Plants rely on transcriptional dynamics to respond to multiple climatic fluctuations and contexts... more Plants rely on transcriptional dynamics to respond to multiple climatic fluctuations and contexts in nature. We analyzed the genome-wide gene expression patterns of rice (Oryza sativa) growing in rainfed and irrigated fields during two distinct tropical seasons and determined simple linear models that relate transcriptomic variation to climatic fluctuations. These models combine multiple environmental parameters to account for patterns of expression in the field of co-expressed gene clusters. We examined the similarities of our environmental models between tropical and temperate field conditions, using previously published data. We found that field type and macroclimate had broad impacts on transcriptional responses to environmental fluctuations, especially for genes involved in photosynthesis and development. Nevertheless, variation in solar radiation and temperature at the timescale of hours had reproducible effects across environmental contexts. These results provide a basis for ...
Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the M... more Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This anal...
The purpose of the study &amp... more The purpose of the study "Phylogeographic relationships among Asian eggplants and new perspectives on eggplant domestication" by Meyer et al. (2012) was to use new and expanded accession sets coupled with molecular data to evaluate possible scenarios of eggplant domestication with as little influence as possible from any previously published nomenclatural scheme, and taking into consideration multiple sources of evidence regarding the history of eggplant in Asia. Samuels (2013) disfavored this system and in his Letter to the Editor attempted to re-evaluate the results according to his system. However, Samuels appears to have misread Meyer et al. and also makes several claims without the support of evidence. We stand by the results of Meyer et al., which are in agreement with the recent and much needed new taxonomic treatment for wild relatives of eggplant.
Fruit of the cultivated eggplant species Solanum melongena, Solanum aethiopicum, and Solanum macr... more Fruit of the cultivated eggplant species Solanum melongena, Solanum aethiopicum, and Solanum macrocarpon, and wild relatives including Solanum anguivi and Solanum incanum, have a high content of hydroxycinnamic acid conjugates with potential human health benefits. Typically, caffeoylquinic acid esters predominate, and in particular 5-O-(E)-caffeoylquinic acid. By contrast, fruit from accession PI 319855 in the USDA eggplant core collection, unambiguously identified as Solanum viarum by morphological characters, were found to include several major, closely related hydroxycinnamic acid conjugates with much longer C18-HPLC retention times than those of 5-O-(E)-caffeoylquinic acid and other monocaffeoylquinic acid isomers. Four of these compounds were isolated from methanolic extracts of lyophilized fruit tissues by C18-HPLC, and structurally elucidated using (1)H and (13)C NMR techniques and HR-TOF-MS. Isomeric compounds 1 and 2 are composed of 5-O-(E)-caffeoylquinic acid with a malonyl group on the 3- or 4-hydroxyl of quinic acid, respectively, plus a 6-O-sinapoylglucose group 1-O-β-D linked with the 4-hydroxyl on the phenyl ring of the caffeoyl moiety (1β,4β-dihydroxy-3β-carboxyacetoxy- and 1β,3β-dihydroxy-4β-carboxyacetoxy-5α-[[3-[4-[1β-(6-O-(E)-sinapoyl-β-D-glucopyranosyl)oxy]-3-hydroxyphenyl]-(E)-1-oxo-2-propenyl]oxy]cyclohexanecarboxylic acid). Compound 3 has the same structure as 1 and 2 without malonation of quinic acid (1β,3β,4β-trihydroxy-5α-[[3-[4-[1β-(6-O-(E)-sinapoyl-β-d-glucopyranosyl)oxy]-3-hydroxyphenyl]-(E)-1-oxo-2-propenyl]oxy]cyclohexanecarboxylic acid). Compound 4 differs from 3 by methylation of the carboxyl group on quinic acid (methyl 1β,3β,4β-trihydroxy-5α-[[3-[4-[1β-(6-O-(E)-sinapoyl-β-D-glucopyranosyl)oxy]-3-hydroxyphenyl]-(E)-1-oxo-2-propenyl]oxy]cyclohexanecarboxylate). Some features of these four new compounds, such as malonation and the specific linkages between caffeoyl, glucosyl, and sinapoyl moieties, are common in acylated and glycosylated phenylpropanoids, but have not previously been reported in complex derivatives of 5-O-(E)-caffeoylquinic acid.
Domestication is a good model for the study of evolutionary processes because of the recent evolu... more Domestication is a good model for the study of evolutionary processes because of the recent evolution of crop species (<12,000 years ago), the key role of selection in their origins, and good archaeological and historical data on their spread and diversification. Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops. Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations that occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations and that are associated with geographical adaptation of crop species.
