Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

Kim, Seungill; Park, Minkyu; Yeom, Seon-In; Kim, Yong Min; Lee, Je Min; Lee, Hyun Ah; Seo, Eun-Young; Choi, Jaeyoung; Cheong, Kwang Ho; Kim, Ki Tae; Jung, Ki Won; Lee, Gir-Won; Oh, Sang Keun; Bae, Chungyun; Kim, Saet Byul; Lee, Hye Young; Kim, Shin Young; Kim, Myungshin; Kang, Byoung-Cheorl; Jo, Yeong Deuk; Yang, Hee Young; Jeong, Hee Jin; Kang, Won Hee; Kwon, Jin Kyung; Shin, Chanseok; Lim, Jae Yun; Park, June Hyun; Huh, Jin Hoe; Kim, June-Sik; Kim, Byung Dong; Cohen, Oded; Paran, Ilan; Suh, Mi Chung; Lee, Saet Buyl; Kim, Yeon Ki; Shin, Younhee; Noh, Seung Jae; Park, Jun Hyung; Seo, Young Sam; Kwon, Suk Yoon; Kim, Hyun A; Park, Jeong Mee; Kim, Hyun Jin; Choi, Sang Bong; Bosland, Paul W.; Reeves, Gregory; Jo, Sung Hwan; Lee, Bong Woo; Cho, Hyung-Taeg; Choi, Hyunjung; Lee, Min Soo; Yu, Yeisoo; Choi, Yang Do; Park, Beom Seok; Deynze, Allen Van; Ashrafi, Hamid; Hill, Theresa; Kim, Woo Taek; Pai, Hyun Sook; Ahn, Hee-Kyung; Yeam, Inhwa; Giovannoni, James J.; Rose, Jocelyn K. C.; Sørensen, Iben; Lee, Sang Jik; Kim, Ryan W.; Choi, Ik Young; Choi, Beom Soon; Lim, Jong Sung; Lee, Yong Hwan; Choi, Doil

doi:10.1038/ng.2877

Cited by 892 publications

(1,003 citation statements)

References 67 publications

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“…We found in silico evidence for the ATG8 h-i group in pepper, but this gene was ruled out based on the pepper annotation pipeline. 54 Duplication events are one of the most important mechanisms for the evolution of life. There are different types of duplications, and these duplications might explain the copy number variation of ATG4 and ATG8 in plants.…”

Section: Discussionmentioning

confidence: 99%

Comparative analyses of ubiquitin-like ATG8 and cysteine protease ATG4 autophagy genes in the plant lineage and cross-kingdom processing of ATG8 by ATG4

et al. 2016

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Autophagy is important for degradation and recycling of intracellular components. In a diversity of genera and species, orthologs and paralogs of the yeast Atg4 and Atg8 proteins are crucial in the biogenesis of double-membrane autophagosomes that carry the cellular cargoes to vacuoles and lysosomes. Although many plant genome sequences are available, the ATG4 and ATG8 sequence analysis is limited to some model plants. We identified 28 ATG4 and 116 ATG8 genes from the available 18 different plant genome sequences. Gene structures and protein domain sequences of ATG4 and ATG8 are conserved in plant lineages. Phylogenetic analyses classified ATG8s into 3 subgroups suggesting divergence from the common ancestor. The ATG8 expansion in plants might be attributed to whole genome duplication, segmental and dispersed duplication, and purifying selection. Our results revealed that the yeast Atg4 processes Arabidopsis ATG8 but not human LC3A (HsLC3A). In contrast, HsATG4B can process yeast and plant ATG8s in vitro but yeast and plant ATG4s cannot process HsLC3A. Interestingly, in Nicotiana benthamiana plants the yeast Atg8 is processed compared to HsLC3A. However, HsLC3A is processed when coexpressed with HsATG4B in plants. Molecular modeling indicates that lack of processing of HsLC3A by plant and yeast ATG4 is not due to lack of interaction with HsLC3A. Our in-depth analyses of ATG4 and ATG8 in the plant lineage combined with results of cross-kingdom ATG8 processing by ATG4 further support the evolutionarily conserved maturation of ATG8. Broad ATG8 processing by HsATG4B and lack of processing of HsLC3A by yeast and plant ATG4s suggest that the cross-kingdom ATG8 processing is determined by ATG8 sequence rather than ATG4.

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Section: Discussionmentioning

confidence: 99%

Comparative analyses of ubiquitin-like ATG8 and cysteine protease ATG4 autophagy genes in the plant lineage and cross-kingdom processing of ATG8 by ATG4

et al. 2016

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“…In addition, members of the Solanaceae serve as model systems for investigating fundamental processes involved in plant growth and development, including the ripening of fleshy fruit (tomato), tuber formation (potato), pollination and petal senescence (petunia), plant pathogen and pest interactions (tomato, potato, and Nicotiana spp), and the biosynthesis of specialized metabolites (tomato, pepper, Nicotiana, Hyocyamus, Datura, and Atropa spp). The development of genomics tools, including genome sequences and transcriptome data sets for several of these model species, is facilitating characterization of these biological processes (Xu et al, 2011;Ashrafi et al, 2012;Bombarely et al, 2012;Tomato Genome Consortium, 2012;Kim et al, 2014;Qin et al, 2014). In this study, a deep transcriptome of A. belladonna, a member of the Solanaceae family often used for investigating tropane alkaloid biosynthesis (Suzuki et al, 1999a(Suzuki et al, , 1999bRothe et al, 2003;Richter et al, 2005), was generated from diverse tissues, facilitating in silico quantitative analyses of gene expression (Tables 1 to 3).…”

