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EST-SSR marker development based on transcriptome sequencing and genetic analyses of Phoebe bournei (Lauraceae)

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Abstract

High-throughput sequencing of the Phoebe bournei transcriptome was performed, and novel SSR markers were identified. A total of 73,518 nonredundant unigenes were assembled and annotated by sequence similarity searching in diverse public databases. A total of 40,853 SSRs were identified from 73,518 unigenes. Twenty-three pairs of polymorphic EST-SSR markers were selected from 98 markers and used for genetic analyses in 75 individuals from three P. bournei populations. The 23 pairs of markers could detect abundant genetic information from the samples (PIC = 0.769), and cross-species amplification was successfully performed in other related species. Three populations had high level of genetic diversity (He = 0.658 in average), of which the population YS from Jiangxi province had the most abundant genetic diversity (He = 0.722). The results of genetic structure analyses showed that the population YS from Jiangxi province had obvious genetic differences from the other two populations, and the genetic information of the population SX from Fujian province was related to that of the population LC from Guangdong province and the population YS. The transcriptomic resources and EST-SSR markers are valuable tools not only for the ecological conservation of P. bournei but also for phylogenetic studies.

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References

  1. Chen Z (2012) Development and application of microsatellite markers in Betula luminifera. Dissertation, Zhejiang Agriculture and Forestry University

  2. Chen SP, Sun WH, Xiong YF, Jiang YT, Liu XD, Liao XY, Zhang DY, Jiang SZ, Li Y, Liu B, Ma L, Yu X, He L, Liu B, Feng JL, Feng LZ, Wang ZW, Zou SQ, Lan SR, Liu ZJ (2020) The Phoebe genome sheds light on the evolution of magnoliids. Hortic Res 7:146

    Article  CAS  Google Scholar 

  3. Cheng XM, Huang XX (2011) Development and application of SSR markers in plants. Chin Agr Sci Bull 27(5):304–307

    Google Scholar 

  4. Ding YJ, Zhang JH, Lu YF, Lin EP, Lou LH, Tong ZK (2015) Development of EST-SSR markers and analysis of genetic diversity in natural populations of endemic and endangered plant Phoebe chekiangensis. Biochem Syst Ecol 63(63):183–189

    Article  CAS  Google Scholar 

  5. Earl DA, VonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4(2):359–361

    Article  Google Scholar 

  6. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14(8):2611–2620

    Article  CAS  Google Scholar 

  7. Ge YJ, Liu YJ, Shen AH, Lin XC (2015) Fengshui forests conserve genetic diversity: a case study of Phoebe bournei (Hemsl.) Yang in southern China. Genet Mol Res 14(1):1986

    Article  CAS  Google Scholar 

  8. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644–652

    Article  CAS  Google Scholar 

  9. He YH, Liang RL, Jiang Y, Sun B (2013) Research progress and development countermeasures of rare tree species Phoebe bournei. Guangxi For Sci 42(04):365–370

    Google Scholar 

  10. Huang YQ, Yin GT, Yang JC, Yu N, Zou WT, Li RS (2020) Construction of core collection of Phoebe bournei based on SSR molecular markers. Mol Plant Breed 18(08):2641–2648

    Google Scholar 

  11. Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23(14):1801–1806

    Article  CAS  Google Scholar 

  12. Jiang XM, Wen Q, Ye JS, Xiao FM, Jiang M (2009) RAPD analysis of genetic diversity of Phoebe bournei natural population. Acta Ecol Sin 29(1):438–444

    CAS  Google Scholar 

  13. Jin JQ, Cui HR, Chen WY, Lu MZ, Yao YL, Xin Y, Gong XC (2006) Data mining for SSRs in ESTs and development of EST-SSR marker in tea plant (Camellia sinensis). J Tea Sci 46(1):35–54

    Google Scholar 

  14. Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, Van de Wiel C, Bredemeijer G, Vosman B, Matthes M, Daly A, Brettschneider R, Bettini P, Buiatti M, Maestri E, Malcevschi A, Marmiroli N, Aert R, Volckaert G, Rueda J, Linacero R, Vazquez A, Karp A (1997) Reproducibility of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Mol Breed 3(5):381–390

    Article  CAS  Google Scholar 

  15. Li ZH, Li BH, Qi CJ, Yu XL, Wu Y (2012) Studies on importance of valuable wood species resources and its development strategy. J Cent S Univ For Technol 32(11):1–8

    Google Scholar 

  16. Li YG, Xu WQ, Zou WT, Jiang DY, Liu XH (2017) Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species. Bot Stud 58:37

