Genetic analysis of salt-marsh sedge Carex scabrifolia Steud. populations using newly developed microsatellite markers

Hodoki, Yoshikuni; Ohbayashi, Kako; Kunii, Hidenobu

doi:10.1007/s10592-008-9678-y

Cited by 7 publications

(3 citation statements)

References 10 publications

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“…The genetic diversity of C. pumila has been shown to be similar to or higher than that of the halophyte Spergularia media (H O : 0.546, H E : 0.698) [48] and other species such as Carex kobomugi (H O : 0.648, H E : 0.451) [23], Carex macrocephala (H O : 0.073, H E : 0.523) [24], and Carex scabrifolia (H O : 0.350, H E : 0.419) [49] of the genus Carex.…”

Section: Development Of Novel Microsatellite Markers For Population S...mentioning

confidence: 86%

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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Section: Development Of Novel Microsatellite Markers For Population S...mentioning

confidence: 86%

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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“…Despite its enormous species diversity, only a few microsatellite markers have been specifically developed in the Carex genus. Initially, microsatellite markers studies targeted only few species (e.g., Carex scabrifolia, C. moorcroftii, C. helodes, C. angustisquama, C. kobomugi, C. macrocephala, C. pumila [27][28][29][30][31][32][33][34]), but more recently, 42 and 17 markers, respectively, were tested for 106 Carex accessions [33,35]. Almost all taxa included in these studies belong to the Carex or Vignea subgenera.…”

Section: Introductionmentioning

confidence: 99%

“…The number of alleles displayed by both populations of C. myosuroides in the case of these 13 SSR markers was lower compared with several other studies reporting SSR markers in the Carex genus. For example, an analysis of 14 microsatellite loci in six populations of C. kobomugi revealed two to eight alleles per marker [27], and another analysis of nine microsatellite loci in four populations of Carex scabrifolia reported two to seven alleles [28], whereas an analysis of 30 SSR markers in three populations of C. pumila discovered four to twelve alleles [34]. The low number of alleles and the high level of monomorphism were also reported by [32], for three populations of C. angustisquama, analysed using 20 SSR markers, resulting an average of one to five alleles per marker.…”

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confidence: 99%

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

et al. 2023

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Genetic analysis of salt-marsh sedge Carex scabrifolia Steud. populations using newly developed microsatellite markers

Abstract: Nine microsatellite loci were isolated and characterized from the clonal salt-marsh sedge Carex scabrifolia, and genetic diversities within four populations were analyzed.

Cited by 7 publications

References 10 publications

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

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

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

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

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