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Transcriptome sequencing and development of novel genic SSR markers for Dendrobium officinale

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Abstract

Dendrobium officinale is a critically endangered and valuable medicinal herb. In this study, two transcriptome libraries were constructed from 2-year-old stems of two cultivated varieties and sequenced with the Ion Torrent PGM™ platform. A total of 51,683 all-transcripts with average length of 505 bp, and 40,405 all-unigenes with N50 of 644 bp were achieved. Totally, 8527 potential genic simple sequence repeats (SSRs) were identified from 7332 (18.15%) unigene sequences, of which 1023 (2.53%) unigenes contained more than one SSR. Finally, 68 locus-specific primer pairs were designed, and 17 of them produced polymorphic products in D. officinale individuals. The number of alleles per locus ranged from 2 to 15, the observed and expected heterozygosity estimates ranged from 0.194 to 0.903 and from 0.360 to 0.893, respectively. These loci were further tested for cross-species transferability to D. huoshanense. All the 17 primer pairs were successfully amplified to yield locus-specific PCR products in D. huoshanense. Due to their high level of polymorphism and transferability, these genic SSR markers are valuable tools not only for germplasm conservation of this species but also for phylogenetic studies of Dendrobium.

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Acknowledgments

This research was supported by the Applied Basic Research Program of Guizhou Province ([2014]200208), the Key Science and Technology Program of Guizhou Province ([2013]3150), the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), and the Collaborative Innovation Plan of Jiangsu Higher Education (CIP).

Authors’ contributions

M X designed the experiments and conducted transcriptome sequencing, drafted the manuscript. XL and J-WW performed the SSR experiments. MX, S-YT, J-QS, and Y-Y Li collected plant materials. MX and J-WW analyzed the data. M-RH help to coordinate the experiments. All authors read and approved the manuscript.

Author information

Authors and Affiliations

  1. Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China

    Meng Xu, Xin Liu, Jian-Wen Wang & Min-Ren Huang

  2. Suzhou Shenyuan Bio-Tech Co., Ltd, Suzhou, 215200, China

    Shi-Yuan Teng & Ji-Qing Shi

  3. Guizhou Academy of Sciences, Guiyang, 550001, China

    Yuan-Yuan Li

Authors
  1. Meng Xu
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  2. Xin Liu
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  3. Jian-Wen Wang
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  4. Shi-Yuan Teng
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  5. Ji-Qing Shi
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  6. Yuan-Yuan Li
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  7. Min-Ren Huang
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Corresponding author

Correspondence to Meng Xu.

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The authors declare that they have no conflict of interest.

Electronic supplementary material

Supplementary Table S1

Summary for the annotation of assembled unigenes (DOC 30 kb)

Supplementary Table S2

Differentially expressed genes between BS and GS (XLS 464 kb)

Supplementary Table S3

GO enrichment statistics of the differentially expressed genes (XLS 1070 kb)

Supplementary Table S4

KEGG enrichment statistic of the differentially expressed genes (XLS 134 kb)

Supplementary Figure S1

KOG functional classification of all unigenes. 8241 (20.40%) unignes showed significant similarity to sequences in KOG databases, and were clustered into 25 categories. (DOC 155 kb)

Supplementary Figure S2

KEGG clssification of assembled unigenes. A total of 9643 unigenes were assigned to 5 KEGG biochemical pathways (Hierarchy1): Cellular Processes (A), Environmental Information Processing (B), Genetic Information Processing (C), Metabolism (D) and Organismal Systems (E). (DOC 265 kb)

Supplementary File S1

Sequence information of 40,405 unigenes (FASTA 19506 kb)

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Xu, M., Liu, X., Wang, JW. et al. Transcriptome sequencing and development of novel genic SSR markers for Dendrobium officinale . Mol Breeding 37, 18 (2017). https://doi.org/10.1007/s11032-016-0613-5

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  • DOI: https://doi.org/10.1007/s11032-016-0613-5

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