ArticleBMC evolutionary biology2017
The complete chloroplast genome of Primulina and two novel strategies for development of high polymorphic loci for population genetic and phylogenetic studies.
Article in BMC evolutionary biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
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- Characterization and Analysis of the Complete Mitochondrial Genome ofCurrent issues in molecular biology · 2025Article
- Comparative chloroplast genomes analysis of nine Primulina (Gesneriaceae) rare species, from karst region of southwest China.Scientific reports · 2024Article
- From light into shadow: comparative plastomes in Petrocosmea and implications for low light adaptation.BMC plant biology · 2024Article
- Genome-wide analysis of the cellulose toolbox of Primulina eburnea, a calcium-rich vegetable.BMC plant biology · 2023Article
- Recombination Variation Shapes Phylogeny and Introgression in Wild Diploid Strawberries.Molecular biology and evolution · 2023Article
- Plastomes of limestone karst gesneriad genera Petrocodon and Primulina, and the comparative plastid phylogenomics of Gesneriaceae.Scientific reports · 2022Article
- Phylogenomic and Macroevolutionary Evidence for an Explosive Radiation of a Plant Genus in the Miocene.Systematic biology · 2022Article
- Comparative chloroplast genome analyses ofFrontiers in plant science · 2022Article
- Jackfruit genome and population genomics provide insights into fruit evolution and domestication history in China.Horticulture research · 2022Article
- Phylogeographic structure ofFrontiers in plant science · 2022Article
- Towards the Well-Tempered Chloroplast DNA Sequences.Plants (Basel, Switzerland) · 2021Article
- Genome-Wide Evidence for Complex Hybridization and Demographic History in a Group ofFrontiers in genetics · 2021Article
- The First Glimpse ofPlants (Basel, Switzerland) · 2020Article
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- Development of 10 single-copy nuclear DNA markers forApplications in plant sciences · 2018Article
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5 authors.
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Abstract
backgroundPrimulina Hance is an emerging model for studying evolutionary divergence, adaptation and speciation of the karst flora. However, phylogenetic relationships within the genus have not been resolved due to low variation detected in the cpDNA regions. Chloroplast genomes can provide important information for phylogenetic and population genetic studies. Recent advances in next-generation sequencing (NGS) techniques greatly facilitate sequencing whole chloroplast genomes for multiple individuals. Consequently, novel strategies for development of highly polymorphic loci for population genetic and phylogenetic studies based on NGS data are needed.
methodsFor development of high polymorphic loci for population genetic and phylogenetic studies, two novel strategies are proposed here. The first protocol develops lineage-specific highly variable markers from the true high variation regions (Con_Seas) across whole cp genomes, instead of traditional noncoding regions. The pipeline has been integrated into a single perl script, and named "Con_Sea_Identification_and_PIC_Calculation". The second method assembles chloroplast fragments (poTs) and sub-super-marker (CpContigs) through our "SACRing" pipeline. This approach can fundamentally alter the strategies used in phylogenetic and population genetic studies based on cp markers, facilitating a transition from traditional Sanger sequencing to RAD-Seq. Both of these scripts are available at https://github.com/scbgfengchao/ .
resultsThree complete Primulina chloroplast genomes were assembled from genome survey data, and then two novel strategies were developed to yield highly polymorphic markers. For experimental evaluation of the first protocol, a set of Primulina species were used for PCR amplification. The results showed that these newly developed markers are more variable than traditional ones, and seem to be a better choice for phylogenetic and population studies in Primulin a. The second method was also successfully applied in population genetic studies of 21 individuals from three natural populations of Primulina.
conclusionsThese two novel strategies may provide a pathway for similar research in other non-model species. The newly developed high polymorphic loci in this study will promote further the phylogenetic and population genetic studies in Primulina and other genera of the family Gesneriaceae.
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