Comparative Sequence Analysis Reveals Extensive Microcolinearity in the Lateral Suppressor Regions of the Tomato, Arabidopsis, and Capsella Genomes

Rossberg, Mathias; Theres, Klaus; Acarkan, Adile; Herrero, Ruben; Schmitt, Thomas; Schumacher, Karin; Schmitz, Gregor; Schmidt, Renate A.

doi:10.2307/3871354

Cited by 13 publications

(12 citation statements)

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“…We found that the region is colinear between A. thaliana and its relatives (Fig. 1), consistent with other studies demonstrating extensive synteny between cruciferous genomes (17)(18)(19)(20). In A. lyrata, A. petraea, A. cebennensis, and B. divaricarpa, the MAM cluster consists of three genes, which we designate MAMa, MAMb, and MAMc.…”

Section: Comparative Sequencing and Phylogenetic Analyses Reveal Complexsupporting

confidence: 90%

Positive selection driving diversification in plant secondary metabolism

Benderoth¹,

Textor

Windsor³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

217

218

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In Arabidopsis thaliana and related plants, glucosinolates are a major component in the blend of secondary metabolites and contribute to resistance against herbivorous insects. Methylthioalkylmalate synthases (MAM) encoded at the MAM gene cluster control an early step in the biosynthesis of glucosinolates and, therefore, are central to the diversification of glucosinolate metabolism. We sequenced bacterial artificial chromosomes containing the MAM cluster from several Arabidopsis relatives, conducted enzyme assays with heterologously expressed MAM genes, and analyzed MAM nucleotide variation patterns. Our results show that gene duplication, neofunctionalization, and positive selection provide the mechanism for biochemical adaptation in plant defense. These processes occur repeatedly in the history of the MAM gene family, indicating their fundamental importance for the evolution of plant metabolic diversity both within and among species.biochemical neofunctionalization ͉ glucosinolate metabolism ͉ methylthioalkylmalate synthase ͉ plant-enemy interactions P lants synthesize an immense number of secondary compounds, so called because their significance for processes of basic growth and development is not immediately evident. More than 200,000 known secondary metabolites provide an increasingly exploited reservoir for the generation of pharmaceutically active agents (1), and many more await discovery. Classic hypotheses that seek to explain this vast metabolic diversity propose a stepwise and reciprocal process of adaptation and counteradaptation between plants and their natural enemies, molded by mutual selection (2). In Arabidopsis thaliana and other crucifers, glucosinolates are a major component in the mélange of secondary metabolites. More than 120 glucosinolates are known, which share a chemical core structure but differ in their amino acid-derived side chain. Glucosinolate composition and quantity varies among and within species (3-5). Upon tissue disruption, myrosinase-catalyzed hydrolysis of glucosinolates generates biologically active compounds, which play an important ecological role in plant defense against herbivorous insects (4, 6-9). However, insects can adapt to glucosinolate profiles or evade deleterious effects from glucosinolate hydrolysis by counteradaptation (9-12). In A. thaliana, a modular genetic system regulates diversity in glucosinolate profiles among accessions and may permit the rapid generation of new glucosinolate combinations in response to challenges imposed by the biotic environment (3). Several genetic loci (3, 9), each present in several alleles, interact epistatically and, together with modifying proteins (7), determine the blend of bioactive products that emerges during glucosinolate hydrolysis (9). One genetic locus central for glucosinolate diversity, the methylthioalkylmalate synthase gene (MAM) cluster, controls an early step in the biosynthesis of aliphatic glucosinolates, the predominant glucosinolate class in A. thaliana. This locus comprises a small family of MAM genes, ...

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Section: Comparative Sequencing and Phylogenetic Analyses Reveal Complexsupporting

confidence: 90%

Positive selection driving diversification in plant secondary metabolism

Benderoth¹,

Textor

Windsor³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

217

218

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“…We found a gene density of one gene every 9 kb, which is similar to previous findings in S. demissum (7.6 kb, [24]) and tomato (8 kb, [36,37]), but lower than A. thaliana (5 kb, [38]) and rice (6 kbp, [39]), and higher than in barley, where only three genes were found in a stretch of 60 kbp genomic DNA [40]. The overall GC content was 37% and 39.5% within the putative gene coding regions.…”

Section: Discussionsupporting

confidence: 91%

“…Similar patterns of interrupted co-linearity on the DNA sequence level were found among cereals [46] and between A. thaliana and rice [47]. In the highly collinear tomato genome [2,5], genomic sequences of 57 kbp and 106 kbp on chromosome 2 [48] and 7 [37], respectively, have been compared to the A. thaliana genomic sequence. These studies revealed syntenic blocks of comparable redundancy and size with respect to the A. thaliana syntenic regions.…”

