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Kim S, Park J, Yeom SI, Kim YM, Seo E, Kim KT, Kim MS, Lee JM, Cheong K, Shin HS, Kim SB, Han K, Lee J, Park M, Lee HA, Lee HY, Lee Y, Oh S, Lee JH, Choi E, Choi E, Lee SE, Jeon J, Kim H, Choi G, Song H, Lee J, Lee SC, Kwon JK, Lee HY, Koo N, Hong Y, Kim RW, Kang WH, Huh JH, Kang BC, Yang TJ, Lee YH, Bennetzen JL, Choi D. New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication. Genome Biol 2017; 18:210. [PMID: 29089032 DOI: 10.1007/s13580-019-00157-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/19/2019] [Accepted: 10/06/2017] [Indexed: 05/24/2023] Open
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.
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Affiliation(s)
- Seungill Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jieun Park
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Seon-In Yeom
- Department of Agricultural Plant Science, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, South Korea
| | - Yong-Min Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Eunyoung Seo
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Ki-Tae Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Myung-Shin Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Je Min Lee
- Department of Horticultural Science, Kyungpook National University, Daegu, 41566, South Korea
| | - Kyeongchae Cheong
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Ho-Sub Shin
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Saet-Byul Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Koeun Han
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Jundae Lee
- Department of Horticulture, Chonbuk National University, Jeonju, 54896, South Korea
| | - Minkyu Park
- Department of Genetics, University of Georgia, Athens, GA, 30602-7223, USA
| | - Hyun-Ah Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Hye-Young Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Youngsill Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Soohyun Oh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Joo Hyun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Eunhye Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Eunbi Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - So Eui Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Hyunbin Kim
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Gobong Choi
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Hyeunjeong Song
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - JunKi Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jin-Kyung Kwon
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Hea-Young Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Namjin Koo
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Yunji Hong
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Ryan W Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Won-Hee Kang
- Department of Agricultural Plant Science, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, South Korea
| | - Jin Hoe Huh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Yong-Hwan Lee
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | | | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
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