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

作者：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

来源：Genome Biology, 2017, 18(1): 210.

DOI：10.1186/s13059-017-1341-9

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

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.

• 出版日期2017-11-1