Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity
- Department of Biochemistry and Molecular Biology, Michigan State University, United States
- Department of Plant Biology, Michigan State University, United States
- University of Wisconsin, United States
- Division of Biological Sciences, University of Missouri, United States
- MSU-DOE Plant Research Laboratory, Michigan State University, United States
- Department of Computational Mathematics, Science, and Engineering, Michigan State University, United States
Figures
Figure 1
Primary metabolites are biosynthetic precursors of tomato trichome acylsugars.
In cultivated tomatoes, the trichome acylsucroses are synthesized by four Sl-ASATs using the primary metabolites – sucrose and different types of acyl-CoAs – as substrates. In this study we provide …
Figure 2 with 1 supplement
Mapping of a genetic locus related to acylsugar variations in tomato interspecific introgression lines.
(A) Electrospray ionization negative (ESI-) mode, base-peak intensity (BPI) LC/MS chromatogram of trichome metabolites from cultivated tomato S. lycopersicum M82 and introgression line IL7-4. The …
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Figure 2—source data 1
Data used to make Figure 2B.
Peak area percentage of seven major trichome acylsugars in M82 and IL7-4.
- https://cdn.elifesciences.org/articles/56717/elife-56717-fig2-data1-v2.xlsx
Figure 2—figure supplement 1
Expression profiles of tomato ACS, ECH, and BAHD acyltransferase family genes used for phylogenetic analysis in this study.
Each column represents one transcriptomic profiling dataset generated by RNA-seq analysis using samples from the cultivated tomato (S. lycopersicum). A total of 372 RNA-seq datasets were used for …
Figure 3 with 2 supplements
CRISPR/Cas9-mediated gene knockout of tomato Sl-AACS1 or Sl-AECH1 eliminates detectable medium chain containing acylsugars.
(A) Combined LC/MS extracted ion chromatograms of trichome metabolites from CRISPR mutants sl-aacs1 and sl-aech1. The medium chain acylsugars that are not detected in the two mutants are denoted by …
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Figure 3—source data 1
Data used to make Figure 3B.
Quantification of seven major trichome acylsugars in the CRISPR mutants sl-aacs1 and sl-aech1, as well as the parent M82.
- https://cdn.elifesciences.org/articles/56717/elife-56717-fig3-data1-v2.xlsx
Figure 3—figure supplement 1
CRISPR-Cas9-mediated gene knockouts in cultivated tomato S. lycopersicum.
The gRNAs targeting Sl-AACS1 (A), Sl-AECH1(B), and Solyc07g043660 (C) in cultivated tomato are highlighted with red lines and text. Two pairs of gRNAs were designed that target Sl-AECH1, which were …
Figure 3—figure supplement 2
The syntenic region of cultivated tomato S. lycopersicum chromosome 7 and 12 harboring the acylsugar and steroidal glycoalkaloid gene clusters.
The gene models are represented by rectangles, with pseudogenes labeled with dotted lines. The lines linking the gene models of the two chromosomes denote putative orthologous genes in the synteny. …
Figure 4 with 2 supplements
Functional analysis of Sl-AACS1 and Sl-AECH1 in N. benthamiana and recombinant Sl-AACS1 enzyme analysis.
(A) Confocal images of co-expression analysis in tobacco leaf epidermal cells using C-terminal CFP-tagged either Sl-AACS1 or Sl-AECH1 and the mitochondrial marker MT-RFP. Arrowheads point to …
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Figure 4—source data 1
Data used to make Figure 4B.
Aliphatic fatty acids of different chain lengths were used as the substrates to test Sl-AACS1 acyl-CoA synthetase activity.
- https://cdn.elifesciences.org/articles/56717/elife-56717-fig4-data1-v2.xlsx
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Figure 4—source data 2
Data used to make Figure 4D and Figure 4—figure supplement 1C.
N. benthamiana leaf membrane lipid acyl chain composition.
- https://cdn.elifesciences.org/articles/56717/elife-56717-fig4-data2-v2.xlsx
Figure 4—figure supplement 1
Characterization of cluster genes using leaf transient expression: protein subcellular targeting and impacts on lipid metabolism.
