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Arvas YE, Marakli S, Kaya Y, Kalendar R. The power of retrotransposons in high-throughput genotyping and sequencing. FRONTIERS IN PLANT SCIENCE 2023; 14:1174339. [PMID: 37180380 PMCID: PMC10167742 DOI: 10.3389/fpls.2023.1174339] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023]
Abstract
The use of molecular markers has become an essential part of molecular genetics through their application in numerous fields, which includes identification of genes associated with targeted traits, operation of backcrossing programs, modern plant breeding, genetic characterization, and marker-assisted selection. Transposable elements are a core component of all eukaryotic genomes, making them suitable as molecular markers. Most of the large plant genomes consist primarily of transposable elements; variations in their abundance contribute to most of the variation in genome size. Retrotransposons are widely present throughout plant genomes, and replicative transposition enables them to insert into the genome without removing the original elements. Various applications of molecular markers have been developed that exploit the fact that these genetic elements are present everywhere and their ability to stably integrate into dispersed chromosomal localities that are polymorphic within a species. The ongoing development of molecular marker technologies is directly related to the deployment of high-throughput genotype sequencing platforms, and this research is of considerable significance. In this review, the practical application to molecular markers, which is a use of technology of interspersed repeats in the plant genome were examined using genomic sources from the past to the present. Prospects and possibilities are also presented.
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Affiliation(s)
- Yunus Emre Arvas
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, Trabzon, Türkiye
| | - Sevgi Marakli
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Türkiye
| | - Yılmaz Kaya
- Agricultural Biotechnology Department, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Türkiye
- Department of Biology, Faculty of Science, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Ruslan Kalendar
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
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2
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Vershinin AV, Elisafenko EA, Evtushenko EV. Genetic Redundancy in Rye Shows in a Variety of Ways. PLANTS (BASEL, SWITZERLAND) 2023; 12:282. [PMID: 36678994 PMCID: PMC9862056 DOI: 10.3390/plants12020282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Fifty years ago Susumu Ohno formulated the famous C-value paradox, which states that there is no correlation between the physical sizes of the genome, i.e., the amount of DNA, and the complexity of the organism, and highlighted the problem of genome redundancy. DNA that does not have a positive effect on the fitness of organisms has been characterized as "junk or selfish DNA". The controversial concept of junk DNA remains viable. Rye is a convenient subject for yet another test of the correctness and scientific significance of this concept. The genome of cultivated rye, Secale cereale L., is considered one of the largest among species of the tribe Triticeae and thus it tops the average angiosperm genome and the genomes of its closest evolutionary neighbors, such as species of barley, Hordeum (by approximately 30-35%), and diploid wheat species, Triticum (approximately 25%). The review provides an analysis of the structural organization of various regions of rye chromosomes with a description of the molecular mechanisms contributing to their size increase during evolution and the classes of DNA sequences involved in these processes. The history of the development of the concept of eukaryotic genome redundancy is traced and the current state of this problem is discussed.
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Affiliation(s)
- Alexander V. Vershinin
- Institute of Molecular and Cellular Biology, SB RAS, Acad. Lavrentiev Ave. 8/2, 630090 Novosibirsk, Russia
| | - Evgeny A. Elisafenko
- Institute of Molecular and Cellular Biology, SB RAS, Acad. Lavrentiev Ave. 8/2, 630090 Novosibirsk, Russia
- Institute of Cytology and Genetics, SB RAS, Acad. Lavrentiev Ave. 10, 630090 Novosibirsk, Russia
| | - Elena V. Evtushenko
- Institute of Molecular and Cellular Biology, SB RAS, Acad. Lavrentiev Ave. 8/2, 630090 Novosibirsk, Russia
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3
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Rajendran NR, Qureshi N, Pourkheirandish M. Genotyping by Sequencing Advancements in Barley. FRONTIERS IN PLANT SCIENCE 2022; 13:931423. [PMID: 36003814 PMCID: PMC9394214 DOI: 10.3389/fpls.2022.931423] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Barley is considered an ideal crop to study cereal genetics due to its close relationship with wheat and diploid ancestral genome. It plays a crucial role in reducing risks to global food security posed by climate change. Genetic variations in the traits of interest in crops are vital for their improvement. DNA markers have been widely used to estimate these variations in populations. With the advancements in next-generation sequencing, breeders could access different types of genetic variations within different lines, with single-nucleotide polymorphisms (SNPs) being the most common type. However, genotyping barley with whole genome sequencing (WGS) is challenged by the higher cost and computational demand caused by the large genome size (5.5GB) and a high proportion of repetitive sequences (80%). Genotyping-by-sequencing (GBS) protocols based on restriction enzymes and target enrichment allow a cost-effective SNP discovery by reducing the genome complexity. In general, GBS has opened up new horizons for plant breeding and genetics. Though considered a reliable alternative to WGS, GBS also presents various computational difficulties, but GBS-specific pipelines are designed to overcome these challenges. Moreover, a robust design for GBS can facilitate the imputation to the WGS level of crops with high linkage disequilibrium. The complete exploitation of GBS advancements will pave the way to a better understanding of crop genetics and offer opportunities for the successful improvement of barley and its close relatives.
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Affiliation(s)
- Nirmal Raj Rajendran
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Naeela Qureshi
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, Estado de Mexico, Mexico
| | - Mohammad Pourkheirandish
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
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4
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Singhal RK, Saha D, Skalicky M, Mishra UN, Chauhan J, Behera LP, Lenka D, Chand S, Kumar V, Dey P, Indu, Pandey S, Vachova P, Gupta A, Brestic M, El Sabagh A. Crucial Cell Signaling Compounds Crosstalk and Integrative Multi-Omics Techniques for Salinity Stress Tolerance in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:670369. [PMID: 34484254 PMCID: PMC8414894 DOI: 10.3389/fpls.2021.670369] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/28/2021] [Indexed: 10/29/2023]
Abstract
In the era of rapid climate change, abiotic stresses are the primary cause for yield gap in major agricultural crops. Among them, salinity is considered a calamitous stress due to its global distribution and consequences. Salinity affects plant processes and growth by imposing osmotic stress and destroys ionic and redox signaling. It also affects phytohormone homeostasis, which leads to oxidative stress and eventually imbalances metabolic activity. In this situation, signaling compound crosstalk such as gasotransmitters [nitric oxide (NO), hydrogen sulfide (H2S), hydrogen peroxide (H2O2), calcium (Ca), reactive oxygen species (ROS)] and plant growth regulators (auxin, ethylene, abscisic acid, and salicylic acid) have a decisive role in regulating plant stress signaling and administer unfavorable circumstances including salinity stress. Moreover, recent significant progress in omics techniques (transcriptomics, genomics, proteomics, and metabolomics) have helped to reinforce the deep understanding of molecular insight in multiple stress tolerance. Currently, there is very little information on gasotransmitters and plant growth regulator crosstalk and inadequacy of information regarding the integration of multi-omics technology during salinity stress. Therefore, there is an urgent need to understand the crucial cell signaling crosstalk mechanisms and integrative multi-omics techniques to provide a more direct approach for salinity stress tolerance. To address the above-mentioned words, this review covers the common mechanisms of signaling compounds and role of different signaling crosstalk under salinity stress tolerance. Thereafter, we mention the integration of different omics technology and compile recent information with respect to salinity stress tolerance.
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Affiliation(s)
| | - Debanjana Saha
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneswar, India
| | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Udit N. Mishra
- Faculty of Agriculture, Sri Sri University, Cuttack, India
| | - Jyoti Chauhan
- Narayan Institute of Agricultural Sciences, Gopal Narayan Singh University, Jamuhar, India
| | - Laxmi P. Behera
- Department of Agriculture Biotechnology, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Devidutta Lenka
- Department of Plant Breeding and Genetics, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Subhash Chand
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Vivek Kumar
- Institute of Agriculture Sciences, Banaras Hindu University, Varanasi, India
| | - Prajjal Dey
- Faculty of Agriculture, Sri Sri University, Cuttack, India
| | - Indu
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Saurabh Pandey
- Department of Agriculture, Guru Nanak Dev University, Amritsar, India
| | - Pavla Vachova
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Aayushi Gupta
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Marian Brestic
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
- Department of Plant Physiology, Slovak University of Agriculture in Nitra, Nitra, Slovakia
| | - Ayman El Sabagh
- Department of Agronomy, Faculty of Agriculture, University of Kafrelsheikh, Kafr El Sheikh, Egypt
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt, Turkey
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5
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Cagirici HB, Budak H, Sen TZ. Genome-wide discovery of G-quadruplexes in barley. Sci Rep 2021; 11:7876. [PMID: 33846409 PMCID: PMC8041835 DOI: 10.1038/s41598-021-86838-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/19/2021] [Indexed: 12/04/2022] Open
Abstract
G-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar G-quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are lacking comprehensive studies of G4 motifs. In this study, genome-wide identification of G4 motifs in barley was performed, followed by a comparison of genomic distribution and molecular functions to other monocot species, such as wheat, maize, and rice. Similar to the reports on human and some plants like wheat, G4 motifs peaked around the 5′ untranslated region (5′ UTR), the first coding domain sequence, and the first intron start sites on antisense strands. Our comparative analyses in human, Arabidopsis, maize, rice, and sorghum demonstrated that the peak points could be erroneously merged into a single peak when large window sizes are used. We also showed that the G4 distributions around genic regions are relatively similar in the species studied, except in the case of Arabidopsis. G4 containing genes in monocots showed conserved molecular functions for transcription initiation and hydrolase activity. Additionally, we provided examples of imperfect G4 motifs.
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Affiliation(s)
- H Busra Cagirici
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, U.S. Department of Agriculture - Agricultural Research Service, 800 Buchanan St, Albany, CA, 94710, USA
| | - Hikmet Budak
- Montana BioAg Inc., Missoula, MT, USA.,Agrogen, LLC., Omaha, NE, USA
| | - Taner Z Sen
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, U.S. Department of Agriculture - Agricultural Research Service, 800 Buchanan St, Albany, CA, 94710, USA.
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Yepuri V, Jalali S, Kancharla N, Reddy VB, Arockiasamy S. Development of genome wide transposable elements based repeat junction markers in Jatropha (Jatropha curcas L.). Mol Biol Rep 2020; 47:5091-5099. [PMID: 32562173 DOI: 10.1007/s11033-020-05579-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 06/10/2020] [Indexed: 11/29/2022]
Abstract
Jatropha curcas is a potential biodiesel crop and a highly adaptable species to various agro-climatic conditions. In this study, we have utilized transposable elements' (TE) repeat junctions (RJs) which are an important constituent of the genome, used to form a genome-wide molecular marker platform owing to its use in genomic studies of plants. We screened our previously generated Jatropha hybrid genome assembly of size 265 Mbp using RJPrimers pipeline software and identified a total of 1274 TE junctions. For the predicted RJs, we designed 2868 polymerase chain reaction (PCR) based RJ markers (RJMs) flanking the junction regions. In addition to marker design, the identified RJs were utilized to detect 225,517 TEs across the genome. The different types of transposable repeat elements mainly were scattered into Retro, LTR, Copia and Gypsy categories. The efficacy of the designed markers was tested by utilizing a subset of RJMs selected randomly. We have validated 96 randomly selected RJ primers in a group of 32 J. curcas genotypes and more than 90% of the markers effectively intensified as amplicons. Of these, 10 primers were shown to be polymorphic in estimating genetic diversity among the 32 Jatropha lines. UPGMA cluster analysis revealed the formation of two clusters such as A and B exhibiting 85.5% and 87% similarity coefficient respectively. The various RJMs identified in this study could be utilized as a significant asset in Jatropha functional genomics including genome determination, mapping and marker-assisted selection.
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Affiliation(s)
- Vijay Yepuri
- Agronomy Division, Reliance Technology Group, Reliance Industries Limited, Navi Mumbai, Maharashtra, 400701, India
| | - Saakshi Jalali
- Agronomy Division, Reliance Technology Group, Reliance Industries Limited, Navi Mumbai, Maharashtra, 400701, India
| | - Nagesh Kancharla
- Agronomy Division, Reliance Technology Group, Reliance Industries Limited, Navi Mumbai, Maharashtra, 400701, India
| | - V B Reddy
- AgriGenome Labs Private Limited, Hyderabad, 500078, India
| | - S Arockiasamy
- Agronomy Division, Reliance Technology Group, Reliance Industries Limited, Navi Mumbai, Maharashtra, 400701, India.
