Skip to main content
Log in

Genome analysis of Zoysia japonica ‘Yaji’ cultivar using PacBio long-read sequencing

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

Abstract

The Zoysia japonica plant is a warm-season turfgrass and a horticultural crop used in various places and an important genetic resource because it is more resilient to stress from high temperature, drought, coastal salt, disease and pests, and trampling. Genome research on Z. japonica is necessary to find molecular markers related to useful traits. This study analyzed the genome of the Z. japonica ‘Yaji’ cultivar plant by PacBio-based long-read sequencing and assembly and annotation. Before performing the PacBio-based long-read NGS analysis, the ‘Yaji’ cultivar was analyzed by the external morphological classification method and the molecular identification method, and it was confirmed that the ‘Yaji’ cultivar was identified as a Z. japonica plant. Construction of genomic DNA libraries and sequencing with the PacBio RSII platform were performed. As a result of the DNA sequencing, 40 SMRT cells were sequenced, and about 38.6 Gb of reads were produced. De novo assembly was done by the Canu assembler. The resulting assembly consisted of 1,350 contigs. The BUSCO analysis results showed that 1390 (96.5%) of 1440 conserved orthologous are present as complete genes in the Z. japonica ‘Yaji’ cultivar genome. The PacBio-based assembly found that the predicted putative gene sequences and the number of the genes showed high identity to the previously reported individual genes. Gene predictions and annotation of Z. japonica ‘Yaji’ cultivar were done with the Augustus gene prediction software and NCBI-nr database. As a result, 50,140 gene sets of the Z. japonica ‘Yaji’ cultivar were obtained. Target prediction of the ‘Yaji’ cultivar was performed for conserved miRNAs using psRNATarget. As a result, 8207 miRNA/target site pairs of the ‘Yaji’ cultivar were predicted. The transposon element of the ‘Yaji’ cultivar genome was predicted with the REPET package. As a result, 2656 transposon elements of LARD, TRIM of class I (RXX), and TIR of class II (DXX) were predicted. Genomic data of Korean Z. japonica plants were obtained by PacBio long-read sequencing. These genome data of Z. japonica plant will provide valuable basic data for developing molecular markers and molecular identification of Zoysia turfgrass research.

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

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

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

Instant access to the full article PDF.

Fig. 1
Fig. 2

Similar content being viewed by others

Data availability

The datasets used and analyzed during the current study are available from the corresponding author on reasonable request.

Abbreviations

BUSCO:

Benchmarking universal single-copy orthologs

BLAST:

Basic local alignment search tool

CEGMA:

Core eukaryote gene mapping approach

Gb:

Gigabase pairs

GC:

Guanine-cytosine

ITS:

NrDNA-internal transcribed spacer

Kb:

Kilobase pairs

Mb:

Megabase pairs

NCBI:

National center for biotechnology information

NGS:

Next-generation sequencing

PacBio:

Pacific biosciences

SMRT:

Single-molecule real-time

SRA:

Sequence read archive

References

  • Adewale BA (2020) Will long-read sequencing technologies replace short-read sequencing technologies in the next 10 years? Afr J Lab Med 9(1):a1340

    Article  CAS  Google Scholar 

  • Ahn SY, Cho KS, Yoo KO, Suh JT (2010) Phylogenetic relationship of Ligularia species based on RAPD and ITS sequence analysis. Kor J Hortic Sci Technol 28:638–647

    Google Scholar 

  • Ahn JH, Kim JS, Kim S, Soh HY, Shin H, Jang H, Ryu JH, Kim A, Yun KY, Kim S, Kim KS, Choi D, Huh JH (2015) De Novo transcriptome analysis to identify anthocyanin biosynthesis genes responsible for tissue-specific pigmentation in zoysiagrass (Zoysia japonica Steud.). PLoS ONE 10(4):e0124497

    Article  PubMed  PubMed Central  Google Scholar 

  • Arumuganathan K, Tallury SP, Fraser ML, Bruneau AH, Qu R (1999) Nuclear DNA content of thirteen turfgrass species by flow cytometry. Crop Sci 39:1518–1521

