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Samoluk SS, Chalup LMI, Chavarro C, Robledo G, Bertioli DJ, Jackson SA, Seijo G. Heterochromatin evolution in Arachis investigated through genome-wide analysis of repetitive DNA. PLANTA 2019; 249:1405-1415. [PMID: 30680457 DOI: 10.1007/s00425-019-03096-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/18/2019] [Indexed: 05/21/2023]
Abstract
The most conspicuous difference among chromosomes and genomes in Arachis species, the patterns of heterochromatin, was mainly modeled by differential amplification of different members of one superfamily of satellite DNAs. Divergence in repetitive DNA is a primary driving force for genome and chromosome evolution. Section Arachis is karyotypically diverse and has six different genomes. Arachis glandulifera (D genome) has the most asymmetric karyotype and the highest reproductive isolation compared to the well-known A and B genome species. These features make A. glandulifera an interesting model species for studying the main repetitive components that accompanied the genome and chromosome diversification in the section. Here, we performed a genome-wide analysis of repetitive sequences in A. glandulifera and investigated the chromosome distribution of the identified satellite DNA sequences (satDNAs). LTR retroelements, mainly the Ty3-gypsy families "Fidel/Feral" and "Pipoka/Pipa", were the most represented. Comparative analyses with the A and B genomes showed that many of the previously described transposable elements (TEs) were differently represented in the D genome, and that this variation accompanied changes in DNA content. In addition, four major satDNAs were characterized. Agla_CL8sat was the major component of pericentromeric heterochromatin, while Agla_CL39sat, Agla_CL69sat, and Agla_CL122sat were found in heterochromatic and/or euchromatic regions. Even though Agla_CL8sat belong to a different family than that of the major satDNA (ATR-2) found in the heterochromatin of the A, K, and F genomes, both satDNAs are members of the same superfamily. This finding suggests that closely related satDNAs of an ancestral library were differentially amplified leading to the major changes in the heterochromatin patterns that accompanied the karyotype and genome differentiation in Arachis.
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Affiliation(s)
- Sergio S Samoluk
- Facultad de Ciencias Agrarias, Instituto de Botánica del Nordeste (UNNE-CONICET), Corrientes, Argentina.
| | - Laura M I Chalup
- Facultad de Ciencias Agrarias, Instituto de Botánica del Nordeste (UNNE-CONICET), Corrientes, Argentina
| | - Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Germán Robledo
- Facultad de Ciencias Agrarias, Instituto de Botánica del Nordeste (UNNE-CONICET), Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - David J Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Guillermo Seijo
- Facultad de Ciencias Agrarias, Instituto de Botánica del Nordeste (UNNE-CONICET), Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
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Morrissey J, Stack JC, Valls R, Motamayor JC. Low-cost assembly of a cacao crop genome is able to resolve complex heterozygous bubbles. HORTICULTURE RESEARCH 2019; 6:44. [PMID: 30962937 PMCID: PMC6441652 DOI: 10.1038/s41438-019-0125-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/08/2018] [Accepted: 01/02/2019] [Indexed: 06/09/2023]
Abstract
Cacao (Theobroma cacao) is a tropical tree that produces the essential raw material for chocolate. Because yields have been stagnant, land use has expanded to provide for increasing chocolate demand. Assembled genomes of key parents could modernize breeding programs in the remote and under-resourced locations where cacao is grown. The MinION, a long read sequencer that runs off of a laptop computer, has the potential to facilitate the assembly of the complex genomes of high-yielding F1 hybrids. Here, we validate the MinION's application to heterozygous crops by creating a de novo genome assembly of a key parent in breeding programs, the clone Pound 7. Our MinION-only assembly was 20% larger than the latest released cacao genome, with 10-fold greater contiguity, and the resolution of complex heterozygosity and repetitive elements. Polishing with Illumina short reads brought the predicted completeness of our assembly to similar levels to the previously released cacao genome assemblies. In contrast to previous cacao genome projects, our assembly required only a small scientific team and limited reagents. Our sequencing and assembly methods could easily be adopted by under-resourced breeding programs, speeding crop improvement in the developing world.