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7
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Ourari M, Coriton O, Martin G, Huteau V, Keller J, Ainouche ML, Amirouche R, Ainouche A. Screening diversity and distribution of Copia retrotransposons reveals a specific amplification of BARE1 elements in genomes of the polyploid Hordeum murinum complex. Genetica 2020; 148:109-123. [PMID: 32361835 DOI: 10.1007/s10709-020-00094-3] [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: 11/04/2019] [Accepted: 04/24/2020] [Indexed: 10/24/2022]
Abstract
We explored diversity, distribution and evolutionary dynamics of Ty1-Copia retrotransposons in the genomes of the Hordeum murinum polyploid complex and related taxa. Phylogenetic and fluorescent in situ hybridization (FISH) analyses of reverse transcriptase sequences identified four Copia families in these genomes: the predominant BARE1 (including three groups or subfamilies, A, B and C), and the less represented RIRE1, IKYA and TAR-1. Within the BARE1 family, BARE1-A elements and a subgroup of BARE1-B elements (named B1) have proliferated in the allopolyploid members of the H. murinum complex (H. murinum and H. leporinum), and in their extant diploid progenitor, subsp. glaucum. Moreover, we found a specific amplification of BARE1-B elements within each Hordeum species surveyed. The low occurrence of RIRE1, IKYA and TAR-1 elements in the allopolyploid cytotypes suggests that they are either weakly represented or highly degenerated in their diploid progenitors. The results demonstrate that BARE1-A and BARE1-B1 Copia elements are particularly well represented in the genomes of the H. murinum complex and constitute its genomic hallmark. No BARE1-A and -B1 homologs were detected in the reference barley genome. The similar distribution of RT-Copia probes across chromosomes of diploid, tetraploid and hexaploid taxa of the murinum complex shows no evidence of proliferation following polyploidization.
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Affiliation(s)
- Malika Ourari
- Laboratory of Ecology and Environment, Department of Environment Biological Sciences, Faculty of Nature and Life Sciences, Université de Bejaia, Targa Ouzemmour, 06000, Bejaia, Algeria
| | - Olivier Coriton
- Institut National de Recherche en Agriculture, Alimentation et Environnement, UMR1349 INRAE-AgroCampus Ouest-Université de Rennes 1, Bât 301, INRA Centre de Bretagne-Normandie, BP 35327, 35653, Le Rheu Cedex, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, 34398, Montpellier, France.,Université de Montpellier, AGAP, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Virginie Huteau
- Institut National de Recherche en Agriculture, Alimentation et Environnement, UMR1349 INRAE-AgroCampus Ouest-Université de Rennes 1, Bât 301, INRA Centre de Bretagne-Normandie, BP 35327, 35653, Le Rheu Cedex, France
| | - Jean Keller
- Université de Toulouse, LRSV, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, 31320, Auzeville-Tolosane, France
| | - Malika-Lily Ainouche
- Université de Rennes 1, UMR-CNRS 6553, EcoBio, Campus Scientifique de Beaulieu, Bât. 14A, 35042, Rennes Cedex, France
| | - Rachid Amirouche
- Université des Sciences et de la Technologie Houari Boumediene, Faculté des Sciences Biologiques, Lab. LBPO, USTHB, BP 32 El-Alia, Bab-Ezzouar, 16111, Alger, Algerie.
| | - Abdelkader Ainouche
- Université de Rennes 1, UMR-CNRS 6553, EcoBio, Campus Scientifique de Beaulieu, Bât. 14A, 35042, Rennes Cedex, France
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Xie J, Zhao Y, Yu L, Liu R, Dou Q. Molecular karyotyping of Siberian wild rye (Elymus sibiricus L.) with oligonucleotide fluorescence in situ hybridization (FISH) probes. PLoS One 2020; 15:e0227208. [PMID: 31951623 PMCID: PMC6968859 DOI: 10.1371/journal.pone.0227208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/14/2019] [Indexed: 12/01/2022] Open
Abstract
Siberian wild rye (Elymus sibiricus L.), an allotetraploid species, is a potentially high-quality perennial forage crop native to temperate regions. We used fluorescently conjugated oligonucleotides, representing ten repetitive sequences, including 6 microsatellite repeats, two satellite repeats, and two ribosomal DNAs, to characterize E. sibiricus chromosomes, using sequential fluorescence in situ hybridization and genomic in situ hybridization assays. Our results showed that microsatellite repeats (AAG)10 or (AGG)10, satellite repeats pAs1 and pSc119.2, and ribosomal 5S rDNA and 45S rDNA are specific markers for unique chromosomes. A referable karyotype ideogram was suggested, by further polymorphism screening, across different E. sibiricus cultivars with a probe mixture of (AAG)10, Oligo-pAs1, and Oligo-pSc119.2. Chromosomal polymorphisms vary between different genomes and between different individual chromosomes. In particular, two distinct forms of chromosome E in H genome were identified in intra- and inter-populations. Here, the significance of these results, for E. sibiricus genome research and breeding, and novel approaches to improve fluorescence in situ hybridization-based karyotyping are discussed.
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Affiliation(s)
- Jihong Xie
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Yan Zhao
- College of Grassland, Resource and Environmental Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Linqing Yu
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Ruijuan Liu
- Key Laboratory of Crop Molecular Breeding, Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, China
| | - Quanwen Dou
- Key Laboratory of Crop Molecular Breeding, Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, China
- * E-mail:
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9
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Divashuk MG, Karlov GI, Kroupin PY. Copy Number Variation of Transposable Elements in Thinopyrum intermedium and Its Diploid Relative Species. PLANTS (BASEL, SWITZERLAND) 2019; 9:E15. [PMID: 31877707 PMCID: PMC7020174 DOI: 10.3390/plants9010015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/05/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022]
Abstract
Diploid and polyploid wild species of Triticeae have complex relationships, and the understanding of their evolution and speciation could help to increase the usability of them in wheat breeding as a source of genetic diversity. The diploid species Pseudoroegneria spicata (St), Thinopyrum bessarabicum (Jb), Dasypyrum villosum (V) derived from a hypothetical common ancestor are considered to be possible subgenome donors in hexaploid species Th. intermedium (JrJvsSt, where indices r, v, and s stand for the partial relation to the genomes of Secale, Dasypyrum, and Pseudoroegneria, respectively). We quantified 10 families of transposable elements (TEs) in P. spicata, Th. bessarabicum, D. villosum (per one genome), and Th. intermedium (per one average subgenome) using the quantitative real time PCR assay and compared their abundance within the studied genomes as well as between them. Sabrina was the most abundant among all studied elements in P. spicata, D. villosum, and Th. intermedium, and among Ty3/Gypsy elements in all studied species. Among Ty1/Copia elements, Angela-A and WIS-A showed the highest and close abundance with the exception of D. villosum, and comprised the majority of all studied elements in Th. bessarabicum. Sabrina, BAGY2, and Angela-A showed similar abundance among diploids and in Th. intermedium hexaploid; Latidu and Barbara demonstrated sharp differences between diploid genomes. The relationships between genomes of Triticeae species based on the studied TE abundance and the role of TEs in speciation and polyploidization in the light of the current phylogenetic models is discussed.
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Affiliation(s)
- Mikhail G. Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (M.G.D.)
- Centre for Molecular Biotechnology, Russian State Agrarian University-Timiryazev Agricultural Academy, Moscow 127550, Russia
| | - Gennady I. Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (M.G.D.)
- Centre for Molecular Biotechnology, Russian State Agrarian University-Timiryazev Agricultural Academy, Moscow 127550, Russia
| | - Pavel Yu. Kroupin
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (M.G.D.)
- Centre for Molecular Biotechnology, Russian State Agrarian University-Timiryazev Agricultural Academy, Moscow 127550, Russia
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10
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Sestili F, Garcia-Molina MD, Gambacorta G, Beleggia R, Botticella E, De Vita P, Savatin DV, Masci S, Lafiandra D. Provitamin A Biofortification of Durum Wheat through a TILLING Approach. Int J Mol Sci 2019; 20:E5703. [PMID: 31739436 PMCID: PMC6888361 DOI: 10.3390/ijms20225703] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 01/06/2023] Open
Abstract
Macro- and micronutrients, essential for the maintenance of human metabolism, are assimilated daily through the diet. Wheat and other major cereals are a good source of nutrients, such as carbohydrates and proteins, but cannot supply a sufficient amount of essential micronutrients, including provitamin A. As vitamin A deficiency (VAD) leads to several serious diseases throughout the world, the biofortification of a major staple crop, such as wheat, represents an effective way to preserve human health in developing countries. In the present work, a key enzyme involved in the branch of carotenoids pathway producing β-carotene, lycopene epsilon cyclase, has been targeted by a Targeting Induced Local Lesions in Genomes (TILLING) approach in a "block strategy" perspective. The null mutant genotype showed a strong reduction in the expression of the lcyE gene and also interesting pleiotropic effects on an enzyme (β-ring hydroxylase) acting downstream in the pathway. Biochemical profiling of carotenoids in the wheat mutant lines showed an increase of roughly 75% in β-carotene in the grains of the complete mutant line compared with the control. In conclusion, we describe here the production and characterization of a new wheat line biofortified with provitamin A obtained through a nontransgenic approach, which also sheds new light on the molecular mechanism governing carotenoid biosynthesis in durum wheat.
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Affiliation(s)
- Francesco Sestili
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100 Viterbo, Italy; (F.S.); (M.D.G.-M.); (G.G.); (E.B.); (D.V.S.); (S.M.)
| | - Maria Dolores Garcia-Molina
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100 Viterbo, Italy; (F.S.); (M.D.G.-M.); (G.G.); (E.B.); (D.V.S.); (S.M.)
| | - Gianluca Gambacorta
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100 Viterbo, Italy; (F.S.); (M.D.G.-M.); (G.G.); (E.B.); (D.V.S.); (S.M.)
| | - Romina Beleggia
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), 71122 Foggia, Italy; (R.B.); (P.D.V.)
| | - Ermelinda Botticella
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100 Viterbo, Italy; (F.S.); (M.D.G.-M.); (G.G.); (E.B.); (D.V.S.); (S.M.)
| | - Pasquale De Vita
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), 71122 Foggia, Italy; (R.B.); (P.D.V.)
| | - Daniel Valentin Savatin
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100 Viterbo, Italy; (F.S.); (M.D.G.-M.); (G.G.); (E.B.); (D.V.S.); (S.M.)
| | - Stefania Masci
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100 Viterbo, Italy; (F.S.); (M.D.G.-M.); (G.G.); (E.B.); (D.V.S.); (S.M.)
| | - Domenico Lafiandra
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100 Viterbo, Italy; (F.S.); (M.D.G.-M.); (G.G.); (E.B.); (D.V.S.); (S.M.)
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11
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Danilova TV, Poland J, Friebe B. Production of a complete set of wheat-barley group-7 chromosome recombinants with increased grain β-glucan content. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3129-3141. [PMID: 31535163 DOI: 10.1007/s00122-019-03411-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
Wheat-barley group-7 recombinant chromosomes were selected using molecular cytogenetics and SNP markers; increased grain β-glucan content was observed in wheat plants with two and four copies of HvCslF6. The soluble dietary fiber (1-3)(1-4) mixed linked β-D-glucan from cereal grains is a valuable component of a healthy diet, which reduces risks of coronary disease and diabetes. Although wheat is an important cereal crop providing a substantial portion of daily calories and protein intake in the human diet, it has a low level of β-glucan. Owing to the plasticity of the polyploid wheat genome, agronomically important traits absent in the wheat primary gene pool can be introgressed from distant relatives. Barley (Hordeum vulgare L.) has a high grain β-glucan content. Earlier, we introgressed this trait into wheat in the form of whole arm compensating Robertsonian translocations (RobT) involving group-7 chromosomes of barley and all three sub-genomes of hexaploid wheat (Triticum aestivum L). In the presented research, we shortened the barley 7HL arms in these RobTs to small pericentromeric segments, using induced wheat-barley homoeologous recombination. The recombinants were selected using SNP markers and molecular cytogenetics. Plants, comprising barley cellulose synthase-like F6 gene (HvCslF6), responsible for β-glucan synthesis, had a higher grain β-glucan content than the wheat control. Three wheat-barley group-7 recombinant chromosomes involving the A, B and D sub-genomes laid the basis for a multiple-copy gene introgression to hexaploid wheat. It is hypothesized that further increases in the β-glucan content in wheat grain can be obtained by increasing the number of HvCslF6 copies through combining several recombinant chromosomes in one line. The wheat lines with four copies of HvCslF6 exceeded the β-glucan content of the lines with two copies.
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Affiliation(s)
- Tatiana V Danilova
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Jesse Poland
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Bernd Friebe
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA.
