Skip to main content
SpringerLink
Log in

Genome-wide DNA polymorphisms of Citrus unshiu Marc. cv. Miyagawa-wase cultivated in different regions based on whole-genome re-sequencing

  • Original Article
  • Published:
Plant Biotechnology Reports Aims and scope Submit manuscript

Abstract

Citrus unshiu Marc. cv. Miyagawa-wase is the most widely cultivated citrus variety in Korea. To determine whether the C. unshiu genome used in this study shows genetic variation compared to the published reference genome (C. unshiu Marc. Miyagawa-wase), we conducted genome re-sequencing of two C. unshiu cultivars (Miyagawa-1 and Miyagawa-2) cultivated on Jeju in Korea. Compared with the reference genome, 1,198,650 and 1,207,084 single-nucleotide polymorphisms (SNPs) and 172,259 and 172,391 insertion/deletion polymorphisms (InDels) were detected in the Miyagawa-1 and -2 genomes, respectively. In SNP and InDel classifications by genome annotation, 367,591 and 369,068 SNPs and 45,362 and 45,464 InDels were located in the genic regions of Miyagawa-1 and -2, respectively. Among the SNPs of Miyagawa-1 and -2, transitions were more frequent than transversions. The majority of InDels was distributed in 1-bp InDels in both cultivars. The comparative number of total SNPs between Miyagawa-1 and -2 was smaller than the number of SNPs between the reference genome and Miyagawa-1 or -2. Gene ontology (GO) analysis showed that 23,164 and 23,049 genes with SNPs and 16,830 and 16,774 genes with InDels were annotated in the GO database. Taken together, Miyagawa-1 and -2 show genome-wide variation, including SNPs and InDels, compared to the published C. unshiu Marc. cv. Miyagawa-wase genome. This study suggests it would be more accurate to use the Miyagawa-1 and -2 genome sequences as a reference when conducting research using C. unshiu cultivated in Korea.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Al Mamun AA, Lombardo MJ, Shee C, Lisewski AM, Gonzalez C, Lin D, Nehring RB, Saint-Ruf C, Gibson JL, Frisch RL, Lichtarge O, Hastings PJ, Rosenberg SM (2012) Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338:1344–1348

    Article  CAS  Google Scholar 

  • Aleza P, Juárez J, Hernández M, Pina JA, Ollitrault P, Navarro L (2009) Recovery and characterization of a Citrus clementina Hort. ex Tan. “Clemenules” haploid plant selected to establish the reference whole Citrus genome sequence. BMC Plant Biol 9:110

    Article  Google Scholar 

  • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H et al (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 25(1):25–29

    Article  CAS  Google Scholar 

  • Baer CF, Miyamoto MM, Denver DR (2007) Mutation rate variation in multicellular eukaryotes: causes and consequences. Nat Rev Genet 8:619–631

    Article  CAS  Google Scholar 

  • Baron E, Richirt J, Villoutreix R, Amsellem L, Roux F (2015) The genetics of intra- and interspecific competitive response and effect in a local population of an annual plant species. Funct Eco 29:1361–1370

  • Bartoli C, Roux F (2017) Genome-wide association studies in plant pathosystems: toward an ecological genomics approach. Front Plant Sci 8:763

    Article  Google Scholar 

  • Bohry D, Ramos HCC, Santos PHD, Boechat MSB, Arêdes FAS, Pirovani AAV, Pereira MG (2021) Discovery of SNPs and InDels in papaya genotypes and its potential for marker assisted selection of fruit quality traits. Sci Rep 11:292

    Article  CAS  Google Scholar 

  • Cox MP, Peterson DA, Biggs PJ (2010) SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinform 11:485

    Article  Google Scholar 

  • De Kort H, Prunier JG, Ducatez S, Honnay O, Baguette M, Stevens VM, Blanchet S (2021) Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations. Nat Commun 12:516

    Article  Google Scholar 

  • Du Y, Luo S, Li X, Yang J, Cui T, Li W, Lixia YL, Feng H, Chen Y, Mu J, Chen X, Shu Q, Guo T, Luo W, Zhou L (2017) Identifcation of substitutions and small insertion–deletions induced by carbon-ion beam irradiation in Arabidopsis thaliana. Front Plant Sci 8:1851

    Article  Google Scholar 

  • Ellstrand NC, Roose ML (1987) Patterns of genetic diversity in clonal plant species. Am J Bot 74(1):123–131

    Article  Google Scholar 

  • Healey A, Furtado A, Cooper T, Henry RJ (2014) Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species. Plant Methods 10:21

    Article  Google Scholar 

  • Jiang C, Mithani A, Belfield EJ, Mott R, Hurst LD, Harberd NP (2014) Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations. Genome Res 24:1821–1829

    Article  CAS  Google Scholar 

  • Kim JE, Oh SK, Lee JH, Lee BM, Jo SH (2014) Genome-wide SNP calling using next generation sequencing data in tomato. Mol Cells 37:36–42

    Article  CAS  Google Scholar 

  • Kim SW, Ahn MS, Kwon YK, Song SY, Kim JK, Ha SH, Kim IJ, Liu JR (2015) Monthly metabolic changes and PLS prediction of carotenoid content of citrus fruit by combined Fourier transform infrared spectroscopy and quantitative HPLC analysis. Plant Biotechnol Rep 9:247–258

