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Transcriptome sequencing and microsatellite marker discovery in Ailanthus altissima (Mill.) Swingle (Simaroubaceae)

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Abstract

Ailanthus altissima Swingle, is a tree species native to East Asia and has a great potential in decorative, bioenergy and industrial applications in many countries. To date, despite its commercial importance, the genomic and genetic resources available for this species are still insufficient. In this study, we characterized the transcriptome of A. altissima and developed thirteen EST-SSRs (expressed sequence tag-simple sequence repeats) based on Illumina paired-end RNA sequencing (RNA-seq). Besides, we developed ten polymorphic chloroplast microsatellite (cpSSR) markers using the available chloroplast genome of A. altissima. The transcriptome data produced 87,797 unigenes, of which 64,891 (73.91%) unigenes were successfully annotated in at least one protein database. For cpSSR markers the number of detected alleles (N) per marker varied from three at cpSSR12 to twelve at cpSSR8, the unbiased haploid diversity indices (uh) varied from 0.111 to 0.485, and haploid diversity indices (h) ranged from 0.101 to 0.444 with an average unbiased haploid diversity index (uh) of 0.274. Overall, a total of 65 different cpSSR alleles were identified at the ten loci among 165 individuals of A. altissima. The allele number per locus for EST-SSRs varied from 2.143 to 9.357, and the values of observed and expected heterozygosity ranged from 0.312 to 1.000 and 0.505 to 0.826, respectively. The molecular markers developed in this study will facilitate future genetic diversity, population structure, long distance-gene transfer and pollen-based gene flow analyses of A. altissima populations from its known distribution ranges in China focusing on planted and natural forest stands.

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Acknowledgements

We would like to acknowledge the National Natural Scientific Foundation of China (Grant No.31500457) and CAS-TWAS President’s Fellowship for International PhD Students for funding this project. The authors are also grateful for the comments of editor and of three anonymous reviewers, which improved the manuscript considerably.

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Authors and Affiliations

  1. Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, 518004, Shenzhen, People’s Republic of China

    Josphat K. Saina & Yi-Ying Liao

  2. Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, 430074, Wuhan, People’s Republic of China

    Josphat K. Saina, Zhi-Zhong Li, Yeshitila Mekbib & Andrew W. Gichira

  3. University of Chinese Academy of Sciences, 100049, Beijing, People’s Republic of China

    Josphat K. Saina, Zhi-Zhong Li, Yeshitila Mekbib & Andrew W. Gichira

  4. Sino-African Joint Research Center, Chinese Academy of Sciences, 430074, Wuhan, People’s Republic of China

    Josphat K. Saina, Yeshitila Mekbib & Andrew W. Gichira

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  1. Josphat K. Saina
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Contributions

Y-YL conceived and designed the experiment; JK.S performed the experiments, analyzed data and wrote the first draft of the manuscript. Z-ZL assisted in data analysis, Y-YL, Z-ZL, AW.G and YM commented on previous versions of the manuscript. Y-YL and Z-ZL collected the plant materials. All authors read and approved the final version of the manuscript.

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Correspondence to Yi-Ying Liao.

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Saina, J.K., Li, ZZ., Mekbib, Y. et al. Transcriptome sequencing and microsatellite marker discovery in Ailanthus altissima (Mill.) Swingle (Simaroubaceae). Mol Biol Rep 48, 2007–2023 (2021). https://doi.org/10.1007/s11033-020-05402-w

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  • DOI: https://doi.org/10.1007/s11033-020-05402-w

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