Background
The analysis of genetic diversity of protected plant species can greatly support conservation efforts.
Plantago maxima
Juss. ex Jacq. is a perennial species distributed along the Eurasian ...steppe. The westernmost range edge of the species’ distribution is located in the Pannonian basin, in Hungary where it is represented by a few, fragmented and highly endangered populations. We studied population diversity of all Hungarian range edge, natural populations, and one established ex situ population. One population from the centre of distribution (Kazakhstan) was implemented in the cpDNA haplotype study to compare the peripheral vs. central populations. We performed morphometric trait-based analysis, chromosome studies (morphometric analyses and FISH) and genetic diversity evaluations using inter simple sequence repeats (ISSR) and cpDNA trnL-trnF to evaluate differences between the in situ and ex situ populations as well as central vs. peripheral populations.
Results
Our results showed no obvious morphological differences among the in situ and ex situ populations in the period between 2018 and 2020. One ex situ subpopulation develops flowers three years in a row from 2019, which is a favourable indicator of the introduction success. Hungarian populations are exclusively diploids (2
n
= 2x = 12). The karyogram consists of 5 metacentric and 1 acrocentric chromosome pair.
Plantago maxima
has one 35S and two 5S rDNA loci, located on the acrocentric chromosome pair. Eight variable ISSR primers yielded 100 fragments, of which 74.6% were polymorphic (mean H
e
= 0.220). A high level of genetic variation within population was observed (92%) while the genetic differentiation among the populations was only 8%. STRUCTURE analysis revealed that the largest Kunpeszér population separated from the rest of the Hungarian populations, indicating a high rate of admixture among the other ones. Based on the trnL-trnF sequence analysis the Hungarian populations represent a single haplotype, which can indicate a reduced diversity due to isolation and recent population decline. By contrast, Kazakh population represents a distinct haplotype compared to the Hungarian samples.
Conclusions
The present study draws the attention to the high conservation value of the
Plantago maxima
populations from the westernmost range edge of the species’ distribution.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Given the 2,400-fold range of genome sizes (0.06-148.9 Gbp (gigabase pair)) of seed plants (angiosperms and gymnosperms) with a broadly similar gene content (amounting to approximately 0.03 Gbp), the ...repeat-sequence content of the genome might be expected to increase with genome size, resulting in the largest genomes consisting almost entirely of repetitive sequences. Here we test this prediction, using the same bioinformatic approach for 101 species to ensure consistency in what constitutes a repeat. We reveal a fundamental change in repeat turnover in genomes above around 10 Gbp, such that species with the largest genomes are only about 55% repetitive. Given that genome size influences many plant traits, habits and life strategies, this fundamental shift in repeat dynamics is likely to affect the evolutionary trajectory of species lineages.
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FZAB, GEOZS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Understanding virus evolution is a fundamental goal of virology, evolutionary biology, and disease epidemiology. We provide a detailed analysis of evolution and origin of Cryphonectria hypovirus 1 ...(CHV1) populations in Europe, based on the complete genome sequence of all European subtypes. Phylogenetic analyses divided European strains into two closely related clades. Strains of the subtype I belong to the first, while strains of the subtypes F1, D and E belong to the second clade suggesting that the subtypes F1, D and E are more closely related than previously thought. Strains of the subtype F2 appeared to be recombinant; subtypes F1/D/E contributed a larger fraction of sequence while subtype I contributed a smaller fraction. The p29 was the most variable domain, while the replication-associated large ORF B protein was the most conserved domain within the CHV1. Low sequence similarity, predominant negative selection and frequent recombination characterise the evolution of CHV1.