    Article  Google Scholar 

  • Bae EJ, Park NC, Lee KS, Lee SM, Choi JS, Yang GM (2010) Distribution and morphology characteristics of native zoysiagrasses (Zoysia spp.) grown in South Korea. Kor Turfgrass Sci 24:97–105

    Google Scholar 

  • Bae EJ, Lee KS, Kim DS, Han EH, Lee SM, Lee DW (2013) Sod production and current status of cultivation management in Korea. Weed Turf Sci 2:95–99

    Article  Google Scholar 

  • Baigalmaa J, Kim MK, Noh JH, Hua S, Yang DC (2009) Phylogenetic analysis of Schizonepeta Spike on the basis of DNA sequences. K J Med Crop Sci 17:46–53

    Google Scholar 

  • Bolle C (2004) The role of GRAS proteins in plant signal transduction and development. Planta 218:683–692

    Article  CAS  PubMed  Google Scholar 

  • CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci USA 106:12794–12797

    Article  PubMed Central  Google Scholar 

  • China Plant BOL Group (2011) Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proc Natl Acad Sci USA 108:19641–19646

    Article  PubMed Central  Google Scholar 

  • Choi JS (2017) Distribution, classification, breeding, and current use of zoysiagrass species and cultivars in Korea. Weed Turf Sci 6:283–291

    Google Scholar 

  • Choi JS, Yang GM (2004) Development of new hybrid cultivar ‘Senock’ in zoysiagrass. Kor Tufgrass Sci 18:201–209

    Google Scholar 

  • Choi JS, Yang GM (2006a) Development of new cultivar ‘Millock’ in zoysiagrass. Kor Tufgrass Sci 20:1–10

    Google Scholar 

  • Choi JS, Yang GM (2006b) Sod production in South Korea. Kor Turfgrass Sci 20:237–251

    Google Scholar 

  • Choi JS, Ahn BJ, Yang GM (1997) Distribution of native Zoysiagrasses (Zoysia spp.) in the south and west coastal regions of Korea and classification using morphological characteristics. J Kor Soc Hort Sci 38:399–407

    Google Scholar 

  • Choi DK, Yang GM, Choi JS (2008) Flowering periods, genetic characteristics, and cross-pollination rate of Zoysia spp in natural open-pollination. Kor Turfgrass Sci 22:13–24

    Google Scholar 

  • Choi JS, Yang GM, Oh CJ, Lee GJ, Bae EJ, Lee KS (2018) Development of new cultivars ‘JangsungChorok’ and ‘JangsungSaetbyeol’ in Zoysiagrass. Weed Turf Sci 7:231–238

    Google Scholar 

  • Chung SJ, Park SJ, Choi YI, Kim IK, Lee KY, Kim HJ, Lee GJ (2013a) SCAR markers were developed to identify zoysiagrass mutants exhibiting fine leaf characteristics. CNU J of Agri Sci 40:115–121

    CAS  Google Scholar 

  • Chung SJ, Park SJ, Kim HJ, Yang GM, Choi JS, OhJangSongLee CJDHIJGJ (2013b) RAPD-SCAR markers linked to medium-leaf zoysiagrass ecotypes. Weed Turf Sci 2(2):191–197

    Article  Google Scholar 

  • Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39:W155–W159

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Day RB, Shibuya N, Minami E (2003) Identification and characterization of two new members of the GRAS gene family in rice responsive to N-acetylchitooligosaccharide elicitor. Biochim Biophys Acta 1625:261–268

    Article  CAS  PubMed  Google Scholar 

  • Feschotte C, Pritham EJ (2007) DNA Transposons and the evolution of eukaryotic genomes. Annu Rev Genet 41:331–368

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Flutre T, Duprat E, Feuillet C, Quesneville H (2011) Considering transposable element diversification in de novo annotation approaches. PLoS ONE 6:e16526

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Forbes I (1952) Chromosome numbers and hybrids in Zoysia. Agron J 44:194–199

    Article  Google Scholar 

  • Gao T, Yao H, Song J, Liu C, Zhu Y, MA X, Pang X, Xu H, Chen S, (2010) Identification of medicinal plants in the family Fabaceae using a potential DNA barcode ITS 2. J Ethnopharmacol 130:116–121