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12
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Danilova TV, Poland J, Friebe B. Production of a complete set of wheat-barley group-7 chromosome recombinants with increased grain β-glucan content. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3129-3141. [PMID: 31535163 DOI: 10.1007/s00122-019-03411-3413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/29/2019] [Indexed: 05/20/2023]
Abstract
Wheat-barley group-7 recombinant chromosomes were selected using molecular cytogenetics and SNP markers; increased grain β-glucan content was observed in wheat plants with two and four copies of HvCslF6. The soluble dietary fiber (1-3)(1-4) mixed linked β-D-glucan from cereal grains is a valuable component of a healthy diet, which reduces risks of coronary disease and diabetes. Although wheat is an important cereal crop providing a substantial portion of daily calories and protein intake in the human diet, it has a low level of β-glucan. Owing to the plasticity of the polyploid wheat genome, agronomically important traits absent in the wheat primary gene pool can be introgressed from distant relatives. Barley (Hordeum vulgare L.) has a high grain β-glucan content. Earlier, we introgressed this trait into wheat in the form of whole arm compensating Robertsonian translocations (RobT) involving group-7 chromosomes of barley and all three sub-genomes of hexaploid wheat (Triticum aestivum L). In the presented research, we shortened the barley 7HL arms in these RobTs to small pericentromeric segments, using induced wheat-barley homoeologous recombination. The recombinants were selected using SNP markers and molecular cytogenetics. Plants, comprising barley cellulose synthase-like F6 gene (HvCslF6), responsible for β-glucan synthesis, had a higher grain β-glucan content than the wheat control. Three wheat-barley group-7 recombinant chromosomes involving the A, B and D sub-genomes laid the basis for a multiple-copy gene introgression to hexaploid wheat. It is hypothesized that further increases in the β-glucan content in wheat grain can be obtained by increasing the number of HvCslF6 copies through combining several recombinant chromosomes in one line. The wheat lines with four copies of HvCslF6 exceeded the β-glucan content of the lines with two copies.
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Affiliation(s)
- Tatiana V Danilova
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Jesse Poland
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Bernd Friebe
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA.
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13
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Habachi-Houimli Y, Khalfallah Y, Mezghani-Khemakhem M, Makni H, Makni M, Bouktila D. Genome-wide identification, characterization, and evolutionary analysis of NBS-encoding resistance genes in barley. 3 Biotech 2018; 8:453. [PMID: 30370194 DOI: 10.1007/s13205-018-1478-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/11/2018] [Indexed: 12/29/2022] Open
Abstract
In this study, a systematic analysis of Nucleotide-Binding Site (NBS) disease resistance (R) gene family in the barley, Hordeum vulgare L. cv. Bowman, genome was performed. Using multiple computational analyses, we could identify 96 regular NBS-encoding genes and characterize them on the bases of structural diversity, conserved protein signatures, genomic distribution, gene duplications, differential expression, selection pressure, codon usage, regulation by microRNAs and phylogenetic relationships. Depending on the presence or absence of CC and LRR domains; the identified NBS genes were assigned to four distinct groups; NBS-LRR (53.1%), CC-NBS-LRR (14.6%), NBS (26%), and CC-NBS (6.3%). NBS-associated domain analysis revealed the presence of signal peptides, zinc fingers, diverse kinases, and other structural features. Eighty-five of the identified NBS-encoding genes were mapped onto the seven barley chromosomes, revealing that 50% of them were located on chromosomes 7H, 2H, and 3H, with a tendency of NBS genes to be clustered in the distal telomeric regions of the barley chromosomes. Nine gene clusters, representing 22.35% of total mapped barley NBS-encoding genes, were found, suggesting that tandem duplication stands for an important mechanism in the expansion of this gene family in barley. Phylogenetic analysis determined 31 HvNBS orthologs from rice and Brachypodium. 87 out of 96 HvNBSs were supported by expression evidence, exhibiting various and quantitatively uneven expression patterns across distinct tissues, organs, and development stages. Fourteen potential miRNA-R gene target pairs were further identified, providing insight into the regulation of NBS genes expression. These findings offer candidate target genes to engineer disease-resistant barley genotypes, and promote our understanding of the evolution of NBS-encoding genes in Poaceae crops.
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Affiliation(s)
- Yosra Habachi-Houimli
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
| | - Yosra Khalfallah
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
| | - Maha Mezghani-Khemakhem
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
| | - Hanem Makni
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
- 2Université de Tunis, Institut Supérieur de l'Animation pour la Jeunesse et la Culture (ISAJC), Bir El Bey, Tunisia
| | - Mohamed Makni
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
| | - Dhia Bouktila
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
- 3Université de Jendouba, Institut Supérieur de Biotechnologie de Béja (ISBB), 9000 Béja, Tunisia
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14
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Lee YI, Yap JW, Izan S, Leitch IJ, Fay MF, Lee YC, Hidalgo O, Dodsworth S, Smulders MJM, Gravendeel B, Leitch AR. Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization. BMC Genomics 2018; 19:578. [PMID: 30068293 PMCID: PMC6090851 DOI: 10.1186/s12864-018-4956-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 07/23/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Satellite DNA is a rapidly diverging, largely repetitive DNA component of many eukaryotic genomes. Here we analyse the evolutionary dynamics of a satellite DNA repeat in the genomes of a group of Asian subtropical lady slipper orchids (Paphiopedilum subgenus Parvisepalum and representative species in the other subgenera/sections across the genus). A new satellite repeat in Paphiopedilum subgenus Parvisepalum, SatA, was identified and characterized using the RepeatExplorer pipeline in HiSeq Illumina reads from P. armeniacum (2n = 26). Reconstructed monomers were used to design a satellite-specific fluorescent in situ hybridization (FISH) probe. The data were also analysed within a phylogenetic framework built using the internal transcribed spacer (ITS) sequences of 45S nuclear ribosomal DNA. RESULTS SatA comprises c. 14.5% of the P. armeniacum genome and is specific to subgenus Parvisepalum. It is composed of four primary monomers that range from 230 to 359 bp and contains multiple inverted repeat regions with hairpin-loop motifs. A new karyotype of P. vietnamense (2n = 28) is presented and shows that the chromosome number in subgenus Parvisepalum is not conserved at 2n = 26, as previously reported. The physical locations of SatA sequences were visualised on the chromosomes of all seven Paphiopedilum species of subgenus Parvisepalum (2n = 26-28), together with the 5S and 45S rDNA loci using FISH. The SatA repeats were predominantly localisedin the centromeric, peri-centromeric and sub-telocentric chromosome regions, but the exact distribution pattern was species-specific. CONCLUSIONS We conclude that the newly discovered, highly abundant and rapidly evolving satellite sequence SatA is specific to Paphiopedilum subgenus Parvisepalum. SatA and rDNA chromosomal distributions are characteristic of species, and comparisons between species reveal that the distribution patterns generate a strong phylogenetic signal. We also conclude that the ancestral chromosome number of subgenus Parvisepalum and indeed of all Paphiopedilum could be either 2n = 26 or 28, if P. vietnamense is sister to all species in the subgenus as suggested by the ITS data.
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Affiliation(s)
- Yung-I Lee
- Biology Department, National Museum of Natural Science, No 1, Kuan-Chien Rd, 40453 Taichung, Taiwan, Republic of China
- Department of Life Sciences, National Chung Hsing University, 40227 Taichung, Taiwan, Republic of China
| | - Jing Wei Yap
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
- Forest Research Institute Malaysia (FRIM), 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Shairul Izan
- Plant Breeding, Wageningen University & Research, P.O. Box 386, NL-6700 AJ Wageningen, The Netherlands
- Department of Crop Science, Faculty of Agriculture, University Putra Malaysia (UPM) Serdang, Serdang, Selangor Malaysia
| | - Ilia J. Leitch
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
| | - Michael F. Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
- School of Plant Biology, University of Western Australia, Crawley, WA 6009 Australia
| | - Yi-Ching Lee
- Biology Department, National Museum of Natural Science, No 1, Kuan-Chien Rd, 40453 Taichung, Taiwan, Republic of China
| | - Oriane Hidalgo
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
| | - Steven Dodsworth
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
| | - Marinus J. M. Smulders
- Plant Breeding, Wageningen University & Research, P.O. Box 386, NL-6700 AJ Wageningen, The Netherlands
| | - Barbara Gravendeel
- Endless Forms Group, Naturalis Biodiversity Center, Vondellaan 55, 2332 AA Leiden, The Netherlands
- Faculty of Science and Technology, University of Applied Sciences Leiden, Zernikedreef 11, 2333 CK Leiden, The Netherlands
- Institute Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Andrew R. Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
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15
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Hou F, Ma B, Xin Y, Kuang L, He N. Horizontal transfers of LTR retrotransposons in seven species of Rosales. Genome 2018; 61:587-594. [PMID: 29958091 DOI: 10.1139/gen-2017-0208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Horizontal transposable element transfer (HTT) events have occurred among a large number of species and play important roles in the composition and evolution of eukaryotic genomes. HTTs are also regarded as effective forces in promoting genomic variation and biological innovation. In the present study, HTT events were identified and analyzed in seven sequenced species of Rosales using bioinformatics methods by comparing sequence conservation and Ka/Ks value of reverse transcriptase (RT) with 20 conserved genes, estimating the dating of HTTs, and analyzing the phylogenetic relationships. Seven HTT events involving long terminal repeat (LTR) retrotransposons, two HTTs between Morus notabilis and Ziziphus jujuba, and five between Malus domestica and Pyrus bretschneideri were identified. Further analysis revealed that these LTR retrotransposons had functional structures, and the copy insertion times were lower than the dating of HTTs, particularly in Mn.Zj.1 and Md.Pb.3. Altogether, the results demonstrate that LTR retrotransposons still have potential transposition activity in host genomes. These results indicate that HTT events are another strategy for exchanging genetic material among species and are important for the evolution of genomes.
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Affiliation(s)
- Fei Hou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China
| | - Bi Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China
| | - Youchao Xin
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China
| | - Lulu Kuang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China
| | - Ningjia He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China
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16
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Horn RL, Marques AJD, Manseau M, Golding B, Klütsch CFC, Abraham K, Wilson PJ. Parallel evolution of site-specific changes in divergent caribou lineages. Ecol Evol 2018; 8:6053-6064. [PMID: 29988428 PMCID: PMC6024114 DOI: 10.1002/ece3.4154] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/06/2018] [Accepted: 04/09/2018] [Indexed: 12/15/2022] Open
Abstract
The parallel evolution of phenotypes or traits within or between species provides important insight into the basic mechanisms of evolution. Genetic and genomic advances have allowed investigations into the genetic underpinnings of parallel evolution and the independent evolution of similar traits in sympatric species. Parallel evolution may best be exemplified among species where multiple genetic lineages, descended from a common ancestor, colonized analogous environmental niches, and converged on a genotypic or phenotypic trait. Modern North American caribou (Rangifer tarandus) originated from three ancestral sources separated during the Last Glacial Maximum (LGM): the Beringian-Eurasian lineage (BEL), the North American lineage (NAL), and the High Arctic lineage (HAL). Historical introgression between the NAL and the BEL has been found throughout Ontario and eastern Manitoba. In this study, we first characterized the functional differentiation in the cytochrome-b (cytB) gene by identifying nonsynonymous changes. Second, the caribou lineages were used as a direct means to assess site-specific parallel changes among lineages. There was greater functional diversity within the NAL despite the BEL having greater neutral diversity. The patterns of amino acid substitutions occurring within different lineages supported the parallel evolution of cytB amino acid substitutions suggesting different selective pressures among lineages. This study highlights the independent evolution of identical amino acid substitutions within a wide-ranging mammal species that have diversified from different ancestral haplogroups and where ecological niches can invoke parallel evolution.
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Affiliation(s)
| | | | - Micheline Manseau
- Science and TechnologyEnvironment and Climate Change CanadaOttawaONCanada
- Natural Resources InstituteUniversity of ManitobaWinnipegMBCanada
| | - Brian Golding
- Department of BiologyMcMaster UniversityHamiltonONCanada
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17
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Dai F, Wang X, Zhang X, Chen Z, Nevo E, Jin G, Wu D, Li C, Zhang G. Assembly and analysis of a qingke reference genome demonstrate its close genetic relation to modern cultivated barley. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:760-770. [PMID: 28871634 PMCID: PMC5814578 DOI: 10.1111/pbi.12826] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/02/2017] [Accepted: 08/14/2017] [Indexed: 05/03/2023]
Abstract
Qingke, the local name of hulless barley in the Tibetan Plateau, is a staple food for Tibetans. The availability of its reference genome sequences could be useful for studies on breeding and molecular evolution. Taking advantage of the third-generation sequencer (PacBio), we de novo assembled a 4.84-Gb genome sequence of qingke, cv. Zangqing320 and anchored a 4.59-Gb sequence to seven chromosomes. Of the 46,787 annotated 'high-confidence' genes, 31 564 were validated by RNA-sequencing data of 39 wild and cultivated barley genotypes with wide genetic diversity, and the results were also confirmed by nonredundant protein database from NCBI. As some gaps in the reference genome of Morex were covered in the reference genome of Zangqing320 by PacBio reads, we believe that the Zangqing320 genome provides the useful supplements for the Morex genome. Using the qingke genome as a reference, we conducted a genome comparison, revealing a close genetic relationship between a hulled barley (cv. Morex) and a hulless barley (cv. Zangqing320), which is strongly supported by the low-diversity regions in the two genomes. Considering the origin of Morex from its breeding pedigree, we then demonstrated a close genomic relationship between modern cultivated barley and qingke. Given this genomic relationship and the large genetic diversity between qingke and modern cultivated barley, we propose that qingke could provide elite genes for barley improvement.