(A) Confocal images of co-expression analysis in N. tabacum leaf epidermal cells using C-terminal CFP-tagged Solyc07g043660 and the mitochondrial marker MT-RFP. Arrowheads point to mitochondria that …
Figure 4—figure supplement 2
The closest homologs of Sl-AECH1 from other Solanum species generate medium chain lipids when transiently expressed in N. benthamiana.
(A) ESI- mode, LC/MS extracted ion chromatograms of two SQDGs with C12 as peaks diagnostic of lipids containing medium chain fatty acids. (B) Mass spectra of two SQDGs contain C12 acyl chain. …
Figure 5 with 2 supplements
AACS1 and AECH1 are evolutionarily conserved in Solanum plants.
(A) A conserved syntenic genomic region containing AACS1 and AECH1 was found in three selected Solanum species. Nodes representing estimated dates since the last common ancestors (Särkinen et al., …
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Figure 5—source data 1
Data used to make Figure 5C and D.
Silencing Sq-AACS1 or Sq-AECH1 in S. quitoense using VIGS leads to reduction of total acylsugars.
- https://cdn.elifesciences.org/articles/56717/elife-56717-fig5-data1-v2.xlsx
Figure 5—figure supplement 1
Stable Sp-AACS1 transformation of the M82 CRISPR mutant sl-aacs1 restores C12 containing acylsugars.
(A) ESI- mode, LC/MS extracted ion chromatograms are shown for seven major acylsugar peaks extracted from trichome of S. lycopersicum M82, sl-aacs1, and two independent T0 generation suppressed sl-aa…
Figure 5—figure supplement 2
Functional analysis of AACS1 and AECH1 in S. pennellii and S. quitoense via CRISPR-Cas9 system and VIGS, respectively.
The design of gRNAs targeting wild tomato S. pennellii LA0716 Sp-AACS1 (A), Sopen07g023250 (B), and Sp-AECH1 (C) is highlighted with red lines and text. The transgenic T0 generation carrying …
Figure 6 with 8 supplements
Evolution of the acylsugar gene cluster is associated with acylsugar acyl chain diversity across the Solanaceae family.
(A) The acylsugar gene cluster syntenic regions of 11 Solanaceae species and two outgroup species Ipomea trifida (Convolvulaceae) and Coffea canephora (Rubiaceae). This is a simplified version …
Figure 6—figure supplement 1
Syntenic regions containing the acylsugar gene cluster.
The species name and chromosome/scaffold identifier are indicated with S. lycopersicum in blue font. Rectangle: protein-coding gene (solid line) or pseudogene (dotted line) colored according to the …
Figure 6—figure supplement 2
Analysis of the evolutionary history of the BAHD acyltransferases in the syntenic regions in different Solanaceae species.
(A) Phylogenetic tree of BAHD acyltransferases homologous to Solyc07g043670. Genes colored with green and labeled with green rectangles are from the syntenic regions of Solanaceae species shown in …
Figure 6—figure supplement 3
Analysis of the evolutionary history of the ECH genes in the syntenic regions in different Solanaceae species.
(A) Phylogenetic tree of ECH genes homologous to Sl-AECH1. Genes colored with orange and labeled with orange rectangles are from the syntenic regions of Solanaceae species shown in panel (B). Genes …
Figure 6—figure supplement 4
Analysis of the evolutionary history of the ACS genes in the syntenic regions in different Solanaceae species.
(A) Phylogenetic tree of ACS genes homologous to Sl-AACS1. Genes colored with blue and labeled with blue rectangles are from the syntenic regions of Solanaceae species shown in panel (B). Genes …
Figure 6—figure supplement 5
Phylogenetic analysis of the BAHD acyltransferase.
The BAHD acyltransferase pseudogene (Cc-BAHD-pseu) in the corresponding syntenic region (Figure 6) of Coffea canephora is one of the closest Coffea sequences sister to the ASAT clade. It indicates …
Figure 6—figure supplement 6
Additional evolutionary analysis of ACS genes in the syntenic regions to understand when the segmental duplication event happened.
(A) Sl-AACS1 homologs obtained from Salpiglossis sinuate trichome transcriptome dataset (Moghe et al., 2017) were added for additional phylogenetic analysis. Genes colored with blue are from the …
Figure 6—figure supplement 7
Ancestral trait state reconstruction analysis.