•Subtypes F1, D and E are more closely related than previously thought.•Strains of the subtype F2 are recombinant originating from subtypes F1/D/E and I.•CHV1 protein domains vary considerably in genetic diversity and selection pressure.•Negative selection and frequent recombination characterise CHV1 evolution.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Transcriptional silencing of 35S rDNA loci inherited from one parental species is occurring relatively frequently in allopolyploids. However, molecular mechanisms by which it is selected for ...transcriptional silencing remain unclear. We applied NGS, silver staining and bisulfite sequencing to study the structure, expression and methylation landscape of 35S rDNA in two allopolyploids of common origin, allotetraploid
Anemone multifida
(2
n
= 4
x
= 32, genome composition BBDD) and allohexaploid
A. baldensis
(2
n
= 6
x
= 48, AABBDD), and their genome donors,
A. sylvestris
(2
n
= 16, AA),
A. cylindrica
(2
n
= 16, BB) and
A. parviflora
(2
n
= 16, DD). The size of the recovered 35S rDNA units varied from 10,489 bp in
A. cylindrica
to 12,084 bp in
A. sylvestris
.
Anemone
showed an organization typical of most ribosomal 35S rDNA composed of NTS, ETS, rRNA genes, TTS and TIS with structural features of plant IGS sequences and all functional elements needed for rRNA gene activity. The NTS was more variable than the ETS and consisted of SRs which are highly variable among
Anemone
. Five to six CpG-rich islands were found within the ETS. CpG island located adjacent to the transcription initiation site (TIS) was highly variable regarding the sequence size and methylation level and exhibited in most of the species lower levels of methylation than CpG islands located adjacent to the 18S rRNA gene. Our results uncover hypomethylation of
A. sylvestris
- and
A. parviflora
-derived 35S rDNA units in allopolyploids
A. multifida
and
A. baldensis
. Hypomethylation of
A. parviflora
-derived 35S rDNA was more prominent in
A. baldensis
than in
A. multifida
. We showed that
A. baldensis
underwent coupled
A. sylvestris
-derived 35S rDNA array expansion and
A. parviflora
-derived 35S rDNA copy number decrease that was accompanied by lower methylation level of
A. sylvestris
-derived 35S rDNA units in comparison to
A. parviflora
-derived 35S rDNA units. These observations suggest that in
A. baldensis
nucleolar dominance is directed toward
A. sylvestris
-derived chromosomes. This work broadens our current knowledge of the 35S rDNA organization in
Anemone
and provides evidence of the progenitor-specific 35S rDNA methylation in nucleolar dominance.
Dalmatian pyrethrum (
(Trevir.) Sch. Bip.), a plant species endemic to the east Adriatic coast, is used worldwide for production of the organic insecticide, pyrethrin. Most studies concerning ...Dalmatian pyrethrum have focused on its morphological and biochemical traits relevant for breeding. However, little is known about the chromosomal evolution and genome organization of this species. Our study aims are to identify, classify, and characterize repetitive DNA in the
genome using clustering analysis of a low coverage genomic dataset. Repetitive DNA represents about 71.63% of the genome.
exhibits linked 5S and 35S rDNA configuration (L-type). FISH reveals amplification of interstitial telomeric repeats (ITRs) in
. Of the three newly identified satellite DNA families, TcSAT1 and TcSAT2 are located subterminally on most of
chromosomes, while TcSAT3 family is located intercalary within the longer arm of two chromosome pairs. FISH reveals high levels of polymorphism of the TcSAT1 and TcSAT2 sites by comparative screening of 28 individuals. TcSAT2 is more variable than TcSAT1 regarding the number and position of FISH signals. Altogether, our data highlights the dynamic nature of DNA sequences associated with subtelomeres in
and suggests that subtelomeres represent one of the most dynamic and rapidly evolving regions in eukaryotic genomes.