    Article  Google Scholar 

  17. Li J, Dong LJ, Lin JY, Liu XS, Liang RL (2019) ISSR analysis of genetic diversity of Phoebe bournei from different geographical populations. Mol Plant Breed 17(23):7822–7828

    Google Scholar 

  18. Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21(9):2128–2129

    Article  CAS  Google Scholar 

  19. Liu YX, Song XC, Jiang XM (2013) Chromosome karyotype analysis of Phoebe neurantha and Phoebe bournei. J Nanjing For Univ 37(05):157–160

    Google Scholar 

  20. Liu CC, Dou Y, Guan XL, Fu Q, Zhang Z, Hu ZH, Zheng J, Lu YZ, Li W (2017) De novo transcriptomic analysis and development of EST-SSRs for Sorbus pohuashanensis (Hance) Hedl. PLoS ONE 12(6):e0179219

    Article  Google Scholar 

  21. Liu D, Liu B, Zeng QM, Chen SP, Liu B, Li Y (2019) SSR analysis of the genetic difference of Phoebe Phoebe superior genotypes. J For Environ 39(05):449–453

    Google Scholar 

  22. Lu YF, Yang AN, Zhang JH, Lou LH, Huang HH, Tong ZK (2018) Development and transferability evaluation of EST-SSR markers based on transcriptome data of Phoebe sheareri. J Agric Biotechnol 26(6):1014–1024

    Google Scholar 

  23. Rosenberg NA (2004) Distruct: a program for the graphical display of population structure. Mol Ecol 4(1):137–138

    Article  Google Scholar 

  24. Shi XD, Zhu XH, Sheng YZ, Zhuang GQ, Chen F (2016) Development of SSR markers based on transcriptome sequence of Phoebe zhennan. Sci Silvae Sin 52(11):71–78

    Google Scholar 

  25. Wang D, Cao LY, Gao JP (2014) Data mining of simple sequence repeats in Codonopsis pilosula transcriptome. Chin Tradit Herb Drugs 45(16):2390–2394

    CAS  Google Scholar 

  26. Wu SH, Jin H, Lai JX (2016) Genetic diversity of Fraxinus chinensisusing SSR makers. Inner Mongolia For Sci Technol 42(2):26–29

    Google Scholar 

  27. Xu M, Li HG (2008) Development and characterization of microsatellite markers from expressed sequence tags for Liriodendron. Mol Plant Breed 6(3):615–618

    CAS  Google Scholar 

  28. Xu XL, Xu LA, Huang MR, Wang ZR (2004) Genetic diversity of microsatellites (SSRs) of natural populations of Quercus variabilis. Hereditas 26(5):683–688

    CAS  PubMed  Google Scholar 

  29. Yi M, Zhang L, Lei L, Cheng ZS, Sun SW, Lai M (2020) SSR analysis of Pinus elliottii transcriptome and development of EST-SSR marker. J Nanjing For Univ 44(2):75–83

    Google Scholar 

  30. Zerbo G, Cleophas Konrad H, Ouedraogo M, Geburek T (2017) Fourteen simple-sequence repeats newly developed for population genetic studies in Prosopis africana (Fabaceae Mimosoideae). BMC Res notes 10(1):1–5

    Article  Google Scholar 

  31. Zhang R, Zhou ZC, Jin GQ, Wang SH, Wang XH (2012) Genetic diversity and differentiation within three species of the family Lauraceae in southeast China. Biochem Syst Ecol 44:317

    Article  CAS  Google Scholar 

  32. Zhou Q, Mu KM, Ni ZX, Liu XH, Li YG, Xu LA (2020) Analysis of genetic diversity of ancient Ginkgo populations using SSR markers. Ind Crop Prod 145:111942

    Article  CAS  Google Scholar 

  33. Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR) anchored polymerase chain reaction amplification. Genomics 20(2):176–183

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This study was supported by the National Key Research & Development Program (No. 2016YFD0600603) of China.

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Authors and Affiliations

  1. Zhejiang Academy of Forestry, Hangzhou, 310023, China

    Qi Zhou & Yin-Gang Li

  2. Nanjing Forestry University, Nanjing, 210037, China

    Peng-Yan Zhou

  3. Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China

    Wen-Tao Zou

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  1. Qi Zhou
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  2. Peng-Yan Zhou
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  3. Wen-Tao Zou
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  4. Yin-Gang Li
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Correspondence to Yin-Gang Li.

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Zhou, Q., Zhou, PY., Zou, WT. et al. EST-SSR marker development based on transcriptome sequencing and genetic analyses of Phoebe bournei (Lauraceae). Mol Biol Rep 48, 2201–2208 (2021). https://doi.org/10.1007/s11033-021-06228-w

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