Domesticated food crops are derived from a phylogenetically diverse assemblage of wild ancestors ... more Domesticated food crops are derived from a phylogenetically diverse assemblage of wild ancestors through artificial selection for different traits. Our understanding of domestication, however, is based upon a subset of well-studied ‘model’ crops, many of them from the Poaceae family. Here, we investigate domestication traits and theories using a broader range of crops. We reviewed domestication information (e.g. center of domestication, plant traits, wild ancestors, domestication dates, domestication traits, early and current uses) for 203 major and minor food crops. Compiled data were used to test classic and contemporary theories in crop domestication. Many typical features of domestication associated with model crops, including changes in ploidy level, loss of shattering, multiple origins, and domestication outside the native range, are less common within this broader dataset. In addition, there are strong spatial and temporal trends in our dataset. The overall time required to domesticate a species has decreased since the earliest domestication events. The frequencies of some domestication syndrome traits (e.g. nonshattering) have decreased over time, while others (e.g. changes to secondary metabolites) have increased. We discuss the influences of the ecological, evolutionary, cultural and technological factors that make domestication a dynamic and ongoing process.
The ways in which geographically separate communities use crops reflect the agricultural and cult... more The ways in which geographically separate communities use crops reflect the agricultural and cultural influences on each community. The eggplant (Solanum melongena L.; Solanaceae), which was domesticated in South and Southeast Asia, has long been used in a variety of medicinal and culinary preparations across many different Asian ethnolinguistic groups. Here, we report the total uses for eggplant and sixteen related species in three regions, India, southern China, and Malesia, and conduct a comparative analysis in order to form hypotheses about how influences on plant use in one region could have affected use and evolutionary trajectories in other regions. Results from literature review and 101 interviews show a total of 77 medicinal attributes for eggplant, with few similar attributes mentioned in different regions, leading us to hypothesize that largely pristine (i.e., without influence from other regions) development of uses, which could serve as selection pressures, occurred for eggplant in India, southern China, and Malesia. Results also show that many Solanum species have been fluidly adopted into uses developed for other species in a single region.
Cross-species comparative genomics approaches have been
employed to map and clone many important ... more Cross-species comparative genomics approaches have been employed to map and clone many important disease resistance (R) genes from Solanum species—especially wild relatives of potato and tomato. These efforts will increase with the recent release of potato genome sequence and the impending release of tomato genome sequence. Most R genes belong to the prominent nucleotide binding site-leucine rich repeat (NBS-LRR) class and conserved NBS-LRR protein motifs enable survey of the R gene space of a plant genome by generation of resistance gene analogs (RGA), polymerase chain reaction fragments derived from R genes. We generated a collection of 97 RGA from the disease-resistant wild potato S. bulbocastanum, complementing smaller collections from other Solanum species. To further comparative genomics approaches, we combined all known Solanum RGA and cloned solanaceous NBS-LRR gene sequences, nearly 800 sequences in total, into a single meta-analysis. We defined R gene diversity bins that reflect both evolutionary relationships and DNA cross-hybridization results. The resulting framework is amendable and expandable, providing the research community with a common vocabulary for present and future study of R gene lineages. Through a series of sequence and hybridization experiments, we demonstrate that all tested R gene lineages are of ancient origin, are shared between Solanum species, and can be successfully accessed via comparative genomics approaches.
The domestication history of eggplant (Solanum melongena L.) has long been debated, with studies ... more The domestication history of eggplant (Solanum melongena L.) has long been debated, with studies unable to narrow down where domestication occurred within a broad region of tropical Asia. The most commonly hypothesized region is India, however China has an equally old written record of eggplant use dating ca. 2000 years before present. Both regions have a high diversity of landraces and populations of putatively wild eggplant: Solanum incanum L. in India and Solanum undatum Lam. in SE Asia. An additional complication is that there is taxonomic confusion regarding the two candidate progenitors. Here, we synthesize historic, morphologic, and molecular data (nrITS sequence and AFLP) to interpret the phylogeographic relationships among candidate progenitors and Asian eggplant landraces in order to test theories of domestication. A minimum of two domestication events is supported: one in India and one in southern China/SE Asia. Results also support separate domestication of S. melongena subsp. ovigerum, a group of morphologically distinct eggplants found in SE Asia, and suggest Asian S. incanum and S. undatum may not be genetically distinct. Routes of the spread of eggplant cultivation throughout Asia are proposed, and evolutionary relationships among allied species are discussed.
This study presents a strategy based on repeatable reversed-phase LC-TOF-MS methods and statistic... more This study presents a strategy based on repeatable reversed-phase LC-TOF-MS methods and statistical tools, including untargeted PCA and targeted PLS/OPLS-DA models, to analyze 31 accessions representing 24 species in the eggplant genus Solanum (Solanaceae), including eight species whose metabolic profiles were studied for the first time. Sixty-two Solanum metabolites were identified after detailed analysis of UV absorbance spectra, mass spectral fragmentation patterns, NMR spectra, and/or co-injection experiments with authentic standards. Among these were two new 5-O-caffeoylquinic acid derivatives that were identified by analyzing their MS/MS fragmentation. Based on these results