结缕草是一种暖季型草坪草和各地广泛使用的园艺作物，是一种重要的遗传资源，因为它更能抵抗高温、干旱、沿海盐碱、病虫害和践踏的胁迫。对Z. japonica 的基因组研究对于寻找与有用性状相关的分子标记是必要的。本研究通过基于 PacBio 的长读长测序和组装和注释分析了Z. japonica 'Yaji' 栽培品种植物的基因组。在进行基于PacBio的长读长NGS分析之前，通过外部形态学分类法和分子鉴定方法对'雅集'品种进行了分析，确认'雅集'品种被鉴定为Z. japonica 植物。使用 PacBio RSII 平台构建基因组 DNA 文库并进行测序。作为 DNA 测序的结果，对 40 个 SMRT 细胞进行了测序，并产生了约 38.6 Gb 的读数。从头组装由 Canu 组装机完成。生成的程序集包含 1,350 个重叠群。BUSCO 分析结果表明，1440 个保守的直系同源基因中有 1390 个（96.5%）作为完整基因存在于Z. japonica 'Yaji' 栽培品种基因组中。基于 PacBio 的组装发现，预测的假定基因序列和基因数量与先前报道的单个基因具有高度同一性。粳稻的基因预测与注释'雅集'品种利用Augustus基因预测软件和NCBI-nr数据库完成。结果，获得了50,140 个Z. japonica 'Yaji' 栽培品种的基因组。使用 psRNATarget 对 'Yaji' 品种的保守 miRNA 进行目标预测。结果，预测了'雅集'品种的 8207 个 miRNA/目标位点对。'Yaji' 品种基因组的转座子元件是用 REPET 包预测的。结果，预测了 LARD、I 类 TRIM (RXX) 和 II 类 TIR (DXX) 的 2656 个转座子元件。通过 PacBio 长读长测序获得韩国Z. japonica植物的基因组数据。这些Z. japonica的基因组数据植物将为结缕草草坪草的分子标记开发和分子鉴定研究提供有价值的基础数据。
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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.
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