Myung-Shin Kim1,2, Geun Young Chae3, Soohyun Oh1, Jihyun Kim1, Hyunggon Mang1, Seungill Kim4, Doil Choi5,6. 1. Plant Immunity Research Center, Plant Genomics and Breeding Institute, Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea. 2. Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea. 3. Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea. 4. Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea. ksi2204@uos.ac.kr. 5. Plant Immunity Research Center, Plant Genomics and Breeding Institute, Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea. doil@snu.ac.kr. 6. Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea. doil@snu.ac.kr.
Abstract
BACKGROUND: Peppers (Capsicum annuum L.) containing distinct capsaicinoids are the most widely cultivated spices in the world. However, extreme genomic diversity among species represents an obstacle to breeding pepper. RESULTS: Here, we report de novo genome assemblies of Capsicum annuum 'Early Calwonder (non-pungent, ECW)' and 'Small Fruit (pungent, SF)' along with their annotations. In total, we assembled 2.9 Gb of ECW and SF genome sequences, representing over 91% of the estimated genome sizes. Structural and functional annotation of the two pepper genomes generated about 35,000 protein-coding genes each, of which 93% were assigned putative functions. Comparison between newly and publicly available pepper gene annotations revealed both shared and specific gene content. In addition, a comprehensive analysis of nucleotide-binding and leucine-rich repeat (NLR) genes through whole-genome alignment identified five significant regions of NLR copy number variation (CNV). Detailed comparisons of those regions revealed that these CNVs were generated by intra-specific genomic variations that accelerated diversification of NLRs among peppers. CONCLUSIONS: Our analyses unveil an evolutionary mechanism responsible for generating CNVs of NLRs among pepper accessions, and provide novel genomic resources for functional genomics and molecular breeding of disease resistance in Capsicum species.
BACKGROUND: Peppers (Capsicum annuum L.) containing distinct capsaicinoids are the most widely cultivated spices in the world. However, extreme genomic diversity among species represents an obstacle to breeding pepper. RESULTS: Here, we report de novo genome assemblies of Capsicum annuum 'Early Calwonder (non-pungent, ECW)' and 'Small Fruit (pungent, SF)' along with their annotations. In total, we assembled 2.9 Gb of ECW and SF genome sequences, representing over 91% of the estimated genome sizes. Structural and functional annotation of the two pepper genomes generated about 35,000 protein-coding genes each, of which 93% were assigned putative functions. Comparison between newly and publicly available pepper gene annotations revealed both shared and specific gene content. In addition, a comprehensive analysis of nucleotide-binding and leucine-rich repeat (NLR) genes through whole-genome alignment identified five significant regions of NLR copy number variation (CNV). Detailed comparisons of those regions revealed that these CNVs were generated by intra-specific genomic variations that accelerated diversification of NLRs among peppers. CONCLUSIONS: Our analyses unveil an evolutionary mechanism responsible for generating CNVs of NLRs among pepper accessions, and provide novel genomic resources for functional genomics and molecular breeding of disease resistance in Capsicum species.
Entities:
Keywords:
Copy number variation; Disease resistance; Genome; Hot pepper; NLR evolution
Authors: Amanda M Hulse-Kemp; Shamoni Maheshwari; Kevin Stoffel; Theresa A Hill; David Jaffe; Stephen R Williams; Neil Weisenfeld; Srividya Ramakrishnan; Vijay Kumar; Preyas Shah; Michael C Schatz; Deanna M Church; Allen Van Deynze Journal: Hortic Res Date: 2018-01-12 Impact factor: 6.793