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De Novo Transcriptome Assembly and EST-SSR Marker Development and Application in Chrysosplenium macrophyllum.
Niyan Xiang1,2, Bojie Lu2, Tao Yuan1
1Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China.
Genes
|February 25, 2023
Summary
New expressed sequence tag simple sequence repeat (EST-SSR) markers were developed for Chrysosplenium macrophyllum, aiding population genetics and evolutionary studies. These markers reveal high genetic diversity and distinct population structures based on geography.
Area of Science:
- Molecular Biology
- Population Genetics
- Bioinformatics
Background:
- Chrysosplenium macrophyllum, a Chinese herbal medicine, lacks sufficient molecular markers for population genetics and evolutionary research.
- Transcriptome sequencing offers a potential avenue for developing novel molecular markers.
Purpose of the Study:
- To develop and validate expressed sequence tag simple sequence repeat (EST-SSR) markers for Chrysosplenium macrophyllum using transcriptome sequencing.
- To analyze the genetic diversity and population structure of C. macrophyllum using the newly developed EST-SSR markers.
Main Methods:
- Transcriptome sequencing of C. macrophyllum using the DNBSEQ-T7 Sequencer.
- Identification and development of EST-SSR markers from transcriptomic sequences.
- Validation of EST-SSR markers on C. macrophyllum and related Chrysosplenium species.
- Analysis of genetic diversity and population structure in 12 populations of C. macrophyllum using polymorphic EST-SSR markers.
Main Results:
- A total of 3127 non-redundant EST-SSR markers were identified for C. macrophyllum.
- The developed EST-SSR markers demonstrated high amplification rates and cross-species transferability within the Chrysosplenium genus.
- Natural populations of C. macrophyllum exhibited high levels of genetic diversity.
- Population structure analysis revealed two distinct genetic clusters correlating with geographical origins.
Conclusions:
- Transcriptome sequencing is effective for developing polymorphic EST-SSR markers in C. macrophyllum.
- The newly developed EST-SSR markers are valuable tools for studying genetic diversity and evolutionary history in Chrysosplenium species.
- Geographical factors play a significant role in shaping the population structure of C. macrophyllum.
