RT Journal Article
SR Electronic
T1 Multiple reference genome sequences of hot pepper reveal the massive evolution of plant disease resistance genes by retroduplication
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 115410
DO 10.1101/115410
A1 Seungill Kim
A1 Jieun Park
A1 Seon-In Yeom
A1 Yong-Min Kim
A1 Eunyoung Seo
A1 Ki-Tae Kim
A1 Myung-Shin Kim
A1 Je Min Lee
A1 Kyeongchae Cheong
A1 Ho-Sub Shin
A1 Saet-Byul Kim
A1 Koeun Han
A1 Jundae Lee
A1 Minkyu Park
A1 Hyun-Ah Lee
A1 Hye-Young Lee
A1 Young-sill Lee
A1 Soohyun Oh
A1 Joo Hyun Lee
A1 Eunhye Choi
A1 Eunbi Choi
A1 So Eui Lee
A1 Jongbum Jeon
A1 Hyunbin Kim
A1 Gobong Choi
A1 Hyeunjeong Song
A1 JunKi Lee
A1 Sang-Choon Lee
A1 Jin-Kyung Kwon
A1 Hea-Young Lee
A1 Namjin Koo
A1 Yunji Hong
A1 Ryan W. Kim
A1 Won-Hee Kang
A1 Jin Hoe Huh
A1 Byoung-Cheorl Kang
A1 Tae-Jin Yang
A1 Yong-Hwan Lee
A1 Jeffrey L. Bennetzen
A1 Doil Choi
YR 2017
UL http://biorxiv.org/content/early/2017/03/09/115410.abstract
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.