, IRD, Montpellier, France
| | - Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory (MBL), Woods Hole, MA, United States
| | - Gennady I. Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Lucia Natali
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Karine Alix
- GQE – Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Gif-sur-Yvette, France
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98
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Pellicer J, Fernández P, Fay MF, Michálková E, Leitch IJ. Genome Size Doubling Arises From the Differential Repetitive DNA Dynamics in the Genus Heloniopsis (Melanthiaceae). Front Genet 2021; 12:726211. [PMID: 34552621 PMCID: PMC8450539 DOI: 10.3389/fgene.2021.726211] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/19/2021] [Indexed: 12/23/2022] Open
Abstract
Plant genomes are highly diverse in size and repetitive DNA composition. In the absence of polyploidy, the dynamics of repetitive elements, which make up the bulk of the genome in many species, are the main drivers underpinning changes in genome size and the overall evolution of the genomic landscape. The advent of high-throughput sequencing technologies has enabled investigation of genome evolutionary dynamics beyond model plants to provide exciting new insights in species across the biodiversity of life. Here we analyze the evolution of repetitive DNA in two closely related species of Heloniopsis (Melanthiaceae), which despite having the same chromosome number differ nearly twofold in genome size [i.e., H. umbellata (1C = 4,680 Mb), and H. koreana (1C = 2,480 Mb)]. Low-coverage genome skimming and the RepeatExplorer2 pipeline were used to identify the main repeat families responsible for the significant differences in genome sizes. Patterns of repeat evolution were found to correlate with genome size with the main classes of transposable elements identified being twice as abundant in the larger genome of H. umbellata compared with H. koreana. In addition, among the satellite DNA families recovered, a single shared satellite (HeloSAT) was shown to have contributed significantly to the genome expansion of H. umbellata. Evolutionary changes in repetitive DNA composition and genome size indicate that the differences in genome size between these species have been underpinned by the activity of several distinct repeat lineages.
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Affiliation(s)
- Jaume Pellicer
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain.,Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Pol Fernández
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, United Kingdom.,School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | | | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
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99
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Lin L, Sharma A, Yu Q. Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome. BMC PLANT BIOLOGY 2021; 21:424. [PMID: 34537020 PMCID: PMC8449440 DOI: 10.1186/s12870-021-03194-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Miniature inverted-repeat transposable elements (MITEs) are non-autonomous DNA transposable elements that play important roles in genome organization and evolution. Genome-wide identification and characterization of MITEs provide essential information for understanding genome structure and evolution. RESULTS We performed genome-wide identification and characterization of MITEs in the pineapple genome. The top two MITE families, accounting for 29.39% of the total MITEs and 3.86% of the pineapple genome, have insertion preference in (TA) n dinucleotide microsatellite regions. We therefore named these MITEs A. comosus microsatellite-associated MITEs (Ac-mMITEs). The two Ac-mMITE families, Ac-mMITE-1 and Ac-mMITE-2, shared sequence similarity in the terminal inverted repeat (TIR) regions, suggesting that these two Ac-mMITE families might be derived from a common or closely related autonomous elements. The Ac-mMITEs are frequently clustered via adjacent insertions. Among the 21,994 full-length Ac-mMITEs, 46.1% of them were present in clusters. By analyzing the Ac-mMITEs without (TA) n microsatellite flanking sequences, we found that Ac-mMITEs were likely derived from Mutator-like DNA transposon. Ac-MITEs showed highly polymorphic insertion sites between cultivated pineapples and their wild relatives. To better understand the evolutionary history of Ac-mMITEs, we filtered and performed comparative analysis on the two distinct groups of Ac-mMITEs, microsatellite-targeting MITEs (mt-MITEs) that are flanked by dinucleotide microsatellites on both sides and mutator-like MITEs (ml-MITEs) that contain 9/10 bp TSDs. Epigenetic analysis revealed a lower level of host-induced silencing on the mt-MITEs in comparison to the ml-MITEs, which partially explained the significantly higher abundance of mt-MITEs in pineapple genome. The mt-MITEs and ml-MITEs exhibited differential insertion preference to gene-related regions and RNA-seq analysis revealed their differential influences on expression regulation of nearby genes. CONCLUSIONS Ac-mMITEs are the most abundant MITEs in the pineapple genome and they were likely derived from Mutator-like DNA transposon. Preferential insertion in (TA) n microsatellite regions of Ac-mMITEs occurred recently and is likely the result of damage-limiting strategy adapted by Ac-mMITEs during co-evolution with their host. Insertion in (TA) n microsatellite regions might also have promoted the amplification of mt-MITEs. In addition, mt-MITEs showed no or negligible impact on nearby gene expression, which may help them escape genome control and lead to their amplification.
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Affiliation(s)
- Lianyu Lin
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Anupma Sharma
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA.
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100
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Comparative Analysis of Transposable Elements in Genus Calliptamus Grasshoppers Revealed That Satellite DNA Contributes to Genome Size Variation. INSECTS 2021; 12:insects12090837. [PMID: 34564277 PMCID: PMC8466570 DOI: 10.3390/insects12090837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/01/2021] [Accepted: 09/14/2021] [Indexed: 12/15/2022]
Abstract
Simple Summary Calliptamus is a genus of grasshoppers belonging to the family Acrididae. The genus Calliptamus includes approximately 17 recognized species. Calliptamus abbreviatus, Calliptamus italicus, and Calliptamus barbarus are three species that are widely found in northern China. These species are polyphagous, feeding on a variety of wild plants as well as crops, particularly legumes. The genome sizes, phylogenetic position, and transcriptome analysis of the genus Calliptamus were already known previous to this research. The repeatome analysis of these species was missing, which is directly linked to the larger genome sizes of the grasshoppers. Here, we classified repetitive DNA sequences at the level of superfamilies and sub-families, and found that LINE, TcMar-Tc1 and Ty3-gypsy LTR retrotransposons dominated the repeatomes of all genomes, accounting for 16–34% of the total genomes of these species. Satellite DNA dynamic evolutionary changes in all three genomes played a role in genome size evolution. This study would be a valuable source for future genome assemblies. Abstract Transposable elements (TEs) play a significant role in both eukaryotes and prokaryotes genome size evolution, structural changes, duplication, and functional variabilities. However, the large number of different repetitive DNA has hindered the process of assembling reference genomes, and the genus level TEs diversification of the grasshopper massive genomes is still under investigation. The genus Calliptamus diverged from Peripolus around 17 mya and its species divergence dated back about 8.5 mya, but their genome size shows rather large differences. Here, we used low-coverage Illumina unassembled short reads to investigate the effects of evolutionary dynamics of satDNAs and TEs on genome size variations. The Repeatexplorer2 analysis with 0.5X data resulted in 52%, 56%, and 55% as repetitive elements in the genomes of Calliptamus barbarus, Calliptamus italicus, and Calliptamus abbreviatus, respectively. The LINE and Ty3-gypsy LTR retrotransposons and TcMar-Tc1 dominated the repeatomes of all genomes, accounting for 16–35% of the total genomes of these species. Comparative analysis unveiled that most of the transposable elements (TEs) except satDNAs were highly conserved across three genomes in the genus Calliptamus grasshoppers. Out of a total of 20 satDNA families, 17 satDNA families were commonly shared with minor variations in abundance and divergence between three genomes, and 3 were Calliptamus barbarus specific. Our findings suggest that there is a significant amplification or contraction of satDNAs at genus phylogeny which is the main cause that made genome size different.
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