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Affiliation(s)
- Fei Dai
- Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina
| | - Xiaolei Wang
- Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina
| | - Xiao‐Qi Zhang
- Western Barley Genetics AllianceWestern Australian State Agricultural Biotechnology CentreSchool of Veterinary and Life SciencesMurdoch UniversityPerthWAAustralia
| | - Zhonghua Chen
- Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina
- School of Science and HealthWestern Sydney UniversityPenrithNSWAustralia
| | - Eviatar Nevo
- Institute of EvolutionUniversity of HaifaHaifaIsrael
| | - Gulei Jin
- Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina
| | - Dezhi Wu
- Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina
| | - Chengdao Li
- Western Barley Genetics AllianceWestern Australian State Agricultural Biotechnology CentreSchool of Veterinary and Life SciencesMurdoch UniversityPerthWAAustralia
| | - Guoping Zhang
- Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina
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18
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Danilova TV, Friebe B, Gill BS, Poland J, Jackson E. Development of a complete set of wheat-barley group-7 Robertsonian translocation chromosomes conferring an increased content of β-glucan. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:377-388. [PMID: 29124282 DOI: 10.1007/s00122-017-3008-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/26/2017] [Indexed: 05/06/2023]
Abstract
A complete set of six compensating Robertsonian translocation chromosomes involving barley chromosome 7H and three chromosomes of hexaploid wheat was produced. Grain β-glucan content increased in lines containing 7HL. Many valuable genes for agronomic performance, disease resistance and increased yield have been transferred from relative species to wheat (Triticum aestivum L.) through whole-arm Robertsonian translocations (RobT). Although of a great value, the sets of available translocations from barley (Hordeum vulgare L.) are limited. Here, we present the production of a complete set of six compensating RobT chromosomes involving barley chromosome 7H and three group-7 chromosomes of wheat. The barley group-7 long-arm RobTs had a higher grain β-glucan content compared to the wheat control. The β-glucan levels varied depending on the temperature and were higher under hot conditions. Implicated in this increase, the barley cellulose synthase-like F6 gene (CslF6) responsible for β-glucan synthesis was physically mapped near the centromere in the long arm of barley chromosome 7H. Likewise, wheat CslF6 homoeologs were mapped near the centromere in the long arms of all group-7 wheat chromosomes. With the set of novel wheat-barley translocations, we demonstrate a valuable increase of β-glucan, along with a resource of genetic stocks that are likely to carry many other important genes from barley into wheat.
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Affiliation(s)
- Tatiana V Danilova
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Bernd Friebe
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA.
| | - Bikram S Gill
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Jesse Poland
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Eric Jackson
- General Mills NTS [AI]2 Lab, Minneapolis, MN, 55426, USA
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19
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Markova DN, Mason-Gamer RJ. Transcriptional activity of PIF and Pong-like Class II transposable elements in Triticeae. BMC Evol Biol 2017; 17:178. [PMID: 28774284 PMCID: PMC5543537 DOI: 10.1186/s12862-017-1028-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 07/26/2017] [Indexed: 11/10/2022] Open
Abstract
Background Transposable elements are major contributors to genome size and variability, accounting for approximately 70–80% of the maize, barley, and wheat genomes. PIF and Pong-like elements belong to two closely-related element families within the PIF/Harbinger superfamily of Class II (DNA) transposons. Both elements contain two open reading frames; one encodes a transposase (ORF2) that catalyzes transposition of the functional elements and their related non-autonomous elements, while the function of the second is still debated. In this work, we surveyed for PIF- and Pong-related transcriptional activity in 13 diploid Triticeae species, all of which have been previously shown to harbor extensive within-genome diversity of both groups of elements. Results The results revealed that PIF elements have considerable transcriptional activity in Triticeae, suggesting that they can escape the initial levels of plant cell control and are regulated at the post-transcriptional level. Phylogenetic analysis of 156 PIF cDNA transposase fragments along with 240 genomic partial transposase sequences showed that most, if not all, PIF clades are transcriptionally competent, and that multiple transposases coexisting within a single genome have the potential to act simultaneously. In contrast, we did not detect any transcriptional activity of Pong elements in any sample. Conclusions The lack of Pong element transcription shows that even closely related transposon families can exhibit wide variation in their transposase transcriptional activity within the same genome. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1028-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dragomira N Markova
- Department of Biological Sciences, University of Illinois at Chicago, M/C 067 840 West Taylor Street, Chicago, IL, 60607, USA. .,Present address: Department of Plant Sciences (mail stop 3), 151 Asmundson Hall, University of California, Davis, CA, 95616, USA.
| | - Roberta J Mason-Gamer
- Department of Biological Sciences, University of Illinois at Chicago, M/C 067 840 West Taylor Street, Chicago, IL, 60607, USA
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20
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Bauer E, Schmutzer T, Barilar I, Mascher M, Gundlach H, Martis MM, Twardziok SO, Hackauf B, Gordillo A, Wilde P, Schmidt M, Korzun V, Mayer KFX, Schmid K, Schön CC, Scholz U. Towards a whole-genome sequence for rye (Secale cereale L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:853-869. [PMID: 27888547 DOI: 10.1111/tpj.13436] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/08/2016] [Accepted: 11/21/2016] [Indexed: 05/18/2023]
Abstract
We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun sequencing of the 7.9-Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high-density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome-wide map of selection signals differentiating the divergent gene pools. This rye whole-genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.
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Affiliation(s)
- Eva Bauer
- Technical University of Munich, Plant Breeding, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany
| | - Ivan Barilar
- Universität Hohenheim, Crop Biodiversity and Breeding Informatics, Fruwirthstr. 21, 70599, Stuttgart, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany
| | - Heidrun Gundlach
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Mihaela M Martis
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Sven O Twardziok
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Bernd Hackauf
- Julius Kühn-Institute, Institute for Breeding Research on Agricultural Crops, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany
| | - Andres Gordillo
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Peer Wilde
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Malthe Schmidt
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Viktor Korzun
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Klaus F X Mayer
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Karl Schmid
- Universität Hohenheim, Crop Biodiversity and Breeding Informatics, Fruwirthstr. 21, 70599, Stuttgart, Germany
| | - Chris-Carolin Schön
- Technical University of Munich, Plant Breeding, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany
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21
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Li G, Wang H, Lang T, Li J, La S, Yang E, Yang Z. New molecular markers and cytogenetic probes enable chromosome identification of wheat-Thinopyrum intermedium introgression lines for improving protein and gluten contents. PLANTA 2016; 244:865-76. [PMID: 27290728 DOI: 10.1007/s00425-016-2554-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/06/2016] [Indexed: 05/19/2023]
Abstract
New molecular markers were developed for targeting Thinopyrum intermedium 1St#2 chromosome, and novel FISH probe representing the terminal repeats was produced for identification of Thinopyrum chromosomes. Thinopyrum intermedium has been used as a valuable resource for improving the disease resistance and yield potential of wheat. A wheat-Th. intermedium ssp. trichophorum chromosome 1St#2 substitution and translocation has displayed superior grain protein and wet gluten content. With the aim to develop a number of chromosome 1St#2 specific molecular and cytogenetic markers, a high throughput, low-cost specific-locus amplified fragment sequencing (SLAF-seq) technology was used to compare the sequences between a wheat-Thinopyrum 1St#2 (1D) substitution and the related species Pseudoroegneria spicata (St genome, 2n = 14). A total of 5142 polymorphic fragments were analyzed and 359 different SLAF markers for 1St#2 were predicted. Thirty-seven specific molecular markers were validated by PCR from 50 randomly selected SLAFs. Meanwhile, the distribution of transposable elements (TEs) at the family level between wheat and St genomes was compared using the SLAFs. A new oligo-nucleotide probe named Oligo-pSt122 from high SLAF reads was produced for fluorescence in situ hybridization (FISH), and was observed to hybridize to the terminal region of 1St#L and also onto the terminal heterochromatic region of Th. intermedium genomes. The genome-wide markers and repetitive based probe Oligo-pSt122 will be valuable for identifying Thinopyrum chromosome segments in wheat backgrounds.
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Affiliation(s)
- Guangrong Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China
| | - Hongjin Wang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China
| | - Tao Lang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China
| | - Jianbo Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China
| | - Shixiao La
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China
| | - Ennian Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China.
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22
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Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data. G3-GENES GENOMES GENETICS 2016; 6:2299-308. [PMID: 27233667 PMCID: PMC4978885 DOI: 10.1534/g3.116.029082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The most abundant transposable elements (TEs) in plant genomes are Class I long terminal repeat (LTR) retrotransposons represented by superfamilies gypsy and copia. Amplification of these superfamilies directly impacts genome structure and contributes to differential patterns of genome size evolution among plant lineages. Utilizing short-read Illumina data and sequence information from a panel of Helianthus annuus (sunflower) full-length gypsy and copia elements, we explore the contribution of these sequences to genome size variation among eight diploid Helianthus species and an outgroup taxon, Phoebanthus tenuifolius. We also explore transcriptional dynamics of these elements in both leaf and bud tissue via RT-PCR. We demonstrate that most LTR retrotransposon sublineages (i.e., families) display patterns of similar genomic abundance across species. A small number of LTR retrotransposon sublineages exhibit lineage-specific amplification, particularly in the genomes of species with larger estimated nuclear DNA content. RT-PCR assays reveal that some LTR retrotransposon sublineages are transcriptionally active across all species and tissue types, whereas others display species-specific and tissue-specific expression. The species with the largest estimated genome size, H. agrestis, has experienced amplification of LTR retrotransposon sublineages, some of which have proliferated independently in other lineages in the Helianthus phylogeny.
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23
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Guyot R, Darré T, Dupeyron M, de Kochko A, Hamon S, Couturon E, Crouzillat D, Rigoreau M, Rakotomalala JJ, Raharimalala NE, Akaffou SD, Hamon P. Partial sequencing reveals the transposable element composition of Coffea genomes and provides evidence for distinct evolutionary stories. Mol Genet Genomics 2016; 291:1979-90. [PMID: 27469896 DOI: 10.1007/s00438-016-1235-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/25/2016] [Indexed: 10/21/2022]
Abstract
The Coffea genus, 124 described species, has a natural distribution spreading from inter-tropical Africa, to Western Indian Ocean Islands, India, Asia and up to Australasia. Two cultivated species, C. arabica and C. canephora, are intensively studied while, the breeding potential and the genome composition of all the wild species remained poorly uncharacterized. Here, we report the characterization and comparison of the highly repeated transposable elements content of 11 Coffea species representatives of the natural biogeographic distribution. A total of 994 Mb from 454 reads were produced with a genome coverage ranging between 3.2 and 15.7 %. The analyses showed that highly repeated transposable elements, mainly LTR retrotransposons (LTR-RT), represent between 32 and 53 % of Coffea genomes depending on their biogeographic location and genome size. Species from West and Central Africa (Eucoffea) contained the highest LTR-RT content but with no strong variation relative to their genome size. At the opposite, for the insular species (Mascarocoffea), a strong variation of LTR-RT was observed suggesting differential dynamics of these elements in this group. Two LTR-RT lineages, SIRE and Del were clearly differentially accumulated between African and insular species, suggesting these lineages were associated to the genome divergence of Coffea species in Africa. Altogether, the information obtained in this study improves our knowledge and brings new data on the composition, the evolution and the divergence of wild Coffea genomes.
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Affiliation(s)
- Romain Guyot
- IRD UMR IPME, CoffeeAdapt, BP 64501, 34394, Montpellier Cedex 5, France.
| | - Thibaud Darré
- IRD UMR DIADE, EvoGeC, BP 64501, 34394, Montpellier Cedex 5, France
| | | | | | - Serge Hamon
- IRD UMR DIADE, EvoGeC, BP 64501, 34394, Montpellier Cedex 5, France
| | | | - Dominique Crouzillat
- Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oe ́, BP 49716, 37097, Tours Cedex 2, France
| | - Michel Rigoreau
- Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oe ́, BP 49716, 37097, Tours Cedex 2, France
| | | | | | | | - Perla Hamon
- IRD UMR DIADE, EvoGeC, BP 64501, 34394, Montpellier Cedex 5, France
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24
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Renny-Byfield S, Page JT, Udall JA, Sanders WS, Peterson DG, Arick MA, Grover CE, Wendel JF. Independent Domestication of Two Old World Cotton Species. Genome Biol Evol 2016; 8:1940-7. [PMID: 27289095 PMCID: PMC4943200 DOI: 10.1093/gbe/evw129] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2016] [Indexed: 11/16/2022] Open
Abstract
Domesticated cotton species provide raw material for the majority of the world's textile industry. Two independent domestication events have been identified in allopolyploid cotton, one in Upland cotton (Gossypium hirsutum L.) and the other to Egyptian cotton (Gossypium barbadense L.). However, two diploid cotton species, Gossypium arboreum L. and Gossypium herbaceum L., have been cultivated for several millennia, but their status as independent domesticates has long been in question. Using genome resequencing data, we estimated the global abundance of various repetitive DNAs. We demonstrate that, despite negligible divergence in genome size, the two domesticated diploid cotton species contain different, but compensatory, repeat content and have thus experienced cryptic alterations in repeat abundance despite equivalence in genome size. Evidence of independent origin is bolstered by estimates of divergence times based on molecular evolutionary analysis of f7,000 orthologous genes, for which synonymous substitution rates suggest that G. arboreum and G. herbaceum last shared a common ancestor approximately 0.4-2.5 Ma. These data are incompatible with a shared domestication history during the emergence of agriculture and lead to the conclusion that G. arboreum and G. herbaceum were each domesticated independently.
