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

Plant Biotechnology Reports - Tập 17 - Trang 275-283 - 2023
Dae-Hwa Yang1, Ok-Cheol Jeong1, Hyeon-Jin Sun1, Hong-Gyu Kang1, Hyo-Yeon Lee1,2
1Subtropical Horticulture Research Institute, Jeju National University, Jeju, Korea
2Faculty of Biotechnology, Jeju National University, Jeju, Korea

Tóm tắt

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.

Tài liệu tham khảo

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 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 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 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 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 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 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 Bolle C (2004) The role of GRAS proteins in plant signal transduction and development. Planta 218:683–692 CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci USA 106:12794–12797 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 Choi JS (2017) Distribution, classification, breeding, and current use of zoysiagrass species and cultivars in Korea. Weed Turf Sci 6:283–291 Choi JS, Yang GM (2004) Development of new hybrid cultivar ‘Senock’ in zoysiagrass. Kor Tufgrass Sci 18:201–209 Choi JS, Yang GM (2006a) Development of new cultivar ‘Millock’ in zoysiagrass. Kor Tufgrass Sci 20:1–10 Choi JS, Yang GM (2006b) Sod production in South Korea. Kor Turfgrass Sci 20:237–251 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 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 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 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 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 Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39:W155–W159 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 Feschotte C, Pritham EJ (2007) DNA Transposons and the evolution of eukaryotic genomes. Annu Rev Genet 41:331–368 Flutre T, Duprat E, Feuillet C, Quesneville H (2011) Considering transposable element diversification in de novo annotation approaches. PLoS ONE 6:e16526 Forbes I (1952) Chromosome numbers and hybrids in Zoysia. Agron J 44:194–199 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 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 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 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 Hebert PDN, Cywinska A, Ball SL, de Waard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B 270:313–321 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 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 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 Hyun YH, Choi BJ, Kim YJ, Joo YK (2012) Analysis of research trend on zoysiagrass (Zoysia spp). Asian J Turfgrass Sci 26:89–95 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 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 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 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 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 Kress WJ, Erickson DL (2008) DNA barcodes: genes, genomics, and bioinformatics. Proc Natl Acad Sci USA 105:2761–2762 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 Kunihisa M, Fukino N, Matsumoto S (2003) Development of cleavage amplified polymorphic sequence (CAPS) markers for identification of strawberry cultivars. Euphytica 134:209–215 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 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 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 Mantere T, Kersten S, Hoischen A (2019) Long-read sequencing emerging in medical genetics. Front Genet 10:426 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 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 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 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 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 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 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 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 Sun HJ, Song IJ, Bae TW, Lee HY (2010) Recent development in biotechnological improvement of Zoysia japonica Steud. J Plant Biotechnol 37:400–407 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 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 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 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 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 White RH, Engelke MC, Anderson SJ, Ruemmele BA, Marcum KB, Taylor GR (2001) Zoysiagrass water relations. Crop Sci 41:133–138 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 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 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 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 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 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 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 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 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 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 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