    Article  CAS  PubMed  Google Scholar 

  • Gehrig H, Gauβmann O, Marx H, Schwarzott D, Kluge M (2001) Molecular phylogeny of the genus Kalanchoe (Crassulaceae) inferred from nucleotide sequences of the ITS-1 and ITS-2 regions. Plant Sci 160:827–835

    Article  CAS  PubMed  Google Scholar 

  • Gehrig JL, Portik DM, Driscoll MD, Jackson E, Chakraborty S, Gratalo D, Ashby M, Valladares R (2022) Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data. Microb Genom 8:000794

    PubMed  PubMed Central  Google Scholar 

  • Han HS, Kim DY, Lee KY, Park WG, Cho IK, Jung JS (2006) Comparative analysis of Acanthopanax senticosus harms from Korea, China and Russia based on the ITS sequences of nuclear ribosomal DNA. Korean J Plant Res 19:54–58

    Google Scholar 

  • Hebert PDN, Cywinska A, Ball SL, de Waard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B 270:313–321

    Article  CAS  Google Scholar 

  • Hoede C, Arnoux S, Moisset M, Chaumier T, Inizan O, Jamilloux V, Quesneville H (2014) PASTEC: an automatic transposable element classification tool. PLoS ONE 9:e91929

    Article  PubMed  PubMed Central  Google Scholar 

  • Hong SY, Cho KS, Yoo KO (2012) Phylogenetic analysis of Korean native aster plants based on internal transcribed spacer (ITS) sequence. Kor J Hort Sci Technol 30:178–184

    CAS  Google Scholar 

  • Hong MJ, Yang DH, Jeong OC, Kim YJ, Park MY, Kang HG, Sun HJ, Kwon YI, Park SY, Yang P, Song PS, Ko SM, Lee HY (2017) Molecular identification of Zoysia japonica and Zoysia sinica (Zoysia Species) based on ITS sequence analyses and CAPS. Hortic Sci Technol 35:344–360

    CAS  Google Scholar 

  • Hyun YH, Choi BJ, Kim YJ, Joo YK (2012) Analysis of research trend on zoysiagrass (Zoysia spp). Asian J Turfgrass Sci 26:89–95

    Google Scholar 

  • Kim KN (2016) Comparison of green color retention of zoysiagrass and cool-season grass under multi-layer system, USGA system, and mono-layer system of sports field. Hortic Sci Technol 34(2):342–353

    Google Scholar 

  • Kim HK, Lee SJ (2010) Turfgrass and golf course. Sunjinmunhwa Publishing 99–180

  • Kim YJ, Yang DH, Park MY, Sun HJ, Song PS, Kang HG, Suh SC, Lee YE (2020) Lee HY (2020) Overexpression of Zoysia ZjCIGR1 gene confers cold stress resistance to zoysiagrass. Plant Biotechnol Rep 14:21–31

    Article  Google Scholar 

  • Kingan SB, Urban J, Lambert CC, Baybayan P, Childers AK, Coates B, Scheffler B, Hackett K, Korlach J, Geib SM (2019) A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system. Gigascience 8:1–10

    Article  CAS  Google Scholar 

  • Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–736

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Korlach J, Gedman G, Kingan SB, Chin CS, Howard JT, Audet JN, Cantin L, Jarvis ED (2017) De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads. GigaScience 6:1–16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kress WJ, Erickson DL (2008) DNA barcodes: genes, genomics, and bioinformatics. Proc Natl Acad Sci USA 105:2761–2762

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci USA 102:8369–8374

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kunihisa M, Fukino N, Matsumoto S (2003) Development of cleavage amplified polymorphic sequence (CAPS) markers for identification of strawberry cultivars. Euphytica 134:209–215

    Article  CAS  Google Scholar 

  • Lee S, Yu HC, Yoon BS, Yang GM, Kim JY, Kim Y, Oh CJ (2013) Soil and morphological characteristics of native zoysiagrasses by the habitats. Weed Turf Sci 2:55–61

