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

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.