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Affiliation(s)
- Simon Renny-Byfield
- Department of Ecology, Evolution and Organismal Biology, Iowa State University DuPont Pioneer, Johnston, IA
| | - Justin T Page
- Plant and Wildlife Science Department, Brigham Young University
| | - Joshua A Udall
- Plant and Wildlife Science Department, Brigham Young University
| | - William S Sanders
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University Department of Computer Science and Engineering, Mississippi State University
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University Department of Plant and Soil Sciences, Mississippi State University
| | - Mark A Arick
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University
| | - Corrinne E Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
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25
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Daneri-Castro SN, Svensson B, Roberts TH. Barley germination: Spatio-temporal considerations for designing and interpreting ‘omics’ experiments. J Cereal Sci 2016. [DOI: 10.1016/j.jcs.2016.05.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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26
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Burkhardt A, Gawde A, Cantrell CL, Baxter HL, Joyce BL, Stewart CN, Zheljazkov VD. Effects of Produced Water on Soil Characteristics, Plant Biomass, and Secondary Metabolites. JOURNAL OF ENVIRONMENTAL QUALITY 2015; 44:1938-1947. [PMID: 26641346 DOI: 10.2134/jeq2015.06.0299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The Powder River Basin in Wyoming and Montana contains the United States' largest coal reserve. The area produces large amounts of natural gas through extraction from water-saturated coalbeds. Determining the impacts of coalbed natural gas-produced efflux water on crops is important when considering its potential use as supplemental irrigation water. We hypothesized that coalbed natural gas water, because of its high salinity and sodicity, would affect plant secondary metabolism (essential oils) and biomass accumulation. A 2-yr field study was conducted in Wyoming to investigate the effects of produced water on two traditional bioenergy feedstocks-corn ( L.) and switchgrass ( L.)-and four novel biofuel feedstock species-spearmint ( L.), Japanese cornmint ( L.), lemongrass [ (Nees ex Steud.) J.F. Watson]), and common wormwood ( L.). The four nontraditional feedstock species were chosen because they contain high-value plant chemicals that can offset production costs. Essential oil content was significantly affected by coalbed natural gas water in lemongrass and spearmint. Oil content differences between two spearmint harvests in the same year indicated that there were significant changes between the growth stage of the plant and essential oil content; the first harvest averaged 0.42 g of oil per 100 g biomass while the second harvest (harvested before flowering) yielded only 0.19 g oil per 100 g dry biomass. Results indicated that produced water can be used for short-period (2 yr) irrigation of crops. However, prolonged use of untreated produced water for irrigation would likely have deleterious long-term effects on the soil and plants unless the water was treated or diluted (mixed) with good-quality water.
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27
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Joyce BL, Zheljazkov VD, Sykes R, Cantrell CL, Hamilton C, Mann DGJ, Rodriguez M, Mielenz JR, Astatkie T, Stewart CN. Ethanol and High-Value Terpene Co-Production from Lignocellulosic Biomass of Cymbopogon flexuosus and Cymbopogon martinii. PLoS One 2015; 10:e0139195. [PMID: 26437026 PMCID: PMC4593581 DOI: 10.1371/journal.pone.0139195] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 09/10/2015] [Indexed: 12/05/2022] Open
Abstract
Cymbopogon flexuosus, lemongrass, and C. martinii, palmarosa, are perennial grasses grown to produce essential oils for the fragrance industry. The objectives of this study were (1) to evaluate biomass and oil yields as a function of nitrogen and sulfur fertilization, and (2) to characterize their utility for lignocellulosic ethanol compared to Panicum virgatum (switchgrass). Mean biomass yields were 12.83 Mg lemongrass ha-1 and 15.11 Mg palmarosa ha-1 during the second harvest year resulting in theoretical biofuel yields of 2541 and 2569 L ethanol ha-1 respectively compared to reported 1749–3691 L ethanol ha-1 for switchgrass. Pretreated lemongrass yielded 198 mL ethanol (g biomass)-1 and pretreated palmarosa yielded 170 mL ethanol (g biomass)-1. Additionally, lemongrass yielded 85.7 kg essential oil ha-1 and palmarosa yielded 67.0 kg ha-1 with an estimated value of USD $857 and $1005 ha-1. These data suggest that dual-use crops such as lemongrass and palmarosa may increase the economic viability of lignocellulosic biofuels.
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Affiliation(s)
- Blake L. Joyce
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, United States of America
| | - Valtcho D. Zheljazkov
- Columbia Basin Agricultural Research Station, Oregon State University, 48037 Co 788 Rd, Adams, OR, 97810, United States of America
- * E-mail: ;
| | - Robert Sykes
- National Renewable Energy Laboratory, Golden, CO, 80401, United States of America
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, United States of America
| | - Charles L. Cantrell
- Agricultural Research Service, United States Department of Agriculture, NPURU, University, MS, 38677, United States of America
| | - Choo Hamilton
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, United States of America
- Oak Ridge National Laboratory, Environmental Science Division, Oak Ridge, TN, 37831, United States of America
| | - David G. J. Mann
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, United States of America
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, United States of America
| | - Miguel Rodriguez
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, United States of America
- Oak Ridge National Laboratory, Environmental Science Division, Oak Ridge, TN, 37831, United States of America
| | - Jonathan R. Mielenz
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, United States of America
- Oak Ridge National Laboratory, Environmental Science Division, Oak Ridge, TN, 37831, United States of America
| | - Tess Astatkie
- Faculty of Agriculture, Dalhousie University, 50 Pictou Road, P.O. Box 550, Truro, NS, B2N 5E3, Canada
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, United States of America
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28
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Muñoz-Amatriaín M, Lonardi S, Luo M, Madishetty K, Svensson JT, Moscou MJ, Wanamaker S, Jiang T, Kleinhofs A, Muehlbauer GJ, Wise RP, Stein N, Ma Y, Rodriguez E, Kudrna D, Bhat PR, Chao S, Condamine P, Heinen S, Resnik J, Wing R, Witt HN, Alpert M, Beccuti M, Bozdag S, Cordero F, Mirebrahim H, Ounit R, Wu Y, You F, Zheng J, Simková H, Dolezel J, Grimwood J, Schmutz J, Duma D, Altschmied L, Blake T, Bregitzer P, Cooper L, Dilbirligi M, Falk A, Feiz L, Graner A, Gustafson P, Hayes PM, Lemaux P, Mammadov J, Close TJ. Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:216-27. [PMID: 26252423 PMCID: PMC5014227 DOI: 10.1111/tpj.12959] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/15/2015] [Accepted: 07/24/2015] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Stefano Lonardi
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - MingCheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Kavitha Madishetty
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Jan T Svensson
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Nordic Genetic Resource Center, SE-23053, Alnarp, Sweden
| | - Matthew J Moscou
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Steve Wanamaker
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Tao Jiang
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Andris Kleinhofs
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Gary J Muehlbauer
- Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Roger P Wise
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service & Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011-1020, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Yaqin Ma
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Molefarming Laboratory USA, Davis, CA, 95616, USA
| | - Edmundo Rodriguez
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Departamento de Ciencias Basicas, Universidad Autonoma Agraria Antonio Narro, Narro 1923, Saltillo, Coah, 25315, México
| | - Dave Kudrna
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Prasanna R Bhat
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Monsanto Research Center, Bangalore, 560092, India
| | - Shiaoman Chao
- USDA-ARS Biosciences Research Lab, Fargo, ND, 58105, USA
| | - Pascal Condamine
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Shane Heinen
- Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Josh Resnik
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Ronald Reagan UCLA Medical Center, Los Angeles, CA, 90095, USA
| | - Rod Wing
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Heather N Witt
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Matthew Alpert
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Turtle Rock Studios, Lake Forest, CA, 92630, USA
| | - Marco Beccuti
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Department of Computer Science, University of Turin, Corso Svizzera 185, 10149, Turin, Italy
| | - Serdar Bozdag
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Deptartment of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, 53233, USA
| | - Francesca Cordero
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Department of Computer Science, University of Turin, Corso Svizzera 185, 10149, Turin, Italy
| | - Hamid Mirebrahim
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Rachid Ounit
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Yonghui Wu
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Google Inc., Mountain View, CA, 94043, USA
| | - Frank You
- USDA-ARS, Albany, CA, 94710, USA
- Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Jie Zheng
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- School of Computer Engineering, Nanyang Technological University, Nanyang Avenue, Singapore, 639798, Singapore
| | - Hana Simková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic
| | - Jaroslav Dolezel
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic
| | - Jane Grimwood
- Hudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Hudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Denisa Duma
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Houston, TX, 77030, USA
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Tom Blake
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
| | | | - Laurel Cooper
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Muharrem Dilbirligi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- International Cooperation Department, The Scientific and Technological Research Council of Turkey, Tunus cad. No: 80, 06100, Kavaklidere, Ankara, Turkey
| | - Anders Falk
- Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Leila Feiz
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
- Boyce Thompson Institute for Plant Research, Cornell University, 533 Tower Road, Ithaca, NY, 14853-1801, USA
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | | | - Patrick M Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Peggy Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Jafar Mammadov
- Department of Crop & Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
- Dow AgroSciences LLC, Indianapolis, IN, 46268-1054, USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
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Aliyeva-Schnorr L, Beier S, Karafiátová M, Schmutzer T, Scholz U, Doležel J, Stein N, Houben A. Cytogenetic mapping with centromeric bacterial artificial chromosomes contigs shows that this recombination-poor region comprises more than half of barley chromosome 3H. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:385-394. [PMID: 26332657 DOI: 10.1111/tpj.13006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/21/2015] [Accepted: 08/24/2015] [Indexed: 06/05/2023]
Abstract
Genetic maps are based on the frequency of recombination and often show different positions of molecular markers in comparison to physical maps, particularly in the centromere that is generally poor in meiotic recombinations. To decipher the position and order of DNA sequences genetically mapped to the centromere of barley (Hordeum vulgare) chromosome 3H, fluorescence in situ hybridization with mitotic metaphase and meiotic pachytene chromosomes was performed with 70 genomic single-copy probes derived from 65 fingerprinted bacterial artificial chromosomes (BAC) contigs genetically assigned to this recombination cold spot. The total physical distribution of the centromeric 5.5 cM bin of 3H comprises 58% of the mitotic metaphase chromosome length. Mitotic and meiotic chromatin of this recombination-poor region is preferentially marked by a heterochromatin-typical histone mark (H3K9me2), while recombination enriched subterminal chromosome regions are enriched in euchromatin-typical histone marks (H3K4me2, H3K4me3, H3K27me3) suggesting that the meiotic recombination rate could be influenced by the chromatin landscape.
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Affiliation(s)
- Lala Aliyeva-Schnorr
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Miroslava Karafiátová
- Institute of Experimental Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Jaroslav Doležel
- Institute of Experimental Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
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Kelly LJ, Renny‐Byfield S, Pellicer J, Macas J, Novák P, Neumann P, Lysak MA, Day PD, Berger M, Fay MF, Nichols RA, Leitch AR, Leitch IJ. Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size. THE NEW PHYTOLOGIST 2015; 208:596-607. [PMID: 26061193 PMCID: PMC4744688 DOI: 10.1111/nph.13471] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 04/20/2015] [Indexed: 05/18/2023]
Abstract
Plants exhibit an extraordinary range of genome sizes, varying by > 2000-fold between the smallest and largest recorded values. In the absence of polyploidy, changes in the amount of repetitive DNA (transposable elements and tandem repeats) are primarily responsible for genome size differences between species. However, there is ongoing debate regarding the relative importance of amplification of repetitive DNA versus its deletion in governing genome size. Using data from 454 sequencing, we analysed the most repetitive fraction of some of the largest known genomes for diploid plant species, from members of Fritillaria. We revealed that genomic expansion has not resulted from the recent massive amplification of just a handful of repeat families, as shown in species with smaller genomes. Instead, the bulk of these immense genomes is composed of highly heterogeneous, relatively low-abundance repeat-derived DNA, supporting a scenario where amplified repeats continually accumulate due to infrequent DNA removal. Our results indicate that a lack of deletion and low turnover of repetitive DNA are major contributors to the evolution of extremely large genomes and show that their size cannot simply be accounted for by the activity of a small number of high-abundance repeat families.
