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RNA sequencing and SSR marker development for genetic diversity research in Woonyoungia septentrionalis (Magnoliaceae)

Abstract

Transcriptome sequencing was performed using Illumina paired-end RNA sequencing technology, for facilitating gene discovery and SSR marker development in an endangered tree, Woonyoungia septentrionalis. A total of 41,578,222 high-quality reads were obtained, and 93,156 non-redundant unigenes were assembled and annotated by sequence similarity searching in diverse public databases. Analyses showed that 36,176 unigenes (38.83%) had at least blast hit against Nr, Nt, KO, SwissProt, PFAM, KO, or GO database; and 2945 unigenes (4.13%) were annotated in all seven databases. Totally, 17,719 genic-SSRs were identified in 14,629 (15.70%) out of 93,156 unigenes. Finally, 51 primers of the 64 designed SSR primers produced clear SSR bands, of which 20 SSR loci were polymorphic in 149 individuals representing four natural populations. Observed and expected heterozygosity varied from 0 to 0.846 and from 0 to 0.792, respectively. At the species level, the Ho and He of the four W. septentrionalis populations were 0.3325 and 0.3559, respectively. The average genetic diversity within populations, H and I were 0.3500 and 0.5937, respectively. Cross-species amplification of the 20 markers was tested in other related species. The transcriptomic resources and genic SSR markers are valuable tools not only for ecological conservation of this species, but also for phylogenetic studies.

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Acknowledgements

This study was supported by the National Key Research and Development Program of China (2016YFC0502605), the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), and the Collaborative Innovation Plan of Jiangsu Higher Education (CIP).

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Correspondence to Meng Xu.

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Xu, M., Li, Z., Wang, J. et al. RNA sequencing and SSR marker development for genetic diversity research in Woonyoungia septentrionalis (Magnoliaceae). Conservation Genet Resour 10, 867–872 (2018). https://doi.org/10.1007/s12686-017-0884-0

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Keywords

  • Endangered tree
  • Genic SSR
  • Genetic diversity
  • Transcriptome sequencing
  • Woonyoungia septentrionalis