New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication

Seungill Kim, Jieun Park, Seon In Yeom, Yong Min Kim, Eunyoung Seo, Ki Tae Kim, Myung Shin Kim, Je Min Lee, Kyeongchae Cheong, Ho Sub Shin, Saet Byul Kim, Koeun Han, Jundae Lee, Minkyu Park, Hyun Ah Lee, Hye Young Lee, Youngsill Lee, Soohyun Oh, Joo Hyun Lee, Eunhye ChoiEunbi Choi, So Eui Lee, Jongbum Jeon, Hyunbin Kim, Gobong Choi, Hyeunjeong Song, Jun Ki Lee, Sang Choon Lee, Jin Kyung Kwon, Hea Young Lee, Namjin Koo, Yunji Hong, Ryan W. Kim, Won Hee Kang, Jin Hoe Huh, Byoung Cheorl Kang, Tae Jin Yang, Yong Hwan Lee, Jeffrey L. Bennetzen, Doil Choi

Research output: Contribution to journalArticlepeer-review

213 Scopus citations


Background: Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants. Results: We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific. Conclusions: Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.

Original languageEnglish
Article number210
JournalGenome Biology
Issue number1
StatePublished - 1 Nov 2017


  • Disease-resistance gene
  • Genome evolution
  • LTR-retrotransposon
  • NLR
  • Retroduplication


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