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Affiliation(s)
- Laura J. Kelly
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonE1 4NSUK
- Jodrell LaboratoryRoyal Botanic GardensKewRichmondTW9 3DSUK
| | - Simon Renny‐Byfield
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonE1 4NSUK
- Department of Plant SciencesUniversity of California DavisDavisCA95616USA
| | - Jaume Pellicer
- Jodrell LaboratoryRoyal Botanic GardensKewRichmondTW9 3DSUK
| | - Jiří Macas
- Biology Centre CASInstitute of Plant Molecular BiologyCZ‐37005České BudějoviceCzech Republic
| | - Petr Novák
- Biology Centre CASInstitute of Plant Molecular BiologyCZ‐37005České BudějoviceCzech Republic
| | - Pavel Neumann
- Biology Centre CASInstitute of Plant Molecular BiologyCZ‐37005České BudějoviceCzech Republic
| | - Martin A. Lysak
- Plant Cytogenomics Research GroupCEITEC – Central European Institute of TechnologyMasaryk UniversityKamenice 5CZ‐62500BrnoCzech Republic
| | - Peter D. Day
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonE1 4NSUK
- Jodrell LaboratoryRoyal Botanic GardensKewRichmondTW9 3DSUK
| | - Madeleine Berger
- Jodrell LaboratoryRoyal Botanic GardensKewRichmondTW9 3DSUK
- School of Biological and Biomedical SciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
- Rothamsted ResearchWest CommonHarpendenHertfordshireAL5 2JQUK
| | - Michael F. Fay
- Jodrell LaboratoryRoyal Botanic GardensKewRichmondTW9 3DSUK
| | - Richard A. Nichols
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonE1 4NSUK
| | - Andrew R. Leitch
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonE1 4NSUK
| | - Ilia J. Leitch
- Jodrell LaboratoryRoyal Botanic GardensKewRichmondTW9 3DSUK
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Markova DN, Mason-Gamer RJ. The Role of Vertical and Horizontal Transfer in the Evolutionary Dynamics of PIF-Like Transposable Elements in Triticeae. PLoS One 2015; 10:e0137648. [PMID: 26355747 PMCID: PMC4565680 DOI: 10.1371/journal.pone.0137648] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/20/2015] [Indexed: 11/19/2022] Open
Abstract
PIF-like transposable elements are members of the PIF/Harbinger superfamily of DNA transposons found in the genomes of many plants, animals, and fungi. The evolution of the gene that encodes the transposase responsible for mobilizing PIF-like elements has been studied in both plants and animals, but the elements' history in flowering plants remains poorly known. In this work, we describe the phylogenetic distribution and evolution of PIF-like elements in the genomes of 21 diploid species from the wheat tribe, Triticeae, and we present the first convincing evidence of horizontal transfer of PIF elements in plant genomes. A phylogenetic analysis of 240 PIF sequences based on the conserved region of the transposase domain revealed at least four main transposase lineages. Their complex evolutionary history can be best explained by a combination of vertical transmission with differential evolutionary success among lineages, and occasional horizontal transfer between phylogenetically distant Triticeae genera. In addition, we identified 127 potentially functional transposase sequences indicating possible recent activity of PIF.
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Affiliation(s)
- Dragomira N. Markova
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Roberta J. Mason-Gamer
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States of America
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Abstract
Pong-like elements are members of the PIF/Harbinger superfamily of DNA transposons that has been described in many plants, animals, and fungi. Most Pong elements contain two open reading frames (ORFs). One encodes a transposase (ORF2) that catalyzes transposition of Pong and related non-autonomous elements, while the function of the second is unknown. Little is known about the evolutionary history of Pong elements in flowering plants. In this work, we present the first comprehensive analysis of the diversity, abundance, and evolution of the Pong-like transposase gene in the genomes of 21 diploid species from the wheat tribe, Triticeae, and we present the first convincing evidence of horizontal transfer of nuclear-encoded Pong elements in any organism. A phylogenetic analysis of nearly 300 Pong sequences based on a conserved region of the transposase domain revealed a complex evolutionary history of Pong elements that can be best explained by ancestral polymorphism, followed by differential evolutionary success of some transposase lineages, and by occasional horizontal transfer between phylogenetically distant genera. In addition, we used transposon display to estimate the abundance of the transposase gene within Triticeae genomes, and our results revealed varying levels of Pong proliferation, with numbers of transposase copies ranging from 22 to 92. Comparisons of Pong transposase abundance to flow cytometry estimates of genome size revealed that larger Triticeae genome size was not correlated with transposase abundance.
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Chaparro C, Gayraud T, de Souza RF, Domingues DS, Akaffou S, Laforga Vanzela AL, Kochko AD, Rigoreau M, Crouzillat D, Hamon S, Hamon P, Guyot R. Terminal-repeat retrotransposons with GAG domain in plant genomes: a new testimony on the complex world of transposable elements. Genome Biol Evol 2015; 7:493-504. [PMID: 25573958 PMCID: PMC4350172 DOI: 10.1093/gbe/evv001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A novel structure of nonautonomous long terminal repeat (LTR) retrotransposons called terminal repeat with GAG domain (TR-GAG) has been described in plants, both in monocotyledonous, dicotyledonous and basal angiosperm genomes. TR-GAGs are relatively short elements in length (<4 kb) showing the typical features of LTR-retrotransposons. However, they carry only one open reading frame coding for the GAG precursor protein involved for instance in transposition, the assembly, and the packaging of the element into the virus-like particle. GAG precursors show similarities with both Copia and Gypsy GAG proteins, suggesting evolutionary relationships of TR-GAG elements with both families. Despite the lack of the enzymatic machinery required for their mobility, strong evidences suggest that TR-GAGs are still active. TR-GAGs represent ubiquitous nonautonomous structures that could be involved in the molecular diversities of plant genomes.
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Affiliation(s)
- Cristian Chaparro
- 2EI UMR5244 Université de Perpignan Via Domitia, UMR 5244 CNRS Ecologie et Evolution des Interactions (2EI), Perpignan, France
| | - Thomas Gayraud
- Institut de Recherche pour le Développement (IRD), UMR DIADE (CIRAD, IRD, UM2), Montpellier, France
| | | | - Douglas Silva Domingues
- Departamento de Botanica, Instituto de Biociencias, Univ Estadual Paulista, UNESP, Rio Claro, SP, Brazil
| | | | | | - Alexandre de Kochko
- Institut de Recherche pour le Développement (IRD), UMR DIADE (CIRAD, IRD, UM2), Montpellier, France
| | | | | | - Serge Hamon
- Institut de Recherche pour le Développement (IRD), UMR DIADE (CIRAD, IRD, UM2), Montpellier, France
| | - Perla Hamon
- Institut de Recherche pour le Développement (IRD), UMR DIADE (CIRAD, IRD, UM2), Montpellier, France
| | - Romain Guyot
- Institut de Recherche pour le Développement (IRD), UMR IPME, Montpellier, France
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Emadzade K, Jang TS, Macas J, Kovařík A, Novák P, Parker J, Weiss-Schneeweiss H. Differential amplification of satellite PaB6 in chromosomally hypervariable Prospero autumnale complex (Hyacinthaceae). ANNALS OF BOTANY 2014; 114:1597-608. [PMID: 25169019 PMCID: PMC4273535 DOI: 10.1093/aob/mcu178] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Chromosomal evolution, including numerical and structural changes, is a major force in plant diversification and speciation. This study addresses genomic changes associated with the extensive chromosomal variation of the Mediterranean Prospero autumnale complex (Hyacinthaceae), which includes four diploid cytotypes each with a unique combination of chromosome number (x = 5, 6, 7), rDNA loci and genome size. METHODS A new satellite repeat PaB6 has previously been identified, and monomers were reconstructed from next-generation sequencing (NGS) data of P. autumnale cytotype B(6)B(6) (2n = 12). Monomers of all other Prospero cytotypes and species were sequenced to check for lineage-specific mutations. Copy number, restriction patterns and methylation levels of PaB6 were analysed using Southern blotting. PaB6 was localized on chromosomes using fluorescence in situ hybridization (FISH). KEY RESULTS The monomer of PaB6 is 249 bp long, contains several intact and truncated vertebrate-type telomeric repeats and is highly methylated. PaB6 is exceptional because of its high copy number and unprecedented variation among diploid cytotypes, ranging from 10(4) to 10(6) copies per 1C. PaB6 is always located in pericentromeric regions of several to all chromosomes. Additionally, two lineages of cytotype B(7)B(7) (x = 7), possessing either a single or duplicated 5S rDNA locus, differ in PaB6 copy number; the ancestral condition of a single locus is associated with higher PaB6 copy numbers. CONCLUSIONS Although present in all Prospero species, PaB6 has undergone differential amplification only in chromosomally variable P. autumnale, particularly in cytotypes B(6)B(6) and B(5)B(5). These arose via independent chromosomal fusions from x = 7 to x = 6 and 5, respectively, accompanied by genome size increases. The copy numbers of satellite DNA PaB6 are among the highest in angiosperms, and changes of PaB6 are exceptionally dynamic in this group of closely related cytotypes of a single species. The evolution of the PaB6 copy numbers is discussed, and it is suggested that PaB6 represents a recent and highly dynamic system originating from a small pool of ancestral repeats.
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Affiliation(s)
- Khatere Emadzade
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Tae-Soo Jang
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Jiří Macas
- Czech Academy of Sciences, Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic
| | - Ales Kovařík
- Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic
| | - Petr Novák
- Czech Academy of Sciences, Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic
| | - John Parker
- Cambridge University Botanic Garden, Cambridge CB2 1JF, UK
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
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Buchmann JP, Löytynoja A, Wicker T, Schulman AH. Analysis of CACTA transposases reveals intron loss as major factor influencing their exon/intron structure in monocotyledonous and eudicotyledonous hosts. Mob DNA 2014; 5:24. [PMID: 25206928 PMCID: PMC4158355 DOI: 10.1186/1759-8753-5-24] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/18/2014] [Indexed: 01/20/2023] Open
Abstract
Background CACTA elements are DNA transposons and are found in numerous organisms. Despite their low activity, several thousand copies can be identified in many genomes. CACTA elements transpose using a ‘cut-and-paste’ mechanism, which is facilitated by a DDE transposase. DDE transposases from CACTA elements contain, despite their conserved function, different exon numbers among various CACTA families. While earlier studies analyzed the ancestral history of the DDE transposases, no studies have examined exon loss and gain with a view of mechanisms that could drive the changes. Results We analyzed 64 transposases from different CACTA families among monocotyledonous and eudicotyledonous host species. The annotation of the exon/intron boundaries showed a range from one to six exons. A robust multiple sequence alignment of the 64 transposases based on their protein sequences was created and used for phylogenetic analysis, which revealed eight different clades. We observed that the exon numbers in CACTA transposases are not specific for a host genome. We found that ancient CACTA lineages diverged before the divergence of monocotyledons and eudicotyledons. Most exon/intron boundaries were found in three distinct regions among all the transposases, grouping 63 conserved intron/exon boundaries. Conclusions We propose a model for the ancestral CACTA transposase gene, which consists of four exons, that predates the divergence of the monocotyledons and eudicotyledons. Based on this model, we propose pathways of intron loss or gain to explain the observed variation in exon numbers. While intron loss appears to have prevailed, a putative case of intron gain was nevertheless observed.
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Affiliation(s)
- Jan P Buchmann
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, PO Box 65, FIN-00014 Helsinki, Finland ; Present address: Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Center, University of Sydney, Sydney NSW 2006, Australia
| | - Ari Löytynoja
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, PO Box 65, FIN-00014 Helsinki, Finland
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, Zurich, Switzerland
| | - Alan H Schulman
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, PO Box 65, FIN-00014 Helsinki, Finland ; Biotechnology and Food Research, MTT Agrifood Research Finland, Myllytie 1, FIN-31600 Jokioinen, Finland
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Moisy C, Schulman AH, Kalendar R, Buchmann JP, Pelsy F. The Tvv1 retrotransposon family is conserved between plant genomes separated by over 100 million years. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1223-35. [PMID: 24590356 DOI: 10.1007/s00122-014-2293-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 02/21/2014] [Indexed: 05/18/2023]
Abstract
Combining several different approaches, we have examined the structure, variability, and distribution of Tvv1 retrotransposons. Tvv1 is an unusual example of a low-copy retrotransposon metapopulation dispersed unevenly among very distant species and is promising for the development of molecular markers. Retrotransposons are ubiquitous throughout the genomes of the vascular plants, but individual retrotransposon families tend to be confined to the level of plant genus or at most family. This restricts the general applicability of a family as molecular markers. Here, we characterize a new plant retrotransposon named Tvv1_Sdem, a member of the Copia superfamily of LTR retrotransposons, from the genome of the wild potato Solanum demissum. Comparative analyses based on structure and sequence showed a high level of similarity of Tvv1_Sdem with Tvv1-VB, a retrotransposon previously described in the grapevine genome Vitis vinifera. Extending the analysis to other species by in silico and in vitro approaches revealed the presence of Tvv1 family members in potato, tomato, and poplar genomes, and led to the identification of full-length copies of Tvv1 in these species. We were also able to identify polymorphism in UTL sequences between Tvv1_Sdem copies from wild and cultivated potatoes that are useful as molecular markers. Combining different approaches, our results suggest that the Tvv1 family of retrotransposons has a monophyletic origin and has been maintained in both the rosids and the asterids, the major clades of dicotyledonous plants, since their divergence about 100 MYA. To our knowledge, Tvv1 represents an unusual plant retrotransposon metapopulation comprising highly similar members disjointedly dispersed among very distant species. The twin features of Tvv1 presence in evolutionarily distant genomes and the diversity of its UTL region in each species make it useful as a source of robust molecular markers for diversity studies and breeding.
