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

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.

SUBMITTER: Kim S

PROVIDER: S-EPMC5664825 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature

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

Kim Seungill S Park Jieun J Yeom Seon-In SI Kim Yong-Min YM Seo Eunyoung E Kim Ki-Tae KT Kim Myung-Shin MS Lee Je Min JM Cheong Kyeongchae K Shin Ho-Sub HS Kim Saet-Byul SB Han Koeun K Lee Jundae J Park Minkyu M Lee Hyun-Ah HA Lee Hye-Young HY Lee Youngsill Y Oh Soohyun S Lee Joo Hyun JH Choi Eunhye E Choi Eunbi E Lee So Eui SE Jeon Jongbum J Kim Hyunbin H Choi Gobong G Song Hyeunjeong H Lee JunKi J Lee Sang-Choon SC Kwon Jin-Kyung JK Lee Hea-Young HY Koo Namjin N Hong Yunji Y Kim Ryan W RW Kang Won-Hee WH Huh Jin Hoe JH Kang Byoung-Cheorl BC Yang Tae-Jin TJ Lee Yong-Hwan YH Bennetzen Jeffrey L JL Choi Doil D

Genome biology 20171101 1

<h4>Background</h4>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.<h4>Results</h4>We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearran ...[more]

PMID: 29089032

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Project description:Due to its high sensitivity and reproducibility, quantitative real-time PCR (qPCR) is practiced as a useful research tool for targeted gene expression analysis. For qPCR operations, the normalization with suitable reference genes (RGs) is a crucial step that eventually determines the reliability of the obtained results. Although pepper is considered an ideal model plant for the study of non-climacteric fruit development, at present no specific RG have been developed or validated for the qPCR analyses of pepper fruit. Therefore, this study aimed to identify stably expressed genes for their potential use as RGs in pepper fruit studies. Initially, a total of 35 putative RGs were selected by mining the pepper transcriptome data sets derived from the PGP (Pepper Genome Platform) and PGD (Pepper Genome Database). Their expression stabilities were further measured in a set of pepper (Capsicum annuum L. var. 007e) fruit samples, which represented four different fruit developmental stages (IM: Immature; MG: Mature green; B: Break; MR: Mature red) using the qPCR analysis. Then, based on the qPCR results, three different statistical algorithms, namely geNorm, Normfinder, and boxplot, were chosen to evaluate the expression stabilities of these putative RGs. It should be noted that nine genes were proven to be qualified as RGs during pepper fruit development, namely CaREV05 (CA00g79660); CaREV08 (CA06g02180); CaREV09 (CA06g05650); CaREV16 (Capana12g002666); CaREV21 (Capana10g001439); CaREV23 (Capana05g000680); CaREV26 (Capana01g002973); CaREV27 (Capana11g000123); CaREV31 (Capana04g002411); and CaREV33 (Capana08g001826). Further analysis based on geNorm suggested that the application of the two most stably expressed genes (CaREV05 and CaREV08) would provide optimal transcript normalization in the qPCR experiments. Therefore, a new and comprehensive strategy for the identification of optimal RGs was developed. This strategy allowed for the effective normalization of the qPCR analysis of the pepper fruit development at the whole pepper genome level. This study not only explored the optimal RGs specific for studying pepper fruit development, but also introduced a referable strategy of RG mining which could potentially be implicated in other plant species.

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

Publications

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

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