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De Novo Transcriptome Assembly and EST-SSR Marker Development and Application in Chrysosplenium macrophyllum.

Niyan Xiang^1,2, 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.

|February 25, 2023

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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.

Keywords:

Chrysosplenium macrophyllum EST-SSR genetic diversity population structure transcriptome transferability

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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.