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Affiliation(s)
- Cédric Moisy
- MTT/BI Plant Genomics Lab, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Biocenter 3, Viikinkaari 1, 00014, Helsinki, Finland,
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Yilmaz S, Marakli S, Gozukirmizi N. BAGY2 retrotransposon analyses in barley calli cultures and regenerated plantlets. Biochem Genet 2014; 52:233-44. [PMID: 24509836 DOI: 10.1007/s10528-014-9643-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 10/25/2013] [Indexed: 11/30/2022]
Abstract
The stability of aging barley calli and regenerated plantlets from those calli was investigated by the BAGY2 retrotransposon-specific IRAP technique. Mature embryos of barley (Hordeum vulgare cv. Golden Promise) were cultured in Murashige and Skoog medium supplemented with 4 mg/L dicamba and maintained on the same medium for 45 and 90 days. Two IRAP-based primers were used, and the levels of variation of DNA isolated from 45- and 90-day-old calli and regenerated plantlets were found to be increased 0-21%, depending on the mature embryo material and the age of the callus. It has been observed that culture conditions cause genetic variations and evident BAGY2 retrotransposon alterations. Internal domains of BAGY2 were also analyzed by qPCR, and copy numbers were found to be increased. These findings are expected to contribute to understanding of how retrotransposons affect features like tissue culture (especially callus tissue) formation and genetic engineering studies.
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Affiliation(s)
- Sibel Yilmaz
- Department of Molecular Biology and Genetics, Istanbul University, Vezneciler, 34134, Istanbul, Turkey,
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Džunková M, Garcia-Garcerà M, Martínez-Priego L, D’Auria G, Calafell F, Moya A. Direct squencing from the minimal number of DNA molecules needed to fill a 454 picotiterplate. PLoS One 2014; 9:e97379. [PMID: 24887077 PMCID: PMC4041646 DOI: 10.1371/journal.pone.0097379] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 04/17/2014] [Indexed: 02/07/2023] Open
Abstract
The large amount of DNA needed to prepare a library in next generation sequencing protocols hinders direct sequencing of small DNA samples. This limitation is usually overcome by the enrichment of such samples with whole genome amplification (WGA), mostly by multiple displacement amplification (MDA) based on φ29 polymerase. However, this technique can be biased by the GC content of the sample and is prone to the development of chimeras as well as contamination during enrichment, which contributes to undesired noise during sequence data analysis, and also hampers the proper functional and/or taxonomic assignments. An alternative to MDA is direct DNA sequencing (DS), which represents the theoretical gold standard in genome sequencing. In this work, we explore the possibility of sequencing the genome of Escherichia coli fs 24 from the minimum number of DNA molecules required for pyrosequencing, according to the notion of one-bead-one-molecule. Using an optimized protocol for DS, we constructed a shotgun library containing the minimum number of DNA molecules needed to fill a selected region of a picotiterplate. We gathered most of the reference genome extension with uniform coverage. We compared the DS method with MDA applied to the same amount of starting DNA. As expected, MDA yielded a sparse and biased read distribution, with a very high amount of unassigned and unspecific DNA amplifications. The optimized DS protocol allows unbiased sequencing to be performed from samples with a very small amount of DNA.
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Affiliation(s)
- Mária Džunková
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Marc Garcia-Garcerà
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Llúcia Martínez-Priego
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
| | - Giussepe D’Auria
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Francesc Calafell
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Andrés Moya
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
- * E-mail:
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Mochida K, Shinozaki K. Unlocking Triticeae genomics to sustainably feed the future. PLANT & CELL PHYSIOLOGY 2013; 54:1931-50. [PMID: 24204022 PMCID: PMC3856857 DOI: 10.1093/pcp/pct163] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/04/2013] [Indexed: 05/23/2023]
Abstract
The tribe Triticeae includes the major crops wheat and barley. Within the last few years, the whole genomes of four Triticeae species-barley, wheat, Tausch's goatgrass (Aegilops tauschii) and wild einkorn wheat (Triticum urartu)-have been sequenced. The availability of these genomic resources for Triticeae plants and innovative analytical applications using next-generation sequencing technologies are helping to revitalize our approaches in genetic work and to accelerate improvement of the Triticeae crops. Comparative genomics and integration of genomic resources from Triticeae plants and the model grass Brachypodium distachyon are aiding the discovery of new genes and functional analyses of genes in Triticeae crops. Innovative approaches and tools such as analysis of next-generation populations, evolutionary genomics and systems approaches with mathematical modeling are new strategies that will help us discover alleles for adaptive traits to future agronomic environments. In this review, we provide an update on genomic tools for use with Triticeae plants and Brachypodium and describe emerging approaches toward crop improvements in Triticeae.
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Affiliation(s)
- Keiichi Mochida
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Kazuo Shinozaki
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
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Jääskeläinen M, Chang W, Moisy C, Schulman AH. Retrotransposon BARE displays strong tissue-specific differences in expression. THE NEW PHYTOLOGIST 2013; 200:1000-8. [PMID: 24033286 DOI: 10.1111/nph.12470] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 07/30/2013] [Indexed: 05/25/2023]
Abstract
The BARE retrotransposon comprises c. 10% of the barley (Hordeum vulgare) genome. It is actively transcribed, translated and forms virus-like particles (VLPs). For retrotransposons, the inheritance of new copies depends critically on where in the plant replication occurs. In order to shed light on the replication strategy of BARE in the plant, we have used immunolocalization and in situ hybridization to examine expression of the BARE capsid protein, Gag, at a tissue-specific level. Gag is expressed in provascular tissues and highly localized in companion cells surrounding the phloem sieve tubes in mature vascular tissues. BARE Gag and RNA was not seen in the shoot apical meristem of young seedlings, but appeared, following transition to flowering, in the developing floral spike. Moreover, Gag has a highly specific localization in pre-fertilization ovaries. The strong presence of Gag in the floral meristems suggests that newly replicated copies there will be passed to the next generation. BARE expression patterns are consistent with transcriptional regulation by predicted response elements in the BARE promoter, and in the ovary with release from epigenetic transcriptional silencing. To our knowledge, this is the first analysis of the expression of native retrotransposon proteins within a plant to be reported.
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Affiliation(s)
- Marko Jääskeläinen
- MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, PO Box 65, Viikinkaari 1, FIN-00014, Helsinki, Finland
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Breen J, Wicker T, Shatalina M, Frenkel Z, Bertin I, Philippe R, Spielmeyer W, Šimková H, Šafář J, Cattonaro F, Scalabrin S, Magni F, Vautrin S, Bergès H, Paux E, Fahima T, Doležel J, Korol A, Feuillet C, Keller B. A physical map of the short arm of wheat chromosome 1A. PLoS One 2013; 8:e80272. [PMID: 24278269 PMCID: PMC3836966 DOI: 10.1371/journal.pone.0080272] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 10/11/2013] [Indexed: 12/31/2022] Open
Abstract
Bread wheat (Triticum aestivum) has a large and highly repetitive genome which poses major technical challenges for its study. To aid map-based cloning and future genome sequencing projects, we constructed a BAC-based physical map of the short arm of wheat chromosome 1A (1AS). From the assembly of 25,918 high information content (HICF) fingerprints from a 1AS-specific BAC library, 715 physical contigs were produced that cover almost 99% of the estimated size of the chromosome arm. The 3,414 BAC clones constituting the minimum tiling path were end-sequenced. Using a gene microarray containing ∼40 K NCBI UniGene EST clusters, PCR marker screening and BAC end sequences, we arranged 160 physical contigs (97 Mb or 35.3% of the chromosome arm) in a virtual order based on synteny with Brachypodium, rice and sorghum. BAC end sequences and information from microarray hybridisation was used to anchor 3.8 Mbp of Illumina sequences from flow-sorted chromosome 1AS to BAC contigs. Comparison of genetic and synteny-based physical maps indicated that ∼50% of all genetic recombination is confined to 14% of the physical length of the chromosome arm in the distal region. The 1AS physical map provides a framework for future genetic mapping projects as well as the basis for complete sequencing of chromosome arm 1AS.
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Affiliation(s)
- James Breen
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | | | - Zeev Frenkel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Isabelle Bertin
- INRA UMR 1095, Genetique Diversite et Ecophysiologie des Cereales, Clermont-Ferrand, France
| | - Romain Philippe
- INRA UMR 1095, Genetique Diversite et Ecophysiologie des Cereales, Clermont-Ferrand, France
| | | | - Hana Šimková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Jan Šafář
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | | | | | | | | | | | | | - Etienne Paux
- INRA UMR 1095, Genetique Diversite et Ecophysiologie des Cereales, Clermont-Ferrand, France
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Jaroslav Doležel
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Catherine Feuillet
- INRA UMR 1095, Genetique Diversite et Ecophysiologie des Cereales, Clermont-Ferrand, France
| | - Beat Keller
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
- * E-mail:
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Buyyarapu R, Kantety RV, Yu JZ, Xu Z, Kohel RJ, Percy RG, Macmil S, Wiley GB, Roe BA, Sharma GC. BAC-pool sequencing and analysis of large segments of A12 and D12 homoeologous chromosomes in upland cotton. PLoS One 2013; 8:e76757. [PMID: 24116150 PMCID: PMC3792896 DOI: 10.1371/journal.pone.0076757] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 08/28/2013] [Indexed: 11/19/2022] Open
Abstract
Although new and emerging next-generation sequencing (NGS) technologies have reduced sequencing costs significantly, much work remains to implement them for de novo sequencing of complex and highly repetitive genomes such as the tetraploid genome of Upland cotton (Gossypium hirsutum L.). Herein we report the results from implementing a novel, hybrid Sanger/454-based BAC-pool sequencing strategy using minimum tiling path (MTP) BACs from Ctg-3301 and Ctg-465, two large genomic segments in A12 and D12 homoeologous chromosomes (Ctg). To enable generation of longer contig sequences in assembly, we implemented a hybrid assembly method to process ~35x data from 454 technology and 2.8-3x data from Sanger method. Hybrid assemblies offered higher sequence coverage and better sequence assemblies. Homology studies revealed the presence of retrotransposon regions like Copia and Gypsy elements in these contigs and also helped in identifying new genomic SSRs. Unigenes were anchored to the sequences in Ctg-3301 and Ctg-465 to support the physical map. Gene density, gene structure and protein sequence information derived from protein prediction programs were used to obtain the functional annotation of these genes. Comparative analysis of both contigs with Arabidopsis genome exhibited synteny and microcollinearity with a conserved gene order in both genomes. This study provides insight about use of MTP-based BAC-pool sequencing approach for sequencing complex polyploid genomes with limited constraints in generating better sequence assemblies to build reference scaffold sequences. Combining the utilities of MTP-based BAC-pool sequencing with current longer and short read NGS technologies in multiplexed format would provide a new direction to cost-effectively and precisely sequence complex plant genomes.
