New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication.
New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication.
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DOI：
10.1186/s13059-017-1341-9
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发表时间：
2017-11-01
期刊：
影响因子：
12.3
通讯作者：
Choi D
中科院分区：
文献类型：
--
作者：
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
转座因子是引起新基因组结构和物种多样性的主要进化力量。转座因子在植物主要抗病基因家族核苷酸结合蛋白和富含亮氨酸重复蛋白（NLRs）扩增中的作用尚未被研究。我们报道了两个高质量的从头基因组（辣椒和辣椒。chinense）和改良的参考基因组（C. annuum）用于辣椒。结果表明，在3号、5号和9号染色体上均检测到了染色体易位。浆果和另外两种胡椒。吉普赛超家族成员athila LTR-逆转录转座子的扩增导致C. baccatum。深入的全基因组基因和重复序列的比较揭示了通过LTR逆转录转座子介导的逆转录复制，NLR的拷贝数大大增加。此外，反转录复制的NLR在被子植物中丰富，并且在大多数情况下是谱系特异性的。本研究揭示了反转录复制在辣椒NLR基因（包括抗病功能基因）大量涌现中起着关键作用。本文的在线版本（doi：10. 1186/s13059 - 017 - 1341 - 9）包含补充材料，可供授权用户使用。
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. 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. Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants. The online version of this article (doi:10.1186/s13059-017-1341-9) contains supplementary material, which is available to authorized users.
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影响因子：
3.7
作者：
Jiang SY;Ramachandran S
通讯作者：
Ramachandran S
DOI：
10.1093/dnares/dsu035
发表时间：
2015-02
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Kim S;Kim MS;Kim YM;Yeom SI;Cheong K;Kim KT;Jeon J;Kim S;Kim DS;Sohn SH;Lee YH;Choi D
通讯作者：
Choi D
DOI：
10.1038/nrg2487
发表时间：
2009-01
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
通讯作者：
--
影响因子：
7.2
作者：
Huang, SW;van der Vossen, EAG;Visser, RGF
通讯作者：
Visser, RGF
影响因子：
11.6
作者：
JIN, YK;BENNETZEN, JL
通讯作者：
BENNETZEN, JL