Section: Discussionmentioning

confidence: 91%

Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments

Ballvora¹,

Jöcker²,

Viehöver

et al. 2007

BMC Genomics

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BackgroundQuantitative phenotypic variation of agronomic characters in crop plants is controlled by environmental and genetic factors (quantitative trait loci = QTL). To understand the molecular basis of such QTL, the identification of the underlying genes is of primary interest and DNA sequence analysis of the genomic regions harboring QTL is a prerequisite for that. QTL mapping in potato (Solanum tuberosum) has identified a region on chromosome V tagged by DNA markers GP21 and GP179, which contains a number of important QTL, among others QTL for resistance to late blight caused by the oomycete Phytophthora infestans and to root cyst nematodes.ResultsTo obtain genomic sequence for the targeted region on chromosome V, two local BAC (bacterial artificial chromosome) contigs were constructed and sequenced, which corresponded to parts of the homologous chromosomes of the diploid, heterozygous genotype P6/210. Two contiguous sequences of 417,445 and 202,781 base pairs were assembled and annotated. Gene-by-gene co-linearity was disrupted by non-allelic insertions of retrotransposon elements, stretches of diverged intergenic sequences, differences in gene content and gene order. The latter was caused by inversion of a 70 kbp genomic fragment. These features were also found in comparison to orthologous sequence contigs from three homeologous chromosomes of Solanum demissum, a wild tuber bearing species. Functional annotation of the sequence identified 48 putative open reading frames (ORF) in one contig and 22 in the other, with an average of one ORF every 9 kbp. Ten ORFs were classified as resistance-gene-like, 11 as F-box-containing genes, 13 as transposable elements and three as transcription factors. Comparing potato to Arabidopsis thaliana annotated proteins revealed five micro-syntenic blocks of three to seven ORFs with A. thaliana chromosomes 1, 3 and 5.ConclusionComparative sequence analysis revealed highly conserved collinear regions that flank regions showing high variability and tandem duplicated genes. Sequence annotation revealed that the majority of the ORFs were members of multiple gene families. Comparing potato to Arabidopsis thaliana annotated proteins suggested fragmented structural conservation between these distantly related plant species.

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“…The results showed that both the group A and group B regions displayed conserved synteny across the sequenced Brassicaceae genomes (Fig. 3), and were consistent with previous studies showing extensive synteny among Brassicaceae species (Rossberg et al, 2001;Boivin et al, 2004;Kuittinen et al, 2004;Franzke et al, 2011;Cheng et al, 2013).…”

Section: Two Ancestral Fmo Gs-ox Loci Contained Tandem Gene Arrays Ansupporting

confidence: 90%

Lineage‐specific evolution of flavin‐containing monooxygenases involved in aliphatic glucosinolate side‐chain modification

Cang

Sheng

Evivie

et al. 2017

J of Sytematics Evolution

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Glucosinolates, a class of specialized metabolites specific to the order Brassicales, have diverse bioactivities that are largely dependent on the structures of their side chains. Flavin‐containing monooxygenases (FMOs) encoded by the FMOGS‐OX genes have been found to catalyze side‐chain modifications during the synthesis of methionine‐derived aliphatic glucosinolates. Seven FMOGS‐OX genes have been identified in Arabidopsis Heynh., but the evolution of these genes in the Brassicaceae, a family including many economically important vegetables, is poorly understood. In this study, the phylogenetic and syntenic relationships of the FMOGS‐OX genes belonging to 12 sequenced Brassicaceae species were analyzed. Our results showed that the FMOGS‐OX genes included two tandem arrays, the FMOGS‐OX2‐4 group (group A) and the FMOGS‐OX5‐7 group (group B). The evolutionary histories of the FMOGS‐OX groups A and B were similar across the Brassicaceae, but two lineage‐specific evolutionary routes developed after these two separate species lineages diverged from Aethionema arabicum (L.) Andrz. ex DC. In the lineage I route, FMOGS‐OX gene copies tended to increase due to frequent tandem duplication events in most species and a whole genome triplication in Camelina sativa (L.) Crantz. In the lineage II route, gene copies decreased due to deletion events. Combining these results with those of previous studies, we speculated that the FMOGS‐OX genes were derived from an ancestral gene with a broad expression distribution and a broad range of substrates, which then underwent subfunctionalization to generate progeny limited in either spatial expression or substrate structure. Furthermore, the absence of FMOGS‐OX5 substrates in some FMOGS‐OX5‐containing species may suggest neofunctionalization of these genes.

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Comparative Sequence Analysis Reveals Extensive Microcolinearity in the Lateral Suppressor Regions of the Tomato, Arabidopsis, and Capsella Genomes

Cited by 13 publications

References 0 publications

Positive selection driving diversification in plant secondary metabolism

Positive selection driving diversification in plant secondary metabolism

Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments

Lineage‐specific evolution of flavin‐containing monooxygenases involved in aliphatic glucosinolate side‐chain modification

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