logo

SCIENCE CHINA Life Sciences, Volume 62, Issue 9: 1257-1260(2019) https://doi.org/10.1007/s11427-019-9822-2

Update soybean Zhonghuang 13 genome to a golden reference

More info
  • ReceivedJul 22, 2019
  • AcceptedAug 19, 2019
  • PublishedAug 21, 2019

Abstract

There is no abstract available for this article.


Funded by

the National Key Research & Development Program of China(2017YFD0101305)

National Natural Science Foundation of China(31525018,31788103)

and the State Key Laboratory of Plant Cell and Chromosome Engineering(PCCE-KF-2019-05)


Acknowledgment

This work was supported by the National Key Research & Development Program of China (2017YFD0101305), National Natural Science Foundation of China (31525018, 31788103), and the State Key Laboratory of Plant Cell and Chromosome Engineering (PCCE-KF-2019-05).


Interest statement

The author(s) declare that they have no conflict of interest.


Supplement

SUPPORTING INFORMATION

Table S1 Comparison of Gmax_ZH13 and Gmax_ZH13_v2.0

Table S2 Genome annotation of protein coding genes and non-coding genes (gff3 format)

Table S3 Chromosome location of TEs with clear structural boundaries

Table S4 Transposable element and repeat sequence composition in the Gmax_ZH13_v2.0 genome

Table S5 Chromosome location of repeat sequences

Table S6 Locations of centromere region for each chromosome

Table S7 Expression pattern of protein coding genes in 27 different soybean samples

Table S8 Expression pattern of miRNA in 27 different soybean samples

Supplemental File 1 Materials and methods

The supporting information is available online at http://life.scichina.com and https://link.springer.com. The supporting materials are published as submitted, without typesetting or editing. The responsibility for scientific accuracy and content remains entirely with the authors.


References

[1] Cantarel B.L., Korf I., Robb S.M.C., Parra G., Ross E., Moore B., Holt C., Sánchez Alvarado A., Yandell M.. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res, 2008, 18: 188-196 CrossRef PubMed Google Scholar

[2] Du, H., and Liang, C. (2018). Assembly of chromosome-scale contigs by efficiently resolving repetitive sequences with long reads. bioRxiv, http://dx.doi.org/10.1101/345983. Google Scholar

[3] Liu T., Fang C., Ma Y., Shen Y., Li C., Li Q., Wang M., Liu S., Zhang J., Zhou Z., et al. Global investigation of the co-evolution of MIRNA genes and microRNA targets during soybean domestication. Plant J, 2016, 85: 396-409 CrossRef PubMed Google Scholar

[4] Shen Y., Liu J., Geng H., Zhang J., Liu Y., Zhang H., Xing S., Du J., Ma S., Tian Z.. De novo assembly of a Chinese soybean genome. Sci China Life Sci, 2018, 61: 871-884 CrossRef PubMed Google Scholar

[5] Wang Z., Tian Z.X.. Genomics progress will facilitate molecular breeding in soybean. Sci China Life Sci, 2015, 58: 813-815 CrossRef PubMed Google Scholar

[6] Yang J., Huang X.. A new high-quality genome sequence in soybean. Sci China Life Sci, 2018, 61: 1604-1605 CrossRef PubMed Google Scholar

  • Figure 1

    Update of Gmax_ZH13_v2.0 genome. A, Pipeline for genome assembly. B, Distribution of genome features. Tracks from outer to inner circles indicate chromosomes, and density of protein coding genes, repeat sequence, snoRNA, tRNA, miRNA, snRNA and rRNA, respectively. The black blocks on the outer circle indicate regions enriched of Cent91/92 (a soybean-specific centromeric repeat). C, Expression profiling of protein coding genes (left panel) and miRNAs (right panel) in 27 samples from different tissues of different development stages. D, An example of miRNA (top panel) to repress its target gene expression (bottom panel).

Copyright 2020 Science China Press Co., Ltd. 《中国科学》杂志社有限责任公司 版权所有

京ICP备18024590号-1