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.
Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea.
BMC Plant Biol. 2021 May 31;21(1):247. doi: 10.1186/s12870-021-03057-8.
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.
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.
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.
含有不同辣椒素的辣椒（Capsicum annuum L.）是世界上种植最广泛的香料。然而，物种间极端的基因组多样性是辣椒育种的一个障碍。
本研究报告了Capsicum annuum 'Early Calwonder（不辣，ECW）'和 'Small Fruit（辣，SF）'的从头基因组组装及其注释。总共组装了 2.9Gb 的 ECW 和 SF 基因组序列，占估计基因组大小的 91%以上。两个辣椒基因组的结构和功能注释分别生成了约 35000 个和 35000 个蛋白质编码基因，其中 93%被赋予了可能的功能。新的和公开可用的辣椒基因注释之间的比较显示了共享和特定的基因内容。此外，通过全基因组比对对核苷酸结合和富含亮氨酸重复（NLR）基因进行了全面分析，鉴定了 NLR 拷贝数变异（CNV）的五个显著区域。对这些区域的详细比较表明，这些 CNV 是由种内基因组变异产生的，加速了辣椒中 NLR 的多样化。
我们的分析揭示了一种导致辣椒品系中 NLRs CNV 的进化机制，并为辣椒属的功能基因组学和抗病性分子育种提供了新的基因组资源。
