Development of SSR markers for Carex curvula (Cyperaceae) and their importance in investigating the species genetic structure

Şuteu, Dana; Pușcaș, Mihai; Băcilă, Ioan; Miclaus, Mihai; Balázs, Zoltan Robert; Choler, Philippe

doi:10.1007/s11033-023-08362-z

Cited by 3 publications

(6 citation statements)

References 11 publications

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“…The cross-amplification experiment was successful, and a total of 183 alleles were detected, with a range of 10 to 19, and an average of 14.07 alleles per locus. The total number of alleles and mean per locus, as revealed by these SSR markers, were higher than the values exhibited by C. curvula, 137 alleles and a mean of 10.53 alleles per locus respectively [36]. Furthermore, our values were relatively high, even compared with previous studies amplifying other SSR loci in different Carex species, such as the study by [35], which found a total of 173 alleles produced by 17 pairs of primers and an average of 10.18 for each locus.…”

contrasting

confidence: 61%

“…These values might be considered to be very low in comparison with the values noted for C. curvula (mean value = 87.97%). However, the present polymorphism results should be treated with caution, given that sample size in each population was lower than that of the C. curvula populations (five individuals) mentioned in [36]. This would suggest that, for an exhaustive assessment of genetic variation in natural populations, increasing the number of sampled individuals per locality would offer a better resolution of the genetic structure of these species.…”

mentioning

confidence: 76%

“…The amplification of the 13 SSR markers previously developed in C. curvula was tested on DNA extracted from 15 populations/14 species of Carex. According to [18] PCR protocol was followed in accordance with the one described by [36], as summarized below:…”

Section: • Biological Validationmentioning

confidence: 99%

“…More details about the primers (including their sequences), the purification of the PCR products, and the subsequent separation that occurred through capillary electrophoresis can be found in [36].…”

Section: • Biological Validationmentioning

confidence: 99%

“…curvula and C. c. subsp. rosae Gilomen), and we tested their applicability in species phylogeography and subspecies delimitation [36].…”

Section: Introductionmentioning

confidence: 99%

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Cross-Species Transferability of Specific SSR Markers from Carex curvula (Cyperaceae) to Other Carex Species

Șuteu,

Pușcaș,

Băcilă

et al. 2024

Diversity

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Microsatellites are codominant markers that, due to their high polymorphism, are a common choice for detecting genetic variability in various organisms, including fungi, plants, and animals. However, the process of developing these markers is both costly and time-consuming. As a result, the cross-species amplification has become a more rapid and more affordable alternative in biological studies. The objective of this study was to assess the applicability of 13 SSR markers, originally designed for Carex curvula, in other 14 species belonging to different sections of the genus. All the markers were successfully transferred with a mean of 90.76%, and 100% transferability was reached in two species (C. baldensis and C. rupestris). The lowest transferability was registered in the G165 marker, which did not produce amplification in six species. Together, the microsatellites amplified a total of 183 alleles, ranging from 10 to 19 alleles per locus, with an average of 14.07. The mean number of different alleles ranged from 0.846 to a maximum of 2.077 per locus. No significant departures from the Hardy–Weinberg equilibrium were detected in polymorphic loci. The transferability of the 13 SSR markers proved highly successful in various Carex species, across different clades and sections of the genus.

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confidence: 61%

mentioning

confidence: 76%

Section: • Biological Validationmentioning

confidence: 99%

Section: • Biological Validationmentioning

confidence: 99%

“…curvula and C. c. subsp. rosae Gilomen), and we tested their applicability in species phylogeography and subspecies delimitation [36].…”

Section: Introductionmentioning

confidence: 99%

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Cross-Species Transferability of Specific SSR Markers from Carex curvula (Cyperaceae) to Other Carex Species

Șuteu,

Pușcaș,

Băcilă

et al. 2024

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Extent of intraspecific trait variability in ecologically central and marginal populations of a dominant alpine plant across European mountains

et al. 2023

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Background and Aims Studying trait variability and restricted gene flow between populations species can reveal species dynamics. Peripheral populations commonly exhibit lower genetic diversity and trait variability due to isolation and ecological marginality, unlike central populations experiencing gene flow and optimal conditions. This study focused on Carex curvula, the dominant species in alpine acidic meadows of European mountains. The species is sparser in dry areas like the Pyrenees and Balkans, compared to the Central-Eastern Alps and Carpathians. We hypothesized that distinct population groups could be identified based on their mean functional trait values and their correlation with the environment; we predict that ecologically marginal populations would have stronger trait correlations, lower within-population trait variability (ITV), and lower genetic diversity than populations of optimal habitats. Methods Sampling was conducted in 34 populations that spanned the entire distribution range of C. curvula. We used hierarchical clustering to identify emergent functional groups of populations, defined by combinations of multiple traits associated with nutrient economy and drought tolerance (e.g., specific leaf area, anatomy). We contrasted the geographic distribution of these groups in relation to environment and genetic structure. We compared pairwise trait relationships, within-population trait variation (ITV), and neutral genetic diversity between groups. Key Results Our study identified emergent functional groups of populations. Those in the southernmost ranges, specifically the Pyrenees and Balkan region, showed drought-tolerant trait syndromes and correlated with indicators of limited water availability. While we noted a decline in population genetic diversity, we did not observe any significant changes in ITV in ecologically marginal (peripheral) populations. Conclusions Our research exemplifies the relationship between ecological marginality and geographical peripherality, which in this case study is linked to genetic depauperation but not reduced ITV. Understanding these relationships is crucial for understanding the biogeographical factors shaping trait variation.

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Genome Assembly and Microsatellite Marker Development Using Illumina and PacBio Sequencing in the Carex pumila (Cyperaceae) from Korea

Kim,

Yu,

Hong

et al. 2023

Genes

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This study is the first to report the characterization of Carex pumila genomic information. Assembly of the genome generated a draft of C. pumila based on PacBio Sequel II and Illumina paired-end sequencing, which was assembled from 2941 contigs with an estimated genome size of 0.346 Gb. The estimate of repeats in the genome was 31.0%, and heterozygosity ranged from 0.426 to 0.441%. The integrity evaluation of the assembly revealed 1481 complete benchmarked universal single-copy orthologs (BUSCO) (91.76%), indicating the high quality of the draft assembly. A total of 23,402 protein-coding genes were successfully predicted and annotated in the protein database. UpsetR plots showed that 7481 orthogroups were shared by all species. The phylogenetic tree showed that C. pumila is a close but distant relative of Ananas comosus. C. pumila had greater contraction (3154) than expansion (392). Among the extended gene families, aquaporins have been found to be enriched. Primers for microsatellite markers determined 30 polymorphic markers out of 100. The average number of alleles amplified by these 30 polymorphic markers was 4 to 12, with an average polymorphism information content (PIC) value of 0.660. In conclusion, our study provides a useful resource for comparative genomics, phylogeny, and future population studies of C. pumila.

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Development of SSR markers for Carex curvula (Cyperaceae) and their importance in investigating the species genetic structure

Cited by 3 publications

References 11 publications

Cross-Species Transferability of Specific SSR Markers from Carex curvula (Cyperaceae) to Other Carex Species

Cross-Species Transferability of Specific SSR Markers from Carex curvula (Cyperaceae) to Other Carex Species

Extent of intraspecific trait variability in ecologically central and marginal populations of a dominant alpine plant across European mountains

Genome Assembly and Microsatellite Marker Development Using Illumina and PacBio Sequencing in the Carex pumila (Cyperaceae) from Korea

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