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De novo assembly and characterization of the floral transcriptome of an economically important tree species, Lindera glauca (Lauraceae), including the development of EST-SSR markers for population genetics

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Abstract

Lindera glauca (Lauraceae) is an economically important East Asian forest tree characterized by a dioecy in China and apomixis in Japan. However, patterns of population genetic diversity and structure of this species remain unknown for this species due to a lack of efficient molecular markers. In this study, we employed Illumina sequencing to analyze the transcriptomes of the female and male flower buds of L. glauca. We retrieved 59,753 and 75,075 unigenes for the female and male buds, respectively. Based on sequence similarity, 44,379 (74.27 %) unigenes for the female and 45,414 (60.49 %) unigenes for the male were matched to public databases. We identified 11,127 putative differentially expressed genes between the female and male buds and 20,048 expressed sequence tag-simple sequence repeats (EST-SSRs). From 3147 primer pairs designed successfully, 120 were selected for validation of polymorphism, and 13 could reliably amplify polymorphic bands and exhibited moderate levels of genetic diversity (e.g., N A = 4.42; H E = 0.56) when surveyed across 96 individuals of altogether six L. glauca populations from China and Japan. One of the three population genetic clusters identified in China was fixed in Japan, suggesting a historical population bottleneck following island immigration. The present study has generated a wealth of transcriptome data for future functional genomic research focused on the variable reproductive system of L. glauca (dioecy, apomixis) as well as EST-SSR markers for population genetics studies and its intriguing evolutionary shift from dioecy to apomixis in the wake of island colonization.

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References

  1. Wang YL, Gao XM, Yu XP, Cheng SL, Kong LH (1994) Study on the resource and its utilizations of Lindera glauca in China. Henan Sci 12:331–334

    Google Scholar 

  2. Niu J, Chen YL, An JY, Hou XY, Cai J, Wang J, Zhang ZX, Lin SZ (2015) Integrated transcriptome sequencing and dynamic analysis reveal carbon source partitioning between terpenoid and oil accumulation in developing Lindera glauca fruits. Sci Rep 5:15017

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Qi J, Xiong B, Ju YX, Hao QZ, Zhang ZX (2015) Study on fruit growth regularity and lipid accumulation of Lindera glauca. Chin Agric Sci Bull 31:29–33

    Google Scholar 

  4. Dupont YL (2002) Evolution of apomixis as a strategy of colonization in the dioecious species Lindera glauca (Lauraceae). Popul Ecol 44:0293–0297

    Article  Google Scholar 

  5. Pannell JR, Dorken ME (2006) Colonisation as a common denominator in plant metapopulations and range expansions: effects on genetic diversity and sexual systems. Landsc Ecol 21:837–848

    Article  Google Scholar 

  6. Rodríguez-Sánchez F, Guzmán B, Valido A, Vargas P, Arroyo J (2009) Late Neogene history of the laurel tree (Laurus L., Lauraceae) based on phylogeographical analyses of Mediterranean and Macaronesian populations. J Biogeogr 36:1270–1281

    Article  Google Scholar 

  7. Niu J, Hou XY, Fang CL, An JY, Ha DL, Qiu L, Ju YX, Zhao HY, Du WZ, Qi J, Zhang ZX, Liu GN, Lin SZ (2015) Transcriptome analysis of distinct Lindera glauca tissues revealed the differences in the unigenes related to terpenoid biosynthesis. Gene 559:22–30

    Article  CAS  PubMed  Google Scholar 

  8. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Guo R, Mao YR, Cai JR, Wang JY, Wu J, Qiu YX (2014) Characterization and cross-species transferability of EST-SSR markers developed from the transcriptome of Dysosma versipellis (Berberidaceae) and their application to population genetic studies. Mol Breed 34:1733–1746

    Article  Google Scholar 

  10. Chen LY, Cao YN, Yuan N, Nakamura K, Wang GM, Qiu YX (2015) Characterization of transcriptome and development of novel EST-SSR makers based on next-generation sequencing technology in Neolitsea sericea (Lauraceae) endemic to East Asian land-bridge islands. Mol Breed 35:1–15

    Article  Google Scholar 

  11. Ai B, Gao Y, Zhang X, Tao J, Kang M, Huang H (2015) Comparative transcriptome resources of eleven Primulina species, a group of ‘stone plants’ from a biodiversity hot spot. Mol Ecol Resour 15:619–632

    Article  CAS  PubMed  Google Scholar 

  12. 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 29:644–652

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Zhou XJ, Wang YY, Xu YN, Yan RS, Zhao P, Liu WZ (2015) De novo characterization of flower bud transcriptomes and the development of EST-SSR markers for the endangered tree Tapiscia sinensis. Int J Mol Sci 16:12855–12870

