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Chromosome-level reference genome of X12, a highly virulent race of the soybean cyst nematode Heterodera glycines

文献类型： 外文期刊

作者： Lian, Yun 1 ; Wei, He 1 ; Wang, Jinshe 1 ; Lei, Chenfang 1 ; Li, Haichao 1 ; Li, Jinying 1 ; Wu, Yongkang 1 ; Wang, Shufe 1 ;

作者机构： 1.Henan Acad Agr Sci, Inst Ind Crops, Minist Agr,Natl Soybean Improvement Ctr, Key Lab Oil Crops Huanghuaihai Plains,Zhengzhou S, Zhengzhou 450002, Henan, Peoples R China

2.Luoyang Acad Agr & Forestry Sci, Luoyang, Peoples R China

关键词： chromosome scale; evolution; genome assembly; Heterodera glycines; Soybean cyst nematode; X12

期刊名称：MOLECULAR ECOLOGY RESOURCES （ 影响因子：7.09； 五年影响因子：8.745 ）

ISSN： 1755-098X

年卷期：

页码：

收录情况： SCI

摘要： Soybean cyst nematode (SCN, Heterodera glycines) is a major pest of soybean that is spreading across major soybean production regions worldwide. Increased SCN virulence has recently been observed in both the United States and China. However, no study has reported a genome assembly for H. glycines at the chromosome scale. Herein, the first chromosome-level reference genome of X12, an unusual SCN race with high infection ability, is presented. Using whole-genome shotgun (WGS) sequencing, Pacific Biosciences (PacBio) sequencing, Illumina paired-end sequencing, 10X Genomics linked reads and high-throughput chromatin conformation capture (Hi-C) genome scaffolding techniques, a 141.01-megabase (Mb) assembled genome was obtained with scaffold and contig N50 sizes of 16.27 Mb and 330.54 kilobases (kb), respectively. The assembly showed high integrity and quality, with over 90% of Illumina reads mapped to the genome. The assembly quality was evaluated using Core Eukaryotic Genes Mapping Approach and Benchmarking Universal Single-Copy Orthologs. A total of 11,882 genes were predicted using de novo, homolog and RNAseq data generated from eggs, second-stage juveniles (J2), third-stage juveniles (J3) and fourth-stage juveniles (J4) of X12, and 79.0% of homologous sequences were annotated in the genome. These high-quality X12 genome data will provide valuable resources for research in a broad range of areas, including fundamental nematode biology, SCN-plant interactions and co-evolution, and also contribute to the development of technology for overall SCN management.

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