DIFFERENTIAL GENOME SIZE AND REPETITIVE DNA EVOLUTION IN DIPLOID SPECIES OF MELAMPODIUM SECT. MELAMPODIUM (ASTERACEAE)
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PROVIDER: PRJEB36721 | ENA |
REPOSITORIES: ENA
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Project description:Plant genomes vary greatly in composition and size mainly due to the diversity of repetitive DNAs and the inherent propensity for their amplification and removal from the host genome. Most studies addressing repeatome dynamics focus on model organisms, whereas few provide comprehensive investigations across the genomes of related taxa. Herein, we analyze the evolution of repeats of the 13 species in Melampodium sect. Melampodium, representing all but two of its diploid taxa, in a phylogenetic context. The investigated genomes range in size from 0.49 to 2.27 pg/1C (ca. 4.5-fold variation), despite having the same base chromosome number (x = 10) and very strong phylogenetic affinities. Phylogenetic analysis performed in BEAST and ancestral genome size reconstruction revealed mixed patterns of genome size increases and decreases across the group. High-throughput genome skimming and the RepeatExplorer pipeline were utilized to determine the repeat families responsible for the differences in observed genome sizes. Patterns of repeat evolution were found to be highly correlated with phylogenetic position, namely taxonomic series circumscription. Major differences found were in the abundances of the SIRE (Ty1-copia), Athila (Ty3-gypsy), and CACTA (DNA transposon) lineages. Additionally, several satellite DNA families were found to be highly group-specific, although their overall contribution to genome size variation was relatively small. Evolutionary changes in repetitive DNA composition and genome size were complex, with independent patterns of genome up- and downsizing throughout the evolution of the analyzed diploids. A model-based analysis of genome size and repetitive DNA composition revealed evidence for strong phylogenetic signal and differential evolutionary rates of major lineages of repeats in the diploid genomes.
| S-EPMC7136903 | biostudies-literature
Project description:Allopolyploidy has played an important role in the evolution of the flowering plants. Genome mergers are often accompanied by significant and rapid alterations of genome size and structure via chromosomal rearrangements and altered dynamics of tandem and dispersed repetitive DNA families. Recent developments in sequencing technologies and bioinformatic methods allow for a comprehensive investigation of the repetitive component of plant genomes. Interpretation of evolutionary dynamics following allopolyploidization requires both the knowledge of parentage and the age of origin of an allopolyploid. Whereas parentage is typically inferred from cytogenetic and phylogenetic data, age inference is hampered by the reticulate nature of the phylogenetic relationships. Treating subgenomes of allopolyploids as if they belonged to different species (i.e., no recombination among subgenomes) and applying cross-bracing (i.e., putting a constraint on the age difference of nodes pertaining to the same event), we can infer the age of allopolyploids within the framework of the multispecies coalescent within BEAST2. Together with a comprehensive characterization of the repetitive DNA fraction using the RepeatExplorer pipeline, we apply the dating approach in a group of closely related allopolyploids and their progenitor species in the plant genus Melampodium (Asteraceae). We dated the origin of both the allotetraploid, Melampodium strigosum, and its two allohexaploid derivatives, Melampodium pringlei and Melampodium sericeum, which share both parentage and the direction of the cross, to the Pleistocene ($<$1.4 Ma). Thus, Pleistocene climatic fluctuations may have triggered formation of allopolyploids possibly in short intervals, contributing to difficulties in inferring the precise temporal order of allopolyploid species divergence of M. sericeum and M. pringlei. The relatively recent origin of the allopolyploids likely played a role in the near-absence of major changes in the repetitive fraction of the polyploids' genomes. The repetitive elements most affected by the postpolyploidization changes represented retrotransposons of the Ty1-copia lineage Maximus and, to a lesser extent, also Athila elements of Ty3-gypsy family.
| S-EPMC6193527 | biostudies-literature
Project description:Flow cytometry was conducted to evaluate genome size diversity among African diploid species of the Coffea genus. The study included 15 species and six new taxa from Congolese and Cameroonian forest regions which have yet to be botanically characterized. Between-population differences were also recorded in some cases. These evaluations using an internal standard were highly correlated with previous results obtained with an external standard, but differences of up to 18 % existed for some species, involving stoichiometric errors. Consequently, genome size variation between species and within species are discussed as true genome size differences or stoichiometric errors. Environmental and phenotypic correlations with genome size are also discussed.
