Zhenyang Liao1, Xunxiao Zhang1, Shengcheng Zhang1, Zhicong Lin1, Xingtan Zhang2, Ray Ming3. 1. College of Life Science, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. 2. College of Life Science, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. zhangxt@fafu.edu.cn. 3. Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. rayming@illinois.edu.
Abstract
BACKGROUND: Structural variations (SVs) are a type of mutations that have not been widely detected in plant genomes and studies in animals have shown their role in the process of domestication. An in-depth study of SVs will help us to further understand the impact of SVs on the phenotype and environmental adaptability during papaya domestication and provide genomic resources for the development of molecular markers. RESULTS: We detected a total of 8083 SVs, including 5260 deletions, 552 tandem duplications and 2271 insertions with deletion being the predominant, indicating the universality of deletion in the evolution of papaya genome. The distribution of these SVs is non-random in each chromosome. A total of 1794 genes overlaps with SV, of which 1350 genes are expressed in at least one tissue. The weighted correlation network analysis (WGCNA) of these expressed genes reveals co-expression relationship between SVs-genes and different tissues, and functional enrichment analysis shows their role in biological growth and environmental responses. We also identified some domesticated SVs genes related to environmental adaptability, sexual reproduction, and important agronomic traits during the domestication of papaya. Analysis of artificially selected copy number variant genes (CNV-genes) also revealed genes associated with plant growth and environmental stress. CONCLUSIONS: SVs played an indispensable role in the process of papaya domestication, especially in the reproduction traits of hermaphrodite plants. The detection of genome-wide SVs and CNV-genes between cultivated gynodioecious populations and wild dioecious populations provides a reference for further understanding of the evolution process from male to hermaphrodite in papaya.
BACKGROUND: Structural variations (SVs) are a type of mutations that have not been widely detected in plant genomes and studies in animals have shown their role in the process of domestication. An in-depth study of SVs will help us to further understand the impact of SVs on the phenotype and environmental adaptability during papaya domestication and provide genomic resources for the development of molecular markers. RESULTS: We detected a total of 8083 SVs, including 5260 deletions, 552 tandem duplications and 2271 insertions with deletion being the predominant, indicating the universality of deletion in the evolution of papaya genome. The distribution of these SVs is non-random in each chromosome. A total of 1794 genes overlaps with SV, of which 1350 genes are expressed in at least one tissue. The weighted correlation network analysis (WGCNA) of these expressed genes reveals co-expression relationship between SVs-genes and different tissues, and functional enrichment analysis shows their role in biological growth and environmental responses. We also identified some domesticated SVs genes related to environmental adaptability, sexual reproduction, and important agronomic traits during the domestication of papaya. Analysis of artificially selected copy number variant genes (CNV-genes) also revealed genes associated with plant growth and environmental stress. CONCLUSIONS: SVs played an indispensable role in the process of papaya domestication, especially in the reproduction traits of hermaphrodite plants. The detection of genome-wide SVs and CNV-genes between cultivated gynodioecious populations and wild dioecious populations provides a reference for further understanding of the evolution process from male to hermaphrodite in papaya.
Authors: Michael A Hardigan; Emily Crisovan; John P Hamilton; Jeongwoon Kim; Parker Laimbeer; Courtney P Leisner; Norma C Manrique-Carpintero; Linsey Newton; Gina M Pham; Brieanne Vaillancourt; Xueming Yang; Zixian Zeng; David S Douches; Jiming Jiang; Richard E Veilleux; C Robin Buell Journal: Plant Cell Date: 2016-01-15 Impact factor: 11.277
Authors: Luca Santuari; Sylvain Pradervand; Amelia-Maria Amiguet-Vercher; Jerôme Thomas; Eavan Dorcey; Keith Harshman; Ioannis Xenarios; Thomas E Juenger; Christian S Hardtke Journal: Genome Biol Date: 2010-01-12 Impact factor: 13.583