Chromosomal genome and population genetic analyses to reveal genetic architecture, breeding history and genes related to cadmium accumulation in Lentinula edodes

BMC Genomics

Qi Tan¹  Lujun Zhang¹  Xiaodong Shang¹  Hailong Yu²  Yu Li²  Bing Peng³  Yongping Fu³  Shijun Xiao⁴ 

[1] Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, 201403, Shanghai, China;Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, 201403, Shanghai, China;Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, 130018, Changchun, China;Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, 130018, Changchun, China;Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, 130018, Changchun, China;Jiaxing Key Laboratory for New Germplasm Breeding of Economic Mycology, 314000, Jiaxing, China;

关键词: Lentinula edodes;    Germplasm evaluation;    Genome;    Population genetic analysis;    GWAS;    Cd accumulation;   

DOI  :  10.1186/s12864-022-08325-x

来源: Springer

【 摘 要 】

BackgroundLentinula edodes (Berk.) is the second most productive mushroom in the world. It contains compounds effective for antiviral, antitumor, antioxidant and immune regulation. Although genomes have previously been reported for this species, a high-quality chromosome-level reference for L. edodes is unavailable. This hinders detailed investigation of population genetics, breeding history of strains and genes related to environmental stress responses.ResultsA high-quality chromosome-level genome was constructed. We separated a monokaryon from protoplasts of the commercial L. edodes strain L808 and assembled the genome of L. edodes using PacBio long-read and Illumina short-read sequencing, along with the high-throughput chromatin conformation capture (Hi-C) technique. We assembled a 45.87 Mb genome, and 99% of the sequences were anchored onto 10 chromosomes. The contig and scaffold N50 length were 2.17 and 4.94 Mb, respectively. Over 96% of the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) were identified, and 9853 protein-coding genes were predicted. We performed population genome resequencing using 34 wild strains and 65 commercial cultivars of L. edodes originating from China, Japan, the United States and Australia. Based on whole-genome variants, we showed substantial differences in the Chinese wild population, which divided into different branches according to the main areas of their geographical distribution. We also determined the breeding history of L. edodes at the molecular level, and demonstrated that the cultivated strains in China mainly originated from wild strains from China and Northeast Asia. Phenotypic analysis showed that 99 strains exhibited differences on the Cd accumulation. Three significant loci in the of L. edodes genome were identified using the genome-wide association study (GWAS) of Cd accumulation traits. Functional genes associated with Cd accumulation traits were related to DNA ligase and aminoacyl tRNA synthetase, indicating that DNA damage repair and in vivo protein translation may be responses to Cd stress.ConclusionsA high-quality chromosome-level genome and population genetic data of L. edodes provide genetic resources for functional genomic, evolutionary and artificial breeding studies for L. edodes.

【 授权许可】

CC BY