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

Kim, Kang-Rae; Yu, Jeong-Nam; Hong, Jeong Min; Kim, Sun-Yu; Park, So Young

doi:10.3390/genes14112063

Cited by 4 publications

(2 citation statements)

References 49 publications

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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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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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Section: Introductionmentioning

confidence: 99%

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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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Novel Efficient Genome-Wide STR Panels for the Conservation of the Endemic Catfishes of Western Ghats: Critically Endangered Hemibagrus punctatus Jerdon (1849) and Vulnerable Horabagrus brachysoma (Günther, 1864)

Divya,

Jose,

Christo

et al. 2024

Biochem Genet

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NmTHC: a hybrid error correction method based on a generative neural machine translation model with transfer learning

Wang,

Chen

2024

BMC Genomics

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Backgrounds The single-pass long reads generated by third-generation sequencing technology exhibit a higher error rate. However, the circular consensus sequencing (CCS) produces shorter reads. Thus, it is effective to manage the error rate of long reads algorithmically with the help of the homologous high-precision and low-cost short reads from the Next Generation Sequencing (NGS) technology. Methods In this work, a hybrid error correction method (NmTHC) based on a generative neural machine translation model is proposed to automatically capture discrepancies within the aligned regions of long reads and short reads, as well as the contextual relationships within the long reads themselves for error correction. Akin to natural language sequences, the long read can be regarded as a special “genetic language” and be processed with the idea of generative neural networks. The algorithm builds a sequence-to-sequence(seq2seq) framework with Recurrent Neural Network (RNN) as the core layer. The before and post-corrected long reads are regarded as the sentences in the source and target language of translation, and the alignment information of long reads with short reads is used to create the special corpus for training. The well-trained model can be used to predict the corrected long read. Results NmTHC outperforms the latest mainstream hybrid error correction methods on real-world datasets from two mainstream platforms, including PacBio and Nanopore. Our experimental evaluation results demonstrate that NmTHC can align more bases with the reference genome without any segmenting in the six benchmark datasets, proving that it enhances alignment identity without sacrificing any length advantages of long reads. Conclusion Consequently, NmTHC reasonably adopts the generative Neural Machine Translation (NMT) model to transform hybrid error correction tasks into machine translation problems and provides a novel perspective for solving long-read error correction problems with the ideas of Natural Language Processing (NLP). More remarkably, the proposed methodology is sequencing-technology-independent and can produce more precise reads.

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

Cited by 4 publications

References 49 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

Novel Efficient Genome-Wide STR Panels for the Conservation of the Endemic Catfishes of Western Ghats: Critically Endangered Hemibagrus punctatus Jerdon (1849) and Vulnerable Horabagrus brachysoma (Günther, 1864)

NmTHC: a hybrid error correction method based on a generative neural machine translation model with transfer learning

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