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Genome survey sequencing and genetic background characterization of yellow horn based on next-generation sequencing

Molecular Biology Reports volume 46, pages 4303–4312 (2019)Cite this article

Abstract

Yellowhorn (Xanthoceras sorbifolium Bunge) is an important wood oil tree species, with high ornamental and medicinal value. Nevertheless, genomic information of yellowhorn is currently unavailable. Here, for the first time, we conducted a genome survey of two yellowhorn cultivars, Zhongshi 4 and Zhongshi 9, which had distinct differences on the phenotype and drought resistance, to obtain knowledge on the genomic information by next generation sequencing (NGS). Meanwhile, its genome size was estimated using flow cytometry. As a result, the whole genome survey of Zhongshi 4 and Zhongshi 9 generated 34.40 and 39.55 GB sequence data. The genome size of Zhongshi 4 and Zhongshi 9 estimated were about 536.58 Mb and 569.52 Mb, which were closed to results of flow cytometry. The heterozygosity rates were calculated to be 0.75% and 0.89%, and the repeat rates were 60.08% and 62.00%. These reads were assembled into 1024,373 and 885,404 contigs with a N50 length of 1005 bp and 1219 bp, respectively, which were further assembled into 714,369 and 686,128 scaffolds with scaffold N50 length of ~ 1963 bp and ~ 1938 bp, total length of 386,915 Kb and 391,904 Kb. These results indicated that there was little difference in genome size and complexity among different cultivars. In addition, 63137 and 65271 high-quality genomic simple sequence repeat (SSR) markers in Zhongshi 4 and Zhongshi 9 were generated. We suggest that the technologies combining Illumina and PacBio, assisted by Hi-C and matching assemble software should be used to one of two yellowhorn cultivars genome sequencing. The result will help to design whole genome sequencing strategies for yellowhorn, and provided a large amount of gene resources for further excavation and utilization of yellowhorn.

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Data availability

The genome sequence reads obtained by Illumina Hiseq are available at NCBI-SRA. The Bioproject accession number is PRJNA483857 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA483857), and the Biosample accession number is SAMN10980100 (Zhongshi 9) (https://www.ncbi.nlm.nih.gov/biosample/SAMN10980100) and SAMN09748200 (Zhongshi 4) (https://www.ncbi.nlm.nih.gov/biosample/SAMN10980200). The Experiment number is SRX 5401612 and Run number is SRR8601604 (Zhongshi 9) and SRR7768199 (Zhongshi 4).

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Funding

This work was financially supported by the Central Public-Interest Scientific Institution Basal Research Fund (CAFYBB2019QD001, CAFYBB2017QB001), the National Natural Science Foundation of China (31800571, 31870594).

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Author notes

  1. Quanxin Bi and Yang Zhao contributed equally to this article.

Affiliations

  1. State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China

    Quanxin Bi, Yang Zhao, Yifan Cui & Libing Wang

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  1. Quanxin Bi
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  2. Yang Zhao
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  3. Yifan Cui
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  4. Libing Wang
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Correspondence to Libing Wang.

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Bi, Q., Zhao, Y., Cui, Y. et al. Genome survey sequencing and genetic background characterization of yellow horn based on next-generation sequencing. Mol Biol Rep 46, 4303–4312 (2019). https://doi.org/10.1007/s11033-019-04884-7

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Keywords

  • Yellowhorn
  • Genome survey
  • Next genome sequencing
  • SSR