    Article  Google Scholar 

  • Li X, Qian Q, Fu Z, Wang Y, Xiong G, Zeng D, Wang X, Liu X, Teng S, Hiroshi F (2003) Control of tillering in rice. Nature 422:618–621

    Article  CAS  PubMed  Google Scholar 

  • Li RF, Wei JH, Wang HZ, He J, Sun ZY (2006) Development of highly regenerable callus lines and agrobacterium-mediated transformation of Chinese lawngrass (Zoysia sinica Hance) with a cold inducible transcription factor, CBF1. Plant Cell Tiss Org 85:297–305

  • Li C, Lin F, An D, Wang W, Huang R (2018) Genome sequencing and assembly by long reads in plants. Genes 9:6. https://doi.org/10.3390/genes9010006

    Article  CAS  Google Scholar 

  • Mantere T, Kersten S, Hoischen A (2019) Long-read sequencing emerging in medical genetics. Front Genet 10:426

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mhiri C, Borges F, Grandbastien MA (2022) Specificities and dynamics of transposable elements in land plants. Biology 11:488. https://doi.org/10.3390/biology11040488

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moon BC, Lee YM, Ji Y, Choi G, Chun JM, Kim HK (2013) Molecular authentication and phylogenetic analysis of plant species for Breeae and Cirsii Herba based on DNA barcodes. Kor J Herbol 28:75–84

    Article  Google Scholar 

  • Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, Ashburner M, Anxolabehere D (2005) Combined evidence annotation of transposable elements in genome sequences. PLoS Comput Biol 1:166–175

    Article  CAS  PubMed  Google Scholar 

  • Sekhar S, Das S, Panda D, Mohanty S, Mishra B, Kumar A, Navadagi DB, Sah RP, Pradhan SK, Samantaray S, Baig MJ, Behera L, Mohapatra T (2022) Identification of microRNAs that provide a low light stress tolerance-mediated signaling pathway during vegetative growth in rice. Plants 11:2558. https://doi.org/10.3390/plants11192558

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212

    Article  PubMed  Google Scholar 

  • Song IJ, Sun HJ, Jeong OC, Yang DH, Jin ID, Kang HG, Ko SM, Kwon YI, Bae TW, Song PS, Lee HY (2017) Development of dwarf type cultivar ‘Halla Green 2’ in Zoysia japonica Steud. Korean J Breed Sci 49:31–35

    Article  Google Scholar 

  • Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B (2006) AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res 34:W435–W439

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stanke M, Diekhans M, Baertsch R, Haussler D (2008) Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24:637–644

    Article  CAS  PubMed  Google Scholar 

  • Sun HJ, Song IJ, Bae TW, Lee HY (2010) Recent development in biotechnological improvement of Zoysia japonica Steud. J Plant Biotechnol 37:400–407

    Article  Google Scholar 

  • Tai TH, Tanksley SD (1990) A rapid and inexpensive method for isolation of total DNA from dehydrated plant tissue. Plant Mol Biol Rep 8:297–303

    Article  Google Scholar 

  • Tanaka H, Hirakawa H, Kosugi S, Nakayama S, Ono A, Watanabe A, Hashiguchi M, Gondo T, Ishigaki G, Muguerza M, Shimizu K, Sawamura N, Inoue T, Shigeki Y, Ohno N, Tabata S, Akashi R, Sato S (2016) Sequencing and comparative analyses of the genomes of zoysiagrasses. DNA Res 23:171–180

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tian G, Wan P, Sun S, Li J, Chen M (2004) Genome-wide analysis of the GRAS gene family in rice and Arabidopsis. Plant Mol Biol 54:519–532

    Article  CAS  PubMed  Google Scholar 

  • Toyama K, Bae CB, Kang JG, Lim YP, Adachi T, Riu KZ, Song PS, Lee HY (2003) Production of herbicide-tolerant zoysiagrass by Agrobacterium-mediated transformation. Mol Cell 16:19–27

    CAS  Google Scholar 

  • Wang X, Jin D, Wang Z, Guo H, Zhang L, Wang L, Li J, Paterson AH (2015) Telomere-centric genome repatterning determines recurring chromosome number reductions during the evolution of eukaryotes. New Phytol 205:378–389

