ArticleBiological research2020
Development of nuclear SSR and chloroplast genome markers in diverse Liriodendron chinense germplasm based on low-coverage whole genome sequencing.
Article in Biological research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed.
- Comparative Analysis of Chloroplast Genomes Reveals Molecular Evolution and Phylogenetic Relationships inInternational journal of molecular sciences · 2026Article
- Mutation Pressure and Gene-Specific Selection Shape Codon Usage Bias in the Chloroplast Genomes ofEcology and evolution · 2026Article
- Complete Chloroplast Genome ofEcology and evolution · 2026Article
- Comparative genomic and phylogenetic analyses ofFrontiers in plant science · 2026Article
- Molecular identification and phylogenetic analysis of Polygonatum Kingianum with different floral colors on the basis of chloroplast genomes.BMC plant biology · 2025Article
- Comprehensive Evaluation and DNA Fingerprints ofPlants (Basel, Switzerland) · 2025Article
- Comparative Chloroplast Genomics ofInternational journal of molecular sciences · 2025Article
- Comprehensive analysis of complete chloroplast genome sequence of Morina L.Scientific reports · 2025Article
- Comprehensive Genetic and Morphological Analysis of Algerian Carob (Plants (Basel, Switzerland) · 2025Article
- Comparative analysis of complete chloroplast genomes ofFrontiers in plant science · 2025Article
- Chloroplast genomic diversity in eleven Pennisetum species.Frontiers in genetics · 2025Article
- Comprehensive SSR study of 14 Zingiberaceae species based on microsatellite capture sequencing (MiCAPs).Frontiers in plant science · 2025Article
- Comprehensive Analysis of the Fourteen Complete Genome Sequences ofJournal of microbiology and biotechnology · 2024Article
- Phylogenomics and plastome evolution of Lithospermeae (Boraginaceae).BMC plant biology · 2024Article
- Chloroplast Genome Variation and Phylogenetic Relationships of Autochthonous Varieties ofInternational journal of molecular sciences · 2024Article
- Comparative Analysis of Chloroplast Genome ofInternational journal of molecular sciences · 2024Article
- Low-coverage whole genome sequencing of diverseFrontiers in plant science · 2024Article
- Whole chloroplast genome-specific non-synonymous SNPs reveal the presence of substantial diversity in the pigeonpea mini-core collection.3 Biotech · 2023Article
- Article
- Complete chloroplast genome molecular structure, comparative and phylogenetic analyses of Sphaeropteris lepifera of Cyatheaceae family: a tree fern from China.Scientific reports · 2023Article
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Abstract
backgroundLiriodendron chinense ranges widely in subtropical China and northern Vietnam; however, it inhabits several small, isolated populations and is now an endangered species due to its limited seed production. The objective of this study was to develop a set of nuclear SSR (simple sequence repeats) and multiple chloroplast genome markers for genetic studies in L. chinense and their characterization in diverse germplasm.
resultsWe performed low-coverage whole genome sequencing of the L. chinense from four genotypes, assembled the chloroplast genome and identified nuclear SSR loci by searching in contigs for SSR motifs. Comparative analysis of the four chloroplast genomes of L. chinense revealed 45 SNPs, 17 indels, 49 polymorphic SSR loci, and five small inversions. Most chloroplast intraspecific polymorphisms were located in the interspaces of single-copy regions. In total, 6147 SSR markers were isolated from low-coverage whole genome sequences. The most common SSR motifs were dinucleotide (70.09%), followed by trinucleotide motifs (23.10%). The motif AG/TC (33.51%) was the most abundant, followed by TC/AG (25.53%). A set of 13 SSR primer combinations were tested for amplification and their ability to detect polymorphisms in a set of 109 L. chinense individuals, representing distinct varieties or germplasm. The number of alleles per locus ranged from 8 to 28 with an average of 21 alleles. The expected heterozygosity (H
conclusionsThe genetic resources characterized and tested in this study provide a valuable tool to detect polymorphisms in L. chinense for future genetic studies and breeding programs.
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