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Identification and development of microsatellite (SSRs) makers of Exbucklandia (HAMAMELIDACEAE) by high-throughput sequencing

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Abstract

Hamamelidaceae (Saxifragales, previously Rosales) comprises approximately six subfamily, 30 genera and 140 species, most of which are Tertiary relicts. Exbucklandia is the only genus of the subfamily Exbucklandioideae, Hamelidaceae, containing only 2–4 species. Of them, the species E. longipetala H. T. Chang is endemic to China and listed as endangered in The Biodiversity Red List of China: Higher Plant, yet some taxonomists put forward that E. longipetala should be merged into E. tonkinensis (Lecomte) H. T. Chang. Currently, there was nearly no phylogeographic studies on this genus possibly due to the deficiency of efficient molecular markers. In this study, we sequenced the genome of E. tonkinensis based on high throughput sequencing technology, and obtained approximately 6 G raw data, which was further de novo assembled into 303,481 contigs. Based on them, 15,326 SSRs were identified from 13,596 contigs, and primers were successfully designed for 10,660 SSRs. A total of 139 paired primers were synthesized, 106 of them were successfully amplified in six Exbucklandia individuals with expected PCR product size, and 24 demonstrated to be polymorphic among three Exbucklandia populations. Accordingly, the expected and observed heterozygosity were between 0.097–0.717 and 0.098–0.583. Based on these efforts, future researches on genetic diversity and population structure of Exbucklandia can be performed to understand its phylogenetic origins and phylogeographic pattern.

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Acknowledgements

We are grateful for collection’s help from Zhao Wanyi, Liu Zhongcheng, the Guangdong Heishiding Natural Reserv and the Limushan National Nature Reserve, Hainan. This work was supported by the National Natural Science Foundation of China (31800175, 31670189, 31570195), Natural Science Foundation of Guangdong Province (2018A0303130109), the Special Program for Science and Technology Basic Research of the Ministry of Science and Technology of China (2013FY111500), the Fourth National Survey on Chinese Material Medical Resources Program for State Administration of Traditional Chinese Medicine of China (2017-152-003) and the Chang Hungta Science Foundation of Sun Yat-sen University.

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Authors and Affiliations

  1. State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China

    Cuiying Huang, Qianyi Yin, Kaikai Meng, Qiang Fan, Sufang Chen & Wenbo Liao

  2. GoldenGate International College, Battisputali, Kathmandu, Nepal

    Dipak Khadka

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  1. Cuiying Huang
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  2. Qianyi Yin
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  3. Dipak Khadka
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  4. Kaikai Meng
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  6. Sufang Chen
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  7. Wenbo Liao
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Correspondence to Sufang Chen or Wenbo Liao.

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Huang, C., Yin, Q., Khadka, D. et al. Identification and development of microsatellite (SSRs) makers of Exbucklandia (HAMAMELIDACEAE) by high-throughput sequencing. Mol Biol Rep 46, 3381–3386 (2019). https://doi.org/10.1007/s11033-019-04800-z

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