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

Cited 49 time in Web of Science Cited 53 time in Scopus
Authors
Kim, Seungill; Park, Jieun; Yeom, Seon-In; Kim, Yong-Min; Seo, Eunyoung; Kim, Ki-Tae; Kim, Myung-Shin; Lee, Je Min; Cheong, Kyeongchae; Shin, Ho-Sub; Kim, Saet-Byul; Han, Koeun; Lee, Jundae; Park, Minkyu; Lee, Hyun-Ah; Lee, Hye-Young; Lee, Youngsill; Oh, Soohyun; Lee, Joo Hyun; Choi, Eunhye; Choi, Eunbi; Lee, So Eui; Jeon, Jongbum; Kim, Hyunbin; Choi, Gobong; Song, Hyeunjeong; Lee, JunKi; Lee, Sang-Choon; Kwon, Jin-Kyung; Lee, Hea-Young; Koo, Namjin; Hong, Yunji; Kim, Ryan W.; Kang, Won-Hee; Huh, Jin Hoe; Kang, Byoung-Cheorl; Yang, Tae-Jin; Lee, Yong-Hwan; Bennetzen, Jeffrey L.; Choi, Doil
Issue Date
2017-11-01
Publisher
BioMed Central
Citation
Genome Biology, 18(1):210
Keywords
NLRRetroduplicationLTR-retrotransposonDisease-resistance geneGenome evolution
Abstract
Abstract

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.
ISSN
1474-760X
Language
English
URI
http://hdl.handle.net/10371/138337
DOI
https://doi.org/10.1186/s13059-017-1341-9
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College of Agriculture and Life Sciences (농업생명과학대학)Dept. of Plant Science (식물생산과학부)Journal Papers (저널논문_식물생산과학부)
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