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B (2003) TIGR gene indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651–652

    Article  CAS  PubMed  Google Scholar 

  15. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676

    Article  CAS  PubMed  Google Scholar 

  16. Ye J, Fang L, Zheng HK, Zhang Y, Chen J, Zhang ZJ, Wang J, Li ST, Li RQ, Bolund L, Wang J (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34:W293–W297

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Zhang J, Feng JJ, Lu J, Yang YZ, Zhang X, Wan DS, Liu JQ (2014) Transcriptome differences between two sister desert poplar species under salt stress. BMC Genomics 15:1

    Article  Google Scholar 

  18. Rozen S, Skaletsky H (1999) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386

    Google Scholar 

  19. Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106

    Article  PubMed  Google Scholar 

  20. Rousset F (2008) Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Resour 8:103–106

    Article  PubMed  Google Scholar 

  21. Chapuis MP, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–631

    Article  CAS  PubMed  Google Scholar 

  22. Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices Version 2.9.3. http://www2.unil.ch/popgen/softwares/fstat.htm

  23. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  25. Takezaki N, Nei M, Tamura K (2010) POPTREE2: software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. Mol Biol Evol 27:747–752

    Article  CAS  PubMed  Google Scholar 

  26. Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol 19:153–170

    Article  CAS  PubMed  Google Scholar 

  27. Jiang X, Wu Y, Xiao F, Xiong Z, Xu H (2014) Transcriptome analysis for leaves of five chemical types in Cinnamomum camphora. Hereditas 36:58–68

    CAS  PubMed  Google Scholar 

  28. Mao YR, Zhang YH, Xu C, Qiu YX (2015) Comparative transcriptome resources of two Dysosma species (Berberidaceae) and molecular evolution of the CYP719A gene in Podophylloideae. Mol Ecol Resour 16:228–241

    Article  PubMed  Google Scholar 

  29. Ellis JR, Burke JM (2007) EST-SSRs as a resource for population genetic analyses. Heredity 99:125–132

    Article  CAS  PubMed  Google Scholar 

  30. Stoeckel S, Grange J, Fernandez-Manjarres F, Bilger I, Frascaria-Lacoste N, Mariette S (2006) Heterozygote excess in a self-incompatible and partially clonal forest tree species—Prunus avium L. Mol Ecol 15:2109–2118

    Article  CAS  PubMed  Google Scholar 

  31. Barrett SCH (1996) The reproductive biology and genetics of island plants. Philos Trans R Soc Lond B 351:725–733

    Article  Google Scholar 

  32. Ronsheim ML, Bever JD (2000) Genetic variation and evolutionary trade-offs for sexual and asexual reproductive modes in Allium vineale (Liliaceae). Am J Bot 87:1769–1777

    Article  CAS  PubMed  Google Scholar 

  33. Obbard DJ, Harris SA, Pannell JR (2006) Sexual systems and population genetic structure in an annual plant: testing the metapopulation model. Am Nat 167:354–366

    Article  PubMed  Google Scholar 

  34. Yuan N, Sun Y, Comes HP, Fu CX, Qiu YX (2014) Understanding population structure and historical demography in a conservation context: population genetics of the endangered Kirengeshoma palmata (Hydrangeaceae). Am J Bot 101:521–529

    Article  PubMed  Google Scholar 

  35. Barrett SCH (2002) The evolution of plant sexual diversity. Nat Rev Gen 3:274–284

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The research was supported by the National Science Foundation of China (Grant No. 3151101152) and the International Cooperation and Exchange of the National Natural Science Foundation of China (Grant Nos. 31511140095, 31561143015). The authors are grateful to Koh Nakamura (Hokkaido University, Japan) for collecting Japanese material of L. glauca, Hans-Peter Comes and two anonymous reviewers for very insightful comments on an earlier version of this manuscript.

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Authors and Affiliations

  1. Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China

    Shanshan Zhu, Yanqian Ding, Zhaoyan Yap & Yingxiong Qiu

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  1. Shanshan Zhu
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  2. Yanqian Ding
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Correspondence to Yingxiong Qiu.

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Zhu, S., Ding, Y., Yap, Z. et al. De novo assembly and characterization of the floral transcriptome of an economically important tree species, Lindera glauca (Lauraceae), including the development of EST-SSR markers for population genetics. Mol Biol Rep 43, 1243–1250 (2016). https://doi.org/10.1007/s11033-016-4056-1

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  • DOI: https://doi.org/10.1007/s11033-016-4056-1

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