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Affiliation(s)
- Joe Morrissey
- Mars Chocolate, 13601 Old Cutler Road, Miami, FL 33158 USA
| | | | - Rebecca Valls
- Mars Chocolate, 13601 Old Cutler Road, Miami, FL 33158 USA
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Bolsheva NL, Melnikova NV, Kirov IV, Dmitriev AA, Krasnov GS, Amosova АV, Samatadze TE, Yurkevich OY, Zoshchuk SA, Kudryavtseva AV, Muravenko OV. Characterization of repeated DNA sequences in genomes of blue-flowered flax. BMC Evol Biol 2019; 19:49. [PMID: 30813893 PMCID: PMC6391757 DOI: 10.1186/s12862-019-1375-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Members of different sections of the genus Linum are characterized by wide variability in size, morphology and number of chromosomes in karyotypes. Since such variability is determined mainly by the amount and composition of repeated sequences, we conducted a comparative study of the repeatomes of species from four sections forming a clade of blue-flowered flax. Based on the results of high-throughput genome sequencing performed in this study as well as available WGS data, bioinformatic analyses of repeated sequences from 12 flax samples were carried out using a graph-based clustering method. RESULTS It was found that the genomes of closely related species, which have a similar karyotype structure, are also similar in the repeatome composition. In contrast, the repeatomes of karyologically distinct species differed significantly, and no similar tandem-organized repeats have been identified in their genomes. At the same time, many common mobile element families have been identified in genomes of all species, among them, Athila Ty3/gypsy LTR retrotransposon was the most abundant. The 30-chromosome members of the sect. Linum (including the cultivated species L. usitatissimum) differed significantly from other studied species by a great number of satellite DNA families as well as their relative content in genomes. CONCLUSIONS The evolution of studied flax species was accompanied by waves of amplification of satellite DNAs and LTR retrotransposons. The observed inverse correlation between the total contents of dispersed repeats and satellite DNAs allowed to suggest a relationship between both classes of repeating sequences. Significant interspecific differences in satellite DNA sets indicated a high rate of evolution of this genomic fraction. The phylogenetic relationships between the investigated flax species, obtained by comparison of the repeatomes, agreed with the results of previous molecular phylogenetic studies.
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Affiliation(s)
- Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya V. Kirov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Аlexandra V. Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga Yu. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Martín-Peciña M, Ruiz-Ruano FJ, Camacho JPM, Dodsworth S. Phylogenetic signal of genomic repeat abundances can be distorted by random homoplasy: a case study from hominid primates. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly077] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- María Martín-Peciña
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | | | - Juan Pedro M Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Steven Dodsworth
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- School of Life Sciences, University of Bedfordshire, University Square, Luton, UK
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Copetti D, Wing RA. The Dark Side of the Genome: Revealing the Native Transposable Element/Repeat Content of Eukaryotic Genomes. MOLECULAR PLANT 2016; 9:1664-1666. [PMID: 27693675 DOI: 10.1016/j.molp.2016.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/12/2016] [Accepted: 09/22/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Dario Copetti
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; International Rice Research Institute, T.T. Chang Genetic Resources Center, Los Baños, Laguna 63108, Philippines
| | - Rod A Wing
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; International Rice Research Institute, T.T. Chang Genetic Resources Center, Los Baños, Laguna 63108, Philippines.
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Coates BS, Abel CA, Perera OP. Estimation of long terminal repeat element content in the Helicoverpa zea genome from high-throughput sequencing of bacterial artificial chromosome pools. Genome 2016; 60:310-324. [PMID: 28177843 DOI: 10.1139/gen-2016-0067] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The lepidopteran pest insect Helicoverpa zea feeds on cultivated corn and cotton across the Americas where control remains challenging owing to the evolution of resistance to chemical and transgenic insecticidal toxins, yet genomic resources remain scarce for this species. A bacterial artificial chromosome (BAC) library having a mean genomic insert size of 145 ± 20 kbp was created from a laboratory strain of H. zea, which provides ∼12.9-fold coverage of a 362.8 ± 8.8 Mbp (0.37 ± 0.09 pg) flow cytometry estimated haploid genome size. Assembly of Illumina HiSeq 2000 reads generated from 14 pools that encompassed all BAC clones resulted in 165 485 genomic contigs (N50 = 3262 bp; 324.6 Mbp total). Long terminal repeat (LTR) protein coding regions annotated from 181 contigs included 30 Ty1/copia, 78 Ty3/gypsy, and 73 BEL/Pao elements, of which 60 (33.1%) encoded all five functional polyprotein (pol) domains. Approximately 14% of LTR elements are distributed non-randomly across pools of BAC clones.
