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Comparative analysis of de novo genomes reveals dynamic intra-species divergence of NLRs in pepper

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Authors
Kim, Myung-Shin; Chae, Geun Young; Oh, Soohyun; Kim, Jihyun; Mang, Hyunggon; Kim, Seungill; Choi, Doil
Issue Date
2021-05-31
Publisher
BMC
Citation
BMC Plant Biology. 2021 May 31;21(1):247
Keywords
Hot pepperGenomeDisease resistanceNLR evolutionCopy number variation
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.
ISSN
1471-2229
Language
English
URI
https://hdl.handle.net/10371/174779
DOI
https://doi.org/10.1186/s12870-021-03057-8
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College of Agriculture and Life Sciences (농업생명과학대학)Dept. of Agriculture, Forestry and Bioresources (농림생물자원학부)Journal Papers (저널논문_농림생물자원학부)
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