Section: Discussionmentioning

confidence: 99%

A Root-Expressed l-Phenylalanine:4-Hydroxyphenylpyruvate Aminotransferase Is Required for Tropane Alkaloid Biosynthesis in Atropa belladonna

et al. 2014

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The tropane alkaloids, hyoscyamine and scopolamine, are medicinal compounds that are the active components of several therapeutics. Hyoscyamine and scopolamine are synthesized in the roots of specific genera of the Solanaceae in a multistep pathway that is only partially elucidated. To facilitate greater understanding of tropane alkaloid biosynthesis, a de novo transcriptome assembly was developed for Deadly Nightshade (Atropa belladonna). Littorine is a key intermediate in hyoscyamine and scopolamine biosynthesis that is produced by the condensation of tropine and phenyllactic acid. Phenyllactic acid is derived from phenylalanine via its transamination to phenylpyruvate, and mining of the transcriptome identified a phylogenetically distinct aromatic amino acid aminotransferase (ArAT), designated Ab-ArAT4, that is coexpressed with known tropane alkaloid biosynthesis genes in the roots of A. belladonna. Silencing of Ab-ArAT4 disrupted synthesis of hyoscyamine and scopolamine through reduction of phenyllactic acid levels. Recombinant Ab-ArAT4 preferentially catalyzes the first step in phenyllactic acid synthesis, the transamination of phenylalanine to phenylpyruvate. However, rather than utilizing the typical keto-acid cosubstrates, 2-oxoglutarate, pyruvate, and oxaloacetate, Ab-ArAT4 possesses strong substrate preference and highest activity with the aromatic keto-acid, 4-hydroxyphenylpyruvate. Thus, Ab-ArAT4 operates at the interface between primary and specialized metabolism, contributing to both tropane alkaloid biosynthesis and the direct conversion of phenylalanine to tyrosine.

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“…Because the divergence of these angiosperm families occurred in the Paleogene and the divergence of their higher level taxonomies all occurred in the Cretaceous ( Fig. 1; Lavin et al, 2005;Stefanovic et al, 2009;D'Hont et al, 2012;Zhang et al, 2012;Peng et al, 2013;Yang et al, 2013;Kim et al, 2014;Wang et al, 2014;Zeng et al, 2014), the observed intensive expansion of NBS genes in angiosperms more likely coincided with the CretaceousPaleogene (K-P) boundary (;66 MYA). This finding suggests that different lineages of angiosperms either underwent a process to reinforce resistance or experienced increased selective pressure from environmental pathogens during this period.…”

Section: Differential Expansion During Angiosperm Evolution Shaped Tnmentioning

confidence: 99%

“…The Solanaceae nTNL genes formed 55 monophyletic lineages with nTNL genes from S. indicum (two RNL lineages The phylogenetic relationship was constructed according to the APG III system (Bremer et al, 2009). The divergence times at different nodes of angiosperms were combined from previous studies (Lavin et al, 2005;Stefanovic et al, 2009;D'Hont et al, 2012;Zhang et al, 2012;Peng et al, 2013;Yang et al, 2013;Kim et al, 2014;Wang et al, 2014;Zeng et al, 2014). The total number of NBS genes and their classification in each species are shown.…”

Section: Phylogenetic Analysis Of Nbs Genes In Major Angiosperm Cladesmentioning

confidence: 99%

Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns

et al. 2016

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Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes make up the largest plant disease resistance gene family (R genes), with hundreds of copies occurring in individual angiosperm genomes. However, the expansion history of NBS-LRR genes during angiosperm evolution is largely unknown. By identifying more than 6,000 NBS-LRR genes in 22 representative angiosperms and reconstructing their phylogenies, we present a potential framework of NBS-LRR gene evolution in the angiosperm. Three anciently diverged NBS-LRR classes (TNLs, CNLs, and RNLs) were distinguished with unique exon-intron structures and DNA motif sequences. A total of seven ancient TNL, 14 CNL, and two RNL lineages were discovered in the ancestral angiosperm, from which all current NBS-LRR gene repertoires were evolved. A pattern of gradual expansion during the first 100 million years of evolution of the angiosperm clade was observed for CNLs. TNL numbers remained stable during this period but were eventually deleted in three divergent angiosperm lineages. We inferred that an intense expansion of both TNL and CNL genes started from the Cretaceous-Paleogene boundary. Because dramatic environmental changes and an explosion in fungal diversity occurred during this period, the observed expansions of R genes probably reflect convergent adaptive responses of various angiosperm families. An ancient whole-genome duplication event that occurred in an angiosperm ancestor resulted in two RNL lineages, which were conservatively evolved and acted as scaffold proteins for defense signal transduction. Overall, the reconstructed framework of angiosperm NBS-LRR gene evolution in this study may serve as a fundamental reference for better understanding angiosperm NBS-LRR genes.

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Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

Cited by 892 publications

References 67 publications

Comparative analyses of ubiquitin-like ATG8 and cysteine protease ATG4 autophagy genes in the plant lineage and cross-kingdom processing of ATG8 by ATG4

Comparative analyses of ubiquitin-like ATG8 and cysteine protease ATG4 autophagy genes in the plant lineage and cross-kingdom processing of ATG8 by ATG4

A Root-Expressed l-Phenylalanine:4-Hydroxyphenylpyruvate Aminotransferase Is Required for Tropane Alkaloid Biosynthesis in Atropa belladonna

Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns

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