    Article  CAS  PubMed  Google Scholar 

  • White RH, Engelke MC, Anderson SJ, Ruemmele BA, Marcum KB, Taylor GR (2001) Zoysiagrass water relations. Crop Sci 41:133–138

    Article  Google Scholar 

  • Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH (2007) A Unified classification system for eukaryotic transposable elements. Nat Rev Genet 8:973–982

    Article  CAS  PubMed  Google Scholar 

  • Yaneshita M, Kaneko S, Sasakuma T (1999) Allotetraploidy of Zoysia species with 2n=40 based on a RFLP genetic map. Theor Appl Genet 98:751–756

    Article  CAS  Google Scholar 

  • Yang GM, Ahn BJ, Choi JS (1995) Identification of native zoysiagrasses (Zoysia spp) using morphological characteristics and esterase isozymes. J Kor Soc Hortic Sci 36:240–247

    Google Scholar 

  • Yang DH, Sun HJ, Goh CH, Song PS, Bae TW, Song IJ, Lim YP, Lim PO, Lee HY (2012) Cloning of a Zoysia ZjLsL and its overexpression to induce axillary meristem initiation and tiller formation in Arabidopsis and bentgrass. Plant Biol 14(3):411–419

    Article  CAS  PubMed  Google Scholar 

  • Yang DH, Sun HJ, Jeong OC, Song IJ, Bae TW, Jin ID, Kang HG, Ko SM, Kwon YI, Song PS, Lee HY (2016) Dwarf zoysiagrass (Zoysia japonica) cultivar ‘Halla Green 1’ developed through mutation breeding. Korean J Breed Sci 48:516–520

    Article  Google Scholar 

  • Yang DH, Sun HJ, Jeong OC, Kang HG, Song IJ, Jin ID, Kang SY, Lee HY (2021a) Development of ‘Halla Green 7’: a zoysiagrass cultivar with greening period extending phenotype at lower temperatures. Korean J Breed Sci 53:458–466

    Article  Google Scholar 

  • Yang DH, Jeong OC, Sun HJ, Kang HG, Jin ID, Lee HY (2021b) Development of ‘Halla Green 10’ in zoysiagrass. Korean J Breed Sci 53:467–474

    Article  Google Scholar 

  • Yao H, Song J, Liu C, Luo K, Han J, Li Y, Pang X, Xu H, Zhu Y, Xiao P, Chen S (2010) Use of ITS2 region as the universal DNA barcode for plants and animals. PLoS ONE 5:e13102

    Article  PubMed  PubMed Central  Google Scholar 

  • Yu K, Zhang T (2013) Construction of customized sub-databases from NCBI-nr database for rapid annotation of huge metagenomic datasets using a combined BLAST and MEGAN approach. PLoS ONE 8(4):e5983110

    Article  Google Scholar 

  • Yu TY, Yeam DY, Kim YJ, Kim SJ (1974) Morphological studies on Korean lawn grasses (Zoysia spp). J Kor Soc Hort Sci 15:79–91

    Google Scholar 

  • Zdobnov EM, Tegenfeldt F, Kuznetsov D, Waterhouse RM, Simão FA, Ioannidis P, Seppey M, Loetscher A, Kriventseva EV (2017) OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs. Nucleic Acids Res 45(D1):D744–D749

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2016R1A6A1A03012862) and (2019R1A6A1A11052070), and by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries (IPET) through Agri-Bioindustry Technology Development Project, funded by the Ministry of Agriculture, Food and Rural Affairs (MAFRA; Grant Number: 315025-3). The grantors had not played any role in writing this report or the decision to submit this article for publication.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Hyo-Yeon Lee.

Additional information

Publisher's Note

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

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yang, DH., Jeong, OC., Sun, HJ. et al. Genome analysis of Zoysia japonica ‘Yaji’ cultivar using PacBio long-read sequencing. Plant Biotechnol Rep 17, 275–283 (2023). https://doi.org/10.1007/s11816-023-00829-6

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11816-023-00829-6

Keywords

Navigation