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Affiliation(s)
- Ramesh Buyyarapu
- Center for Molecular Biology, Department of Biological and Environmental Sciences, Alabama Agricultural & Mechanical University, Normal, Alabama, United States of America
| | - Ramesh V. Kantety
- Center for Molecular Biology, Department of Biological and Environmental Sciences, Alabama Agricultural & Mechanical University, Normal, Alabama, United States of America
| | - John Z. Yu
- United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, Texas, United States of America
| | - Zhanyou Xu
- United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, Texas, United States of America
| | - Russell J. Kohel
- United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, Texas, United States of America
| | - Richard G. Percy
- United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, Texas, United States of America
| | - Simone Macmil
- Gene Structure and Function Laboratory, University of Otago, Dunedin, New Zealand
| | - Graham B. Wiley
- Arthritis & Immunology Department, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Bruce A. Roe
- Advanced Center for Genome Technology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Govind C. Sharma
- Center for Molecular Biology, Department of Biological and Environmental Sciences, Alabama Agricultural & Mechanical University, Normal, Alabama, United States of America
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Spannagl M, Martis MM, Pfeifer M, Nussbaumer T, Mayer KFX. Analysing complex Triticeae genomes - concepts and strategies. PLANT METHODS 2013; 9:35. [PMID: 24011260 PMCID: PMC3847682 DOI: 10.1186/1746-4811-9-35] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/10/2013] [Indexed: 05/20/2023]
Abstract
The genomic sequences of many important Triticeae crop species are hard to assemble and analyse due to their large genome sizes, (in part) polyploid genomes and high repeat content. Recently, the draft genomes of barley and bread wheat were reported thanks to cost-efficient and fast NGS technologies. The genome of barley is estimated to be 5 Gb in size whereas the genome of bread wheat accounts for 17 Gb and harbours an allo-hexaploid genome. Direct assembly of the sequence reads and access to the gene content is hampered by the repeat content. As a consequence, novel strategies and data analysis concepts had to be developed to provide much-needed whole genome sequence surveys and access to the gene repertoires. Here we describe some analytical strategies that now enable structuring of massive NGS data generated and pave the way towards structured and ordered sequence data and gene order. Specifically we report on the GenomeZipper, a synteny driven approach to order and structure NGS survey sequences of grass genomes that lack a physical map. In addition, to access and analyse the gene repertoire of allo-hexaploid bread wheat from the raw sequence reads, a reference-guided approach was developed utilizing representative genes from rice, Brachypodium distachyon, sorghum and barley. Stringent sub-assembly on the reference genes prevented collapsing of homeologous wheat genes and allowed to estimate gene retention rate and determine gene family sizes. Genomic sequences from the wheat sub-genome progenitors enabled to discriminate a large number of sub-assemblies between the wheat A, B or D sub-genome using machine learning algorithms. Many of the concepts outlined here can readily be applied to other complex plant and non-plant genomes.
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Affiliation(s)
- Manuel Spannagl
- MIPS/IBIS, Helmholtz Center Munich, National Research Center for Environment and Health, Ingolstaedter Landstr. 1, Neuherberg, Germany
| | - Mihaela M Martis
- MIPS/IBIS, Helmholtz Center Munich, National Research Center for Environment and Health, Ingolstaedter Landstr. 1, Neuherberg, Germany
| | - Matthias Pfeifer
- MIPS/IBIS, Helmholtz Center Munich, National Research Center for Environment and Health, Ingolstaedter Landstr. 1, Neuherberg, Germany
| | - Thomas Nussbaumer
- MIPS/IBIS, Helmholtz Center Munich, National Research Center for Environment and Health, Ingolstaedter Landstr. 1, Neuherberg, Germany
| | - Klaus FX Mayer
- MIPS/IBIS, Helmholtz Center Munich, National Research Center for Environment and Health, Ingolstaedter Landstr. 1, Neuherberg, Germany
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Chang W, Jääskeläinen M, Li SP, Schulman AH. BARE retrotransposons are translated and replicated via distinct RNA pools. PLoS One 2013; 8:e72270. [PMID: 23940808 PMCID: PMC3735527 DOI: 10.1371/journal.pone.0072270] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 07/14/2013] [Indexed: 01/02/2023] Open
Abstract
The replication of Long Terminal Repeat (LTR) retrotransposons, which can constitute over 80% of higher plant genomes, resembles that of retroviruses. A major question for retrotransposons and retroviruses is how the two conflicting roles of their transcripts, in translation and reverse transcription, are balanced. Here, we show that the BARE retrotransposon, despite its organization into just one open reading frame, produces three distinct classes of transcripts. One is capped, polyadenylated, and translated, but cannot be copied into cDNA. The second is not capped or polyadenylated, but is destined for packaging and ultimate reverse transcription. The third class is capped, polyadenylated, and spliced to favor production of a subgenomic RNA encoding only Gag, the protein forming virus-like particles. Moreover, the BARE2 subfamily, which cannot synthesize Gag and is parasitic on BARE1, does not produce the spliced sub-genomic RNA for translation but does make the replication competent transcripts, which are packaged into BARE1 particles. To our knowledge, this is first demonstration of distinct RNA pools for translation and transcription for any retrotransposon.
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Affiliation(s)
- Wei Chang
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Marko Jääskeläinen
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Song-ping Li
- Genome-Scale Biology Program, University of Helsinki, Biomedicum, Helsinki, Finland
| | - Alan H. Schulman
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
- * E-mail:
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Klemme S, Banaei-Moghaddam AM, Macas J, Wicker T, Novák P, Houben A. High-copy sequences reveal distinct evolution of the rye B chromosome. THE NEW PHYTOLOGIST 2013; 199:550-558. [PMID: 23614816 DOI: 10.1111/nph.12289] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 03/16/2013] [Indexed: 05/02/2023]
Abstract
B chromosomes (Bs) are supernumerary chromosomes that vary in number among individuals of the same species. Because of their dispensable nature, their non-Mendelian inheritance and their origin from A chromosomes (As), one might assume that Bs followed a different evolutionary pathway from As, this being reflected in differences in their high-copy DNA constitution. We provide detailed insight into the composition and distribution of rye (Secale cereale) B-located high-copy sequences. A- and B-specific high-copy sequences were identified in silico. Mobile elements and satellite sequences were verified by fluorescence in situ hybridization (FISH). Replication was analyzed via EdU incorporation. Although most repeats are similarly distributed along As and Bs, several transposons are either amplified or depleted on the B. An accumulation of B-enriched satellites was found mostly in the nondisjunction control region of the B, which is transcriptionally active and late-replicating. All B-enriched sequences are not unique to the B but are also present in other Secale species, suggesting the origin of the B from As of the same genus. Our findings highlight the differences between As and Bs. Although Bs originated from As, they have since taken a separate evolutionary pathway.
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Affiliation(s)
- Sonja Klemme
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, 06466, Germany
| | | | - Jiri Macas
- Biology Centre ASCR, Institute of Plant Molecular Biology, Branišovská 31/1160, České Budějovice, 370 05, Czech Republic
| | - Thomas Wicker
- University of Zurich, Institute of Plant Biology, Zurich, 8008, Switzerland
| | - Petr Novák
- Biology Centre ASCR, Institute of Plant Molecular Biology, Branišovská 31/1160, České Budějovice, 370 05, Czech Republic
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, 06466, Germany
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Bonchev G, Parisod C. Transposable elements and microevolutionary changes in natural populations. Mol Ecol Resour 2013; 13:765-75. [DOI: 10.1111/1755-0998.12133] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 05/31/2013] [Accepted: 06/04/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Georgi Bonchev
- Laboratory of evolutionary botany Institute of biology University of Neuchâtel Rue Emile‐Argand 11 CH‐2000 Neuchâtel Switzerland
- Institute of plant physiology and genetics Bulgarian academy of sciences G. Bonchev Street, Bldg 24 Sofia 1113 Bulgaria
| | - Christian Parisod
- Laboratory of evolutionary botany Institute of biology University of Neuchâtel Rue Emile‐Argand 11 CH‐2000 Neuchâtel Switzerland
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Silvar C, Perovic D, Nussbaumer T, Spannagl M, Usadel B, Casas A, Igartua E, Ordon F. Towards positional isolation of three quantitative trait loci conferring resistance to powdery mildew in two Spanish barley landraces. PLoS One 2013; 8:e67336. [PMID: 23826271 PMCID: PMC3691219 DOI: 10.1371/journal.pone.0067336] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/17/2013] [Indexed: 01/09/2023] Open
Abstract
Three quantitative trait loci (QTL) conferring broad spectrum resistance to powdery mildew, caused by the fungus Blumeria graminis f. sp. hordei, were previously identified on chromosomes 7HS, 7HL and 6HL in the Spanish barley landrace-derived lines SBCC097 and SBCC145. In the present work, a genome-wide putative linear gene index of barley (Genome Zipper) and the first draft of the physical, genetic and functional sequence of the barley genome were used to go one step further in the shortening and explicit demarcation on the barley genome of these regions conferring resistance to powdery mildew as well as in the identification of candidate genes. First, a comparative analysis of the target regions to the barley Genome Zippers of chromosomes 7H and 6H allowed the development of 25 new gene-based molecular markers, which slightly better delimit the QTL intervals. These new markers provided the framework for anchoring of genetic and physical maps, figuring out the outline of the barley genome at the target regions in SBCC097 and SBCC145. The outermost flanking markers of QTLs on 7HS, 7HL and 6HL defined a physical area of 4 Mb, 3.7 Mb and 3.2 Mb, respectively. In total, 21, 10 and 16 genes on 7HS, 7HL and 6HL, respectively, could be interpreted as potential candidates to explain the resistance to powdery mildew, as they encode proteins of related functions with respect to the known pathogen defense-related processes. The majority of these were annotated as belonging to the NBS-LRR class or protein kinase family.
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Affiliation(s)
- Cristina Silvar
- Department of Ecology, Plant and Animal Biology, University of Coruña, A Coruña, Spain.
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Weiss-Schneeweiss H, Emadzade K, Jang TS, Schneeweiss G. Evolutionary consequences, constraints and potential of polyploidy in plants. Cytogenet Genome Res 2013; 140:137-50. [PMID: 23796571 PMCID: PMC3859924 DOI: 10.1159/000351727] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Polyploidy, the possession of more than 2 complete genomes, is a major force in plant evolution known to affect the genetic and genomic constitution and the phenotype of an organism, which will have consequences for its ecology and geography as well as for lineage diversification and speciation. In this review, we discuss phylogenetic patterns in the incidence of polyploidy including possible underlying causes, the role of polyploidy for diversification, the effects of polyploidy on geographical and ecological patterns, and putative underlying mechanisms as well as chromosome evolution and evolution of repetitive DNA following polyploidization. Spurred by technological advances, a lot has been learned about these aspects both in model and increasingly also in nonmodel species. Despite this enormous progress, long-standing questions about polyploidy still cannot be unambiguously answered, due to frequently idiosyncratic outcomes and insufficient integration of different organizational levels (from genes to ecology), but likely this will change in the near future. See also the sister article focusing on animals by Choleva and Janko in this themed issue.
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Affiliation(s)
- H. Weiss-Schneeweiss
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
| | - K. Emadzade
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
| | - T.-S. Jang
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
| | - G.M. Schneeweiss
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
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Genomics approaches for crop improvement against abiotic stress. ScientificWorldJournal 2013; 2013:361921. [PMID: 23844392 PMCID: PMC3690750 DOI: 10.1155/2013/361921] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 04/22/2013] [Indexed: 12/13/2022] Open
Abstract
As sessile organisms, plants are inevitably exposed to one or a combination of stress factors every now and then throughout their growth and development. Stress responses vary considerably even in the same plant species; stress-susceptible genotypes are at one extreme, and stress-tolerant ones are at the other. Elucidation of the stress responses of crop plants is of extreme relevance, considering the central role of crops in food and biofuel production. Crop improvement has been a traditional issue to increase yields and enhance stress tolerance; however, crop improvement against abiotic stresses has been particularly compelling, given the complex nature of these stresses. As traditional strategies for crop improvement approach their limits, the era of genomics research has arisen with new and promising perspectives in breeding improved varieties against abiotic stresses.
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50
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Renny-Byfield S, Kovarik A, Kelly LJ, Macas J, Novak P, Chase MW, Nichols RA, Pancholi MR, Grandbastien MA, Leitch AR. Diploidization and genome size change in allopolyploids is associated with differential dynamics of low- and high-copy sequences. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:829-39. [PMID: 23517128 DOI: 10.1111/tpj.12168] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 02/23/2013] [Accepted: 03/01/2013] [Indexed: 05/18/2023]
Abstract
Recent advances have highlighted the ubiquity of whole-genome duplication (polyploidy) in angiosperms, although subsequent genome size change and diploidization (returning to a diploid-like condition) are poorly understood. An excellent system to assess these processes is provided by Nicotiana section Repandae, which arose via allopolyploidy (approximately 5 million years ago) involving relatives of Nicotiana sylvestris and Nicotiana obtusifolia. Subsequent speciation in Repandae has resulted in allotetraploids with divergent genome sizes, including Nicotiana repanda and Nicotiana nudicaulis studied here, which have an estimated 23.6% genome expansion and 19.2% genome contraction from the early polyploid, respectively. Graph-based clustering of next-generation sequence data enabled assessment of the global genome composition of these allotetraploids and their diploid progenitors. Unexpectedly, in both allotetraploids, over 85% of sequence clusters (repetitive DNA families) had a lower abundance than predicted from their diploid relatives; a trend seen particularly in low-copy repeats. The loss of high-copy sequences predominantly accounts for the genome downsizing in N. nudicaulis. In contrast, N. repanda shows expansion of clusters already inherited in high copy number (mostly chromovirus-like Ty3/Gypsy retroelements and some low-complexity sequences), leading to much of the genome upsizing predicted. We suggest that the differential dynamics of low- and high-copy sequences reveal two genomic processes that occur subsequent to allopolyploidy. The loss of low-copy sequences, common to both allopolyploids, may reflect genome diploidization, a process that also involves loss of duplicate copies of genes and upstream regulators. In contrast, genome size divergence between allopolyploids is manifested through differential accumulation and/or deletion of high-copy-number sequences.
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Affiliation(s)
- Simon Renny-Byfield
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London E1 4NS, UK
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