Four traits were inferred for their ancestral states using the maximum likelihood model Mk1 in Mesquite 3.6. They are the presence of medium chain acylsugars, presence of ACS in the synteny, …
Figure 6—figure supplement 8
Phylogenetic distribution of acylsugar acyl chains with different lengths across the Solanaceae family.
(A) The collated results of acylsugar acyl chain distribution across different Solanaceae species. Red rectangles indicate detectable acyl chains in the acylsugars produced in the tested species and …
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Solanum lycopersicum M82) | Sl-AACS1 | This paper | GeneBank: MT078737 | Characterized and named in the results |
| Gene (Solanum lycopersicum M82) | Sl-AECH1 | This paper | GeneBank: MT078736 | Characterized and named in the results |
| Gene (Solanum pennellii LA0716) | Sp-AACS1 | This paper | GeneBank: MT078735 | Characterized and named in the results |
| Gene (Solanum pennellii LA0716) | Sp-AECH1 | This paper | GeneBank: MT078734 | Characterized and named in the results |
| Gene (Solanum quitoense) | Sq-AACS1 | This paper | GeneBank: MT078732 | Characterized and named in the results |
| Gene (Solanum quitoense) | Sq-AECH1 | This paper | GeneBank: MT078731 | Characterized and named in the results |
| Gene (Solanum quitoense) | Sq_c35719 | This paper | GeneBank: MT078733 | Characterized and named in the results |
| Software, algorithm | Trimmomatic | http://www.usadellab.org/cms/index.php?page=trimmomatic | RRID:SCR_011848 | |
| Software, algorithm | TopHat | http://ccb.jhu.edu/software/tophat/index.shtml | RRID:SCR_013035 | |
| Software, algorithm | Cufflinks | http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/ | RRID:SCR_014597 | |
| Software, algorithm | MCScanX-transposed | http://chibba.pgml.uga.edu/mcscan2/transposed/ | ||
| Software, algorithm | RAxML | https://github.com/stamatak/standard-RAxML | RRID:SCR_006086 | |
| Software, algorithm | Mesquite | https://www.mesquiteproject.org/ | RRID:SCR_017994 |
Additional files
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Supplementary file 1
Co-expression analysis of tomato genes from ACS, ECH, and BAHD acyltransferase families used for phylogenetic analysis in this study.
The values of Pearson’s correlation coefficient of the expression profiles between any of the two genes were shown in the table. The coefficient values were generated using the FPKM values of these genes in the 372 RNA-seq samples as shown in Figure 2—figure supplement 1. The orange box highlights a group of co-expressed genes involved in acylsugar biosynthesis, such as Sl-ASATs, Sl-AACS1, and Sl-AECH1. The purple box points out another group of co-expressed genes that are root hair specific.
- https://cdn.elifesciences.org/articles/56717/elife-56717-supp1-v2.xlsx
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Supplementary file 2
Gene expression levels of all analyzed transcripts in Solanum pennellii LA0716.
logFC: log2 fold change in stem trichomes versus shaved stems. logCPM: log (counts per million) in trichomes versus shaved stems. The F and Q-value test the significance of differential expression via a quasi- general linear model. The values noted in the sample columns represent the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) analyzed via Cufflinks.
- https://cdn.elifesciences.org/articles/56717/elife-56717-supp2-v2.xlsx
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Supplementary file 3
Synthesized gene fragments and primers used in this study.
- https://cdn.elifesciences.org/articles/56717/elife-56717-supp3-v2.xlsx
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Supplementary file 4
The date used to generate the synteny figure shown in Figure 6—figure supplement 1.
- https://cdn.elifesciences.org/articles/56717/elife-56717-supp4-v2.zip
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Supplementary file 5
The sequence alignment documents used to generate the phylogenetic trees for Figure 6—figure supplements 2, 3, 4, 5 and 6.
- https://cdn.elifesciences.org/articles/56717/elife-56717-supp5-v2.zip
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Transparent reporting form
- https://cdn.elifesciences.org/articles/56717/elife-56717-transrepform-v2.docx
