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Tree Genetics & Genomes

, 15:9 | Cite as

Transcriptome sequencing and EST-SSR marker development in Salix babylonica and S. suchowensis

  • Xueyao Tian
  • Jiwei Zheng
  • Zhongyi Jiao
  • Jie Zhou
  • Kaiyue He
  • Baosong Wang
  • Xudong HeEmail author
Original Article
  • 45 Downloads
Part of the following topical collections:
  1. Germplasm Diversity

Abstract

As the largest genus in the family Salicaceae, Salix L. has great potential in industrial, ornamental, and bioenergy-related applications. Despite their comprehensive importance, the genetic and genomic resources available for various willow species are still insufficient. In the present study, the transcriptomes of S. babylonica and S. suchowensis were sequenced using Roche 454 pyrosequencing and screened for expressed sequence tagged simple sequence repeat (EST-SSR) markers. A total of 280,074 and 267,030 reads with an average length of 432 bp and 398 bp were obtained for S. babylonica and S. suchowensis, respectively. The de novo assemblies yielded 40,271 unigenes for S. babylonica and 55,083 unigenes for S. suchowensis, of which 32,506 and 42,482 unigenes were respectively annotated in at least one of the four reference databases. A total of 1479 differentially expressed genes were identified between the two species. A set of 1083 SSR markers (424 for S. babylonica and 659 for S. suchowensis) were developed from the expressed sequence assemblies. Of the 300 randomly selected EST-SSR markers, 295 (98.3%) were polymorphic among different individuals of S. babylonica and of S. eriocephala. High rates of cross-species/genus amplification were also observed within 16 different species. In conclusion, this transcriptomic analysis provides novel resources for functional genomic research and can be used to improve the efficiency of genetics and breeding applications for these Salix species.

Keywords

Transcriptome De novo assembly EST-SSR Salix Willow 

Notes

Acknowledgments

The authors are grateful to Shanghai BIOZERON Biotechnology Co., Ltd. for their assistance with the bioinformatics analysis.

Data archiving statement

All 454 pyrosequencing reads obtained for S. babylonica and S. suchowensis were submitted to the sequence read archive (SRA) database at NCBI (accession numbers: SRX389383 and SRX388824, respectively). The primer sequences for the 1083 EST-SSRs have also been deposited in the Probe database of GenBank (IDs Pr032826580-Pr032827662).

Funding information

This work was financially supported by the Fund for Independent Innovation of Agricultural Sciences and Technology in Jiangsu Province (No. CX(14)2024), Jiangsu Provincial Natural Science Foundation (BK20141039), Six Talent Peak project in Jiangsu Province (2016-NY-036), and 333 High-level Personnel Training Project in Jiangsu Province (No. BRA2017518).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11295_2018_1315_MOESM1_ESM.xlsx (313 kb)
ESM 1 (XLSX 312 kb)
11295_2018_1315_MOESM2_ESM.xlsx (89 kb)
ESM 2 (XLSX 89 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Xueyao Tian
    • 1
    • 2
  • Jiwei Zheng
    • 2
    • 3
  • Zhongyi Jiao
    • 2
  • Jie Zhou
    • 2
    • 3
  • Kaiyue He
    • 1
  • Baosong Wang
    • 2
    • 3
  • Xudong He
    • 2
    • 3
    Email author
  1. 1.College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
  2. 2.Department of Tree Genetics and BreedingJiangsu Academy of ForestryNanjingChina
  3. 3.Willow Nursery of the Jiangsu Provincial Platform for Conservation and Utilization of Agricultural GermplasmJiangsu Academy of ForestryNanjingChina

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