is a native European crayfish species found in both freshwater and brackish environments. It has commercial importance for fisheries and aquaculture industries. Up till now, most studies concerning
...have focused onto gaining knowledge about its phylogeny and population genetics. However, little is known about the chromosomal evolution and genome organization of this species. Therefore, we performed clustering analysis of a low coverage genomic dataset to identify and characterize repetitive DNA in the
genome. In addition, the karyogram of
(2
= 180) is presented here for the first time consisting of 75 metacentric, 14 submetacentric, and a submetacentric/metacentric heteromorphic chromosome pair. We determined the genome size to be at ~18.7 gigabase pairs. Repetitive DNA represents about 54.85% of the genome. Satellite DNA repeats are the most abundant type of repetitive DNA, making up to ~28% of the total amount of repetitive elements, followed by the Ty3/
retroelements (~15%). Our study established a surprisingly high diversity of satellite repeats in
. The genome of
is by far the most satellite-rich genome discovered to date with 258 satellite families described. Of the five mapped satellite DNA families on chromosomes, PlSAT3-411 co-localizes with the AT-rich DAPI positive probable (peri)centromeric heterochromatin on all chromosomes, while PlSAT14-79 co-localizes with the AT-rich DAPI positive (peri)centromeric heterochromatin on one chromosome and is also located subterminally and intercalary on some chromosomes. PlSAT1-21 is located intercalary in the vicinity of the (peri)centromeric heterochromatin on some chromosomes, while PlSAT6-70 and PlSAT7-134 are located intercalary on some
chromosomes. The FISH results reveal amplification of interstitial telomeric repeats (ITRs) in
. The prevalence of repetitive elements, especially the satellite DNA repeats, may have provided a driving force for the evolution of the
genome.
Phylogenetic relationships within tribe Phyllantheae, the largest tribe of the family Phyllanthaceae, were examined with special emphasis on the large genus PHYLLANTHUS: Nuclear ribosomal ITS and ...plastid matK DNA sequence data for 95 species of tribe Phyllantheae, including representatives of all subgenera of Phyllanthus (except Cyclanthera) and several hitherto unplaced infrageneric groups, were analyzed. Results for ITS and matK are generally concordant, although some species are placed differently in the plastid and ITS trees, indicating that hybridization/paralogy is involved. Results confirm paraphyly of Phyllanthus in its traditional circumscription with embedded Breynia, Glochidion, Reverchonia, and SAUROPUS: We favor the inclusion of the embedded taxa in Phyllanthus over further generic segregation. Monophyletic Phyllanthus comprises an estimated 1269 species, making it one of the "giant" genera. Phyllanthus maderaspatensis is sister to all other species of Phyllanthus, and the genus appears to be of paleotropical origin. Subgenera Isocladus, Kirganelia, and Phyllanthus are polyphyletic, whereas other subgenera appear to be monophyletic. Monotypic Reverchonia is sister to P. abnormis, arborescent section Emblica to herbaceous Urinaria, free-floating aquatic P. fluitans to the weed P. caroliniensis, and the phyllocladous section Choretropsis to the delicate leafy P. claussenii. The unique branching architecture known as "phyllanthoid branching" found in most Phyllanthus taxa has been lost (and/or has been derived) repeatedly. Taxonomic divisions within Phyllantheae based on similar pollen morphology are confirmed, and related taxa share similar distributions. We recommend recognition of six clades at generic level: Flueggea s.l. (including Richeriella), Lingelsheimia, Margaritaria, Phyllanthus s.l. (including Breynia, Glochidion, Reverchonia, and Sauropus), P. diandrus, and Savia section HETEROSAVIA:
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
In this article, the authors have constructed a plasmid to compare intraplasmid recombination efficiency in Agrobacterium tumefaciens and Escherichia coli. The plasmid contains two directly repeated ...copies of spectinomycin resistance gene, one lacking 5' and the other lacking 3' end. These two copies share a 570-bp region of homology and are separated by the ampicillin resistance gene. Homologous recombination between repeated copies of incomplete spectinomycin resistance genes results in the restoration of spectinomycin resistance. During this process, ampicillin resistance gene is either deleted or incomplete spectinomycin genes are amplified along with the ampicillin resistance gene. This experimental system enabled researchers to follow for the first time the generation of deletions and amplifications during intraplasmid recombination in A. tumefaciens. They show here that predominantly RecA-independent mechanism contributes to the formation of deletion and amplification products in both, A. tumefaciens and E. coli. Additionally, deletion and amplification products were detected at similar frequencies, suggesting that amplifications and deletions probably occur by a similar mechanism.
