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Genome Biol. 2017 Nov 1;18(1):210. doi: 10.1186/s13059-017-1341-9.

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

Author information

1
Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
2
Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea.
3
Department of Agricultural Plant Science, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, South Korea.
4
Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea.
5
Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea.
6
Department of Horticultural Science, Kyungpook National University, Daegu, 41566, South Korea.
7
Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea.
8
Department of Horticulture, Chonbuk National University, Jeonju, 54896, South Korea.
9
Department of Genetics, University of Georgia, Athens, GA, 30602-7223, USA.
10
Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea. doil@snu.ac.kr.

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.

KEYWORDS:

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

PMID:
29089032
PMCID:
PMC5664825
DOI:
10.1186/s13059-017-1341-9
[Indexed for MEDLINE]
Free PMC Article

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