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Affiliation(s)
- Brad S Coates
- a USDA-ARS, Corn Insects & Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, IA 50011, USA.,b Department of Entomology, Iowa State University, Ames, IA 50011, USA
| | - Craig A Abel
- a USDA-ARS, Corn Insects & Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Omaththage P Perera
- c USDA-ARS, Southern Insect Management Research Unit, 141 Experiment Station Road, P.O. Box 346, Stoneville, MS 38776, USA
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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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Twyford AD. Will Benchtop Sequencers Resolve the Sequencing Trade-off in Plant Genetics? FRONTIERS IN PLANT SCIENCE 2016; 7:433. [PMID: 27092154 PMCID: PMC4822345 DOI: 10.3389/fpls.2016.00433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/21/2016] [Indexed: 06/05/2023]
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Scossa F, Brotman Y, de Abreu E Lima F, Willmitzer L, Nikoloski Z, Tohge T, Fernie AR. Genomics-based strategies for the use of natural variation in the improvement of crop metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:47-64. [PMID: 26566824 DOI: 10.1016/j.plantsci.2015.05.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/29/2015] [Accepted: 05/31/2015] [Indexed: 05/08/2023]
Abstract
Next-generation genomics holds great potential in the study of plant phenotypic variation. With several crop reference genomes now available, the affordable costs of de novo genome assembly or target resequencing offer the opportunity to mine the enormous amount of genetic diversity hidden in crop wild relatives. Wide introgressions from these wild ancestors species or land races represent a possible strategy to improve cultivated varieties. In this review, we discuss the mechanisms underlying metabolic diversity within plant species and the possible strategies (and barriers) to introgress novel metabolic traits into cultivated varieties. We show how deep genomic surveys uncover various types of structural variants from extended gene pools of major crops and highlight how this variation may be used for the improvement of crop metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany; Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Frutticoltura, Via di Fioranello 52, 00134 Rome, Italy.
| | - Yariv Brotman
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | | | - Lothar Willmitzer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Zoran Nikoloski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
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Vera M, Bello X, Álvarez-Dios JA, Pardo BG, Sánchez L, Carlsson J, Carlsson JE, Bartolomé C, Maside X, Martinez P. Screening of repetitive motifs inside the genome of the flat oyster (Ostrea edulis): Transposable elements and short tandem repeats. Mar Genomics 2015; 24 Pt 3:335-41. [DOI: 10.1016/j.margen.2015.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/03/2015] [Accepted: 08/25/2015] [Indexed: 10/23/2022]
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Ågren JA, Greiner S, Johnson MTJ, Wright SI. No evidence that sex and transposable elements drive genome size variation in evening primroses. Evolution 2015; 69:1053-62. [PMID: 25690700 DOI: 10.1111/evo.12627] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 01/13/2015] [Indexed: 01/05/2023]
Abstract
Genome size varies dramatically across species, but despite an abundance of attention there is little agreement on the relative contributions of selective and neutral processes in governing this variation. The rate of sex can potentially play an important role in genome size evolution because of its effect on the efficacy of selection and transmission of transposable elements (TEs). Here, we used a phylogenetic comparative approach and whole genome sequencing to investigate the contribution of sex and TE content to genome size variation in the evening primrose (Oenothera) genus. We determined genome size using flow cytometry for 30 species that vary in genetic system and find that variation in sexual/asexual reproduction cannot explain the almost twofold variation in genome size. Moreover, using whole genome sequences of three species of varying genome sizes and reproductive system, we found that genome size was not associated with TE abundance; instead the larger genomes had a higher abundance of simple sequence repeats. Although it has long been clear that sexual reproduction may affect various aspects of genome evolution in general and TE evolution in particular, it does not appear to have played a major role in genome size evolution in the evening primroses.
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Affiliation(s)
- J Arvid Ågren
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada.
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How Big is that Genome? Estimating Genome Size and Coverage from k-mer Abundance Spectra. STRING PROCESSING AND INFORMATION RETRIEVAL 2015. [DOI: 10.1007/978-3-319-23826-5_20] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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