Phylogenetic relationships within the genus Pulsatilla as reconstructed by StarBEAST2 based on DNA-sequences of two nuclear and three plastid DNA regions. The main lineages including the outgroups ...are highlighted by different colours. Photographs by Volker Debus (4), Andriy Korolyuk (13, 18), Olga Mochalova (5), Susann Nilsson (7,8,19,21), Zsolt Raksányi (9), Gábor Sramkó (1,2,3,6,10,11,12,14,15,16,22), Polina A. Volkova (20), Valentin Yakubov (17).
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•The evolutionary history of Pulsatilla has been reconstructed.•Explosive diversification of Pulsatilla s.s. started at ca 3 Ma.•Ancestral area of Pulsatilla was in central Asian mountains.•A revised classification of the genus is provided.
Pulsatilla (Anemoneae, Ranunculaceae) is sister to Anemone s.s. and contains ca 40 perennial species of considerable horticultural and medical importance. We sequenced 31 of those species, plus nine subspecies, two cultivars and six outgroups, for two nuclear regions (high-copy nrITS and low-copy MLH1) and three plastid regions (rbcL, accD–psaI, trnL intron) in order to generate the first comprehensive species-level phylogeny of the genus. Phylogenetic trees were constructed using both concatenation-based (maximum likelihood and Bayesian inference) and coalescence methods. The better supported among the internal nodes were subjected to molecular clock dating and ancestral area reconstruction, and karyotypic characters identified by us using Fluorescence In Situ Hybridization were mapped across the tree. The preferred species tree from the coalescence analysis formed the basis of a new infrageneric classification based on monophyly plus degree of divergence. The earliest divergent of the three subgenera, Kostyczewianae, is represented by only a single species that is morphologically intermediate between Anemone s.s. and ‘core’ Pulsatilla. Subgenus Pulsatilla is considerably richer in species than its sister subgenus Preonanthus and contains three monophyletic sections. Species possessing nodding flowers and pectinately dissected leaves are phylogenetically derived compared with groups possessing erect flowers and palmately lobed leaves. Pulsatilla separated from Anemone s.s. at ca 25 Ma. Our results indicate a central Asian mountain origin of the genus and an initial diversification correlated with late Tertiary global cooling plus regional mountain uplift, aridification and consequent expansion of grasslands. The more rapid and extensive diversification within subgenus Pulsatilla began at ca 3 Ma and continued throughout the Quaternary, driven not only by major perturbations in global climate but also by well-documented polyploidy.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The structure and organization of the 5S ribosomal DNA units of the silver fir, Abies alba Mill., as well as their position in the chromosome complement were investigated. PCR amplification of the ...gene and nontranscribed spacer region, sequence analysis and Southern hybridization, using a homologous probe, detected DNA sequences of approximately 550 bp and 700 bp. Sequence analysis of the spacers revealed that the difference in length between the sequences occurred in the middle spacer region as a result of the amplification of a 75-bp sequence of the short unit class, which is organized in four 54- to 68-bp tandem repeats in the long spacer unit. The 5S rDNA transcribed region is 120 bp long and shows high sequence similarity with other gymnosperm species. The comparative analysis of 5' and 3' flanking sequences of 5S rRNA genes of silver fir and other gymnosperms indicates that A. alba spacer units have the same rate of evolution and are more closely related to Larix and Pseudotsuga than to Pinus and Picea. Southern hybridization and fluorescence in situ hybridization of metaphase chromosomes of A. alba suggest that the short and long spacer units are organized as separate tandem arrays at two chromosomal loci on chromosomes V and XI.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
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