    Article  CAS  Google Scholar 

  • Kim WJ, Ryu J, Im J, Kim SH, Kang SY, Lee JH, Jo SH, Ha BK (2018) Molecular characterization of proton beam-induced mutations in soybean using genotyping-by-sequencing. Mol Genet Genomics 293:1169–1180

    Article  CAS  Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760

    Article  CAS  Google Scholar 

  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079

    Article  Google Scholar 

  • Li Y, Cao K, Li N, Zhu G, Fang W, Chen C, Wang X, Guo J, Wang Q, Ding T, Wang J, Guan L, Wang J, Liu K, Guo W, Arús P, Huang S, Fei Z, Wang L (2021) Genomic analyses provide insights into peach local adaptation and responses to climate change. Genome Res 31:592–606

    Article  Google Scholar 

  • Liu TJ, Zhou JJ, Chen FY, Gan ZM, Li YP, Zhang JZ, Hu CG (2018) Identification of the genetic variation and gene exchange between Citrus Trifoliata and Citrus Clementina. Biomolecules 8:182

    Article  Google Scholar 

  • Martin M (2011) Cutadpat: cutadapt removes adapter sequences from high-throughput sequencing reads. Embnet J 17:10–12

    Article  Google Scholar 

  • Park HS, Sawamura M (2002) Comparison of the cold-pressed peel oil composition between Korean and Japanese Satsuma mandarin (Citrus unshiu Marcov. forma Miyagawa-wase) by GC, GC-MS and GC-O. J Food Sci Natr 7:5–11

    Google Scholar 

  • Rando OJ, Verstrepen KJ (2007) Timescales of genetic and epigenetic inheritance. Cell 128:655–668

    Article  CAS  Google Scholar 

  • Sanczuk P, Govaert S, Meeussen C, De Pauw K, Vanneste T et al. (2021) Small scale environmental variation modulates plant defence syndromes of understorey plants in deciduous forests of Europe. Global Ecol Biogeogr 30:205–219

  • Shelake RM, Pramanik D, Kim JY (2019) Evolution of plant mutagenesis tools: a shifting paradigm from random to targeted genome editing. Plant Biotechnol Rep 13:423–445

    Article  Google Scholar 

  • Shimizu T, Tanizawa Y, Mochizuki T, Nagasaki H, Yoshioka T, Toyoda A, Fujiyama A, Kaminuma E, Nakamura Y (2017) Draft sequencing of the heterozygous diploid genome of satsuma (Citrus unshiu Marc.) using a hybrid assembly approach. Front Genet 8:180

    Article  Google Scholar 

  • Shinozaki K, Yamaguchi-Shinozaki K (1997) Gene expression and signal transduction in water-stress response. Plant Physiol 115:327–334

    Article  CAS  Google Scholar 

  • Shor E, Fox CA, Broach JR (2013) The yeast environmental stress response regulates mutagenesis induced by proteotoxic stress. PLoS Genet 9:e1003680

    Article  CAS  Google Scholar 

  • Subrahmaniam HJ, Libourel C, Journet EP, Morel JB, Munos S, Niebel A, Raffaele S, Roux F (2018) The genetics underlying natural variation of plant–plant interactions, a beloved but forgotten member of the family of biotic interactions. Plant J 93:747–770

    Article  CAS  Google Scholar 

  • Thudi M, Khan AW, Kumar V, Gaur PM, Katta K, Garg V, Roorkiwal M, Samineni S, Varshney RK (2016) Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.). BMC Plant Biol 16:10

    Article  Google Scholar 

  • Xu G, Chen L, Ruan X, Chen D, Zhu A et al (2012) The draft genome of sweet orange (Citrus sinensis). Nat Genet 45(1):59–67

    Article  Google Scholar 

  • Zhang QJ, Zhu T, Xia EH, Shi C, Liu YL, Zhang Y, Liu Y, Jiang WK, Zhao YJ, Mao SY et al (2014) Rapid diversification of five Oryza AA genomes associated with rice adaptation. Proc Natl Acad Sci USA 111:4954–4962

    Article  Google Scholar 

Download references

Acknowledgements

This research was supported by the 2021 Scientific Promotion Program funded by Jeju National University. The Subtropical Horticulture Research Institute and Research Institute for Subtropical Agriculture and Biotechnology provided facilities and equipment to conduct this research.

Author information

Authors and Affiliations

  1. Subtropical Horticulture Research Institute, Jeju National University, Jeju, 63243, Korea

    Chang-Ho Eun & In-Jung Kim

  2. Faculty of Biotechnology, College of Applied Life Sciences and Research Institute for Subtropical Agriculture and Biotechnology, SARI, Jeju National University, Jeju, 63243, Korea

    In-Jung Kim

Authors
  1. Chang-Ho Eun
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. In-Jung Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to In-Jung Kim.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (PDF 234 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Eun, CH., Kim, IJ. Genome-wide DNA polymorphisms of Citrus unshiu Marc. cv. Miyagawa-wase cultivated in different regions based on whole-genome re-sequencing. Plant Biotechnol Rep 15, 551–559 (2021). https://doi.org/10.1007/s11816-021-00696-z

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11816-021-00696-z

Keywords

Search

Navigation