PT  - JOURNAL ARTICLE
AU  - Seungill Kim
AU  - Jieun Park
AU  - Seon-In Yeom
AU  - Yong-Min Kim
AU  - Eunyoung Seo
AU  - Ki-Tae Kim
AU  - Myung-Shin Kim
AU  - Je Min Lee
AU  - Kyeongchae Cheong
AU  - Ho-Sub Shin
AU  - Saet-Byul Kim
AU  - Koeun Han
AU  - Jundae Lee
AU  - Minkyu Park
AU  - Hyun-Ah Lee
AU  - Hye-Young Lee
AU  - Young-sill Lee
AU  - Soohyun Oh
AU  - Joo Hyun Lee
AU  - Eunhye Choi
AU  - Eunbi Choi
AU  - So Eui Lee
AU  - Jongbum Jeon
AU  - Hyunbin Kim
AU  - Gobong Choi
AU  - Hyeunjeong Song
AU  - JunKi Lee
AU  - Sang-Choon Lee
AU  - Jin-Kyung Kwon
AU  - Hea-Young Lee
AU  - Namjin Koo
AU  - Yunji Hong
AU  - Ryan W. Kim
AU  - Won-Hee Kang
AU  - Jin Hoe Huh
AU  - Byoung-Cheorl Kang
AU  - Tae-Jin Yang
AU  - Yong-Hwan Lee
AU  - Jeffrey L. Bennetzen
AU  - Doil Choi
TI  - Multiple reference genome sequences of hot pepper reveal the massive evolution of plant disease resistance genes by retroduplication
AID  - 10.1101/115410
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 115410
4099  - http://biorxiv.org/content/early/2017/03/09/115410.short
4100  - http://biorxiv.org/content/early/2017/03/09/115410.full
AB  - Transposable elements (TEs) provide major evolutionary forces leading to new genome structure and species diversification. However, the role of TEs in the expansion of disease resistance gene families has been unexplored in plants. Here, we report high-quality de novo genomes for two peppers (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum). Dynamic genome rearrangements involving translocations among chromosome 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 exhibited great abundance across the angiosperms, with most cases lineage-specific and thus recent events. Our study revealed that retroduplication has played key roles in the emergence of new disease-resistance genes in plants.