| S-EPMC4244848 | biostudies-other
Project description:The species-rich and widespread genus Taraxacum F. H. Wiggers, 1780 (Asteraceae subfamily Cichorioideae) is one of the most taxonomically complex plant genera in the world, mainly due to its combination of different sexual and asexual reproduction strategies. Polyploidy is usually confined to apomictic microspecies, varying from 3x to 6x (rarely 10x). In this study, we focused on Taraxacum sect. Taraxacum (= T.sect.Ruderalia; T.officinale group), i.e., the largest group within the genus. We counted chromosome numbers and measured the DNA content for species sampled in Central Europe, mainly in Czechia. The chromosome number of the 28 species (T.aberrans Hagendijk, Soest & Zevenbergen, 1974, T.atroviride Štěpánek & Trávníček, 2008, T.atrox Kirschner & Štěpánek, 1997, T.baeckiiforme Sahlin, 1971, T.chrysophaenum Railonsala, 1957, T.coartatum G.E. Haglund, 1942, T.corynodes G.E. Haglund, 1943, T.crassum H. Øllgaard & Trávníček, 2003, T.deltoidifrons H. Øllgaard, 2003, T.diastematicum Marklund, 1940, T.gesticulans H. Øllgaard, 1978, T.glossodon Sonck & H. Øllgaard, 1999, T.guttigestans H. Øllgaard in Kirschner & Štěpánek, 1992, T.huelphersianum G.E. Haglund, 1935, T.ingens Palmgren, 1910, T.jugiferum H. Øllgaard, 2003, T.laticordatum Marklund, 1938, T.lojoense H. Lindberg, 1944 (= T.debrayi Hagendijk, Soest & Zevenbergen, 1972, T.lippertianum Sahlin, 1979), T.lucidifrons Trávníček, ineditus, T.obtusifrons Marklund, 1938, T.ochrochlorum G.E. Haglund, 1942, T.ohlsenii G.E. Haglund, 1936, T.perdubium Trávníček, ineditus, T.praestabile Railonsala, 1962, T.sepulcrilobum Trávníček, ineditus, T.sertatum Kirschner, H. Øllgaard & Štěpánek, 1997, T.subhuelphersianum M.P. Christiansen, 1971, T.valens Marklund, 1938) is 2n = 3x = 24. The DNA content ranged from 2C = 2.60 pg (T.atrox) to 2C = 2.86 pg (T.perdubium), with an average value of 2C = 2.72 pg. Chromosome numbers are reported for the first time for 26 species (all but T.diastematicum and T.obtusifrons), and genome size estimates for 26 species are now published for the first time.
| S-EPMC6160755 | biostudies-other
Project description:Deconstructing ribosomal DNA: from the sequence to the chromosome across the Tree-of-Life (rDNA-LIFE)
| PRJNA764566 | ENA
Project description:Halothane/Isoflurane repetitive exposures
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Project description:The genus Taraxacum is one of the largest and taxonomically most complicated apomictic genera. Currently, it is considered to consist of over 2800 species placed within 60 sections. Due to the large number of species, and their uniform morphological design and plasticity of leaves, the identification of plants at the species level is challenging even for specialists. This problem significantly hinders the study of their properties and the rational use of these valuable medicinal and nutritional plants. This paper presents the results of research on the morphology and micromorphology of achenes of 28 Taraxacum species of sect. Palustria and for comparison one species per section of: Erythrosperma, Naevosa, Piesis, and Taraxacum. The achenes were measured with a stereoscopic microscope and a biometric program, and micromorphological studies were performed by scanning electron microscopy. It has been shown that traits associated with achene morphology and micromorphology have a high diagnostic value, allowing us to distinguish sections as well as species within the sect. Palustria. Based on the examined achene features, a dichotomous key for determining the studied species was constructed.
| S-EPMC7661953 | biostudies-literature
Project description:The evolution of the karyotype and genome size was examined in species of Crepis sensu lato. The phylogenetic relationships, inferred from the plastid and nrITS DNA sequences, were used as a framework to infer the patterns of karyotype evolution. Five different base chromosome numbers (x = 3, 4, 5, 6, and 11) were observed. A phylogenetic analysis of the evolution of the chromosome numbers allowed the inference of x = 6 as the ancestral state and the descending dysploidy as the major direction of the chromosome base number evolution. The derived base chromosome numbers (x = 5, 4, and 3) were found to have originated independently and recurrently in the different lineages of the genus. A few independent events of increases in karyotype asymmetry were inferred to have accompanied the karyotype evolution in Crepis. The genome sizes of 33 Crepis species differed seven-fold and the ancestral genome size was reconstructed to be 1C = 3.44 pg. Both decreases and increases in the genome size were inferred to have occurred within and between the lineages. The data suggest that, in addition to dysploidy, the amplification/elimination of various repetitive DNAs was likely involved in the genome and taxa differentiation in the genus.
| S-EPMC8472258 | biostudies-literature
Project description:Background and aimsChanges in the amount of repetitive DNA (dispersed and tandem repeats) are considered the main contributors to genome size variation across plant species in the absence of polyploidy. However, the study of repeatome dynamism in groups showing contrasting genomic features and complex evolutionary histories is needed to determine whether other processes underlying genome size variation may have been overlooked. The main aim here was to elucidate which mechanism best explains genome size evolution in Anacyclus (Asteraceae).MethodsUsing data from Illumina sequencing, we analysed the repetitive DNA in all species of Anacyclus, a genus with a reticulate evolutionary history, which displays significant genome size and karyotype diversity albeit presenting a stable chromosome number.Key resultsBy reconstructing ancestral genome size values, we inferred independent episodes of genome size expansions and contractions during the evolution of the genus. However, analysis of the repeatome revealed a similar DNA repeat composition across species, both qualitative and quantitative. Using comparative methods to study repeatome dynamics in the genus, we found no evidence for repeat activity causing genome size variation among species.ConclusionsOur results, combined with previous cytogenetic data, suggest that genome size differences in Anacyclus are probably related to chromosome rearrangements involving losses or gains of chromosome fragments, possibly associated with homoploid hybridization. These could represent balanced rearrangements that do not disrupt gene dosage in merged genomes, for example via chromosome segment exchanges.
| S-EPMC7103019 | biostudies-literature
Project description:Repetitive sequences in parasitic plants
| PRJEB34450 | ENA