Insights into genomic evolution from the chromosomal and mitochondrial genomes of Ustilaginoidea virens

Phytopathology Research

Yuejiao Li¹  Zaixu Zhao¹  Wenxian Sun²  Kang Zhang³  Shaojie Li⁴  Tom Hsiang⁵  Ziding Zhang⁶  Nan Yao⁷ 

[1] Department of Plant Pathology, The Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, 100193, Beijing, China;Department of Plant Pathology, The Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, 100193, Beijing, China;College of Plant Protection, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China;Department of Plant Pathology, The Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, 100193, Beijing, China;Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, No.12 Zhongguancun South Street, Haidian District, 100081, Beijing, China;Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China;School of Environmental Sciences, University of Guelph, N1G 2W1, Guelph, Ontario, Canada;State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China;State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China;

关键词: Ustilaginoidea virens;    Comparative genomics;    Structural variations;    Genomic evolution;   

DOI  :  10.1186/s42483-021-00086-x

来源: Springer

【 摘 要 】

Ustilaginoidea virens, the causal agent of rice false smut, is an economically important filamentous fungal pathogen. A high-quality reference genome of U. virens promotes understanding of molecular mechanisms underlying its virulence and pathogenicity. Here, we report the first chromosome-level assembly of U. virens genome consisting of seven chromosomes ranging from 2.4 to 7.5 Mb. The assembly has dramatic improvements over previous assemblies, including considerably longer contigs, higher proportion of repetitive elements and more functionally annotated genes. Phylogenetic analyses revealed an extremely low intraspecific sequence divergence in U. virens. By contrast, intraspecific genome comparisons uncovered dynamic genomic alterations including massive structural variations and widespread lineage-specific regions (LSRs) among U. virens strains, which were mainly generated by recent burst of retrotransposons. Genomic plasticity created by structural variations and LSRs might drive rapid evolution of U. virens. High-quality mitochondrial genomes of eight U. virens strains exhibit size variations from 94 to 102 kb. Consistently, U. virens contains conserved lengths of exons and highly dynamic mobile introns, which contribute to intraspecific size variations due to gain/loss of homing endonuclease genes. This study highlights unique characteristics in nuclear and mitochondrial genomic divergence and provides new insights into genomic and mitochondrial evolution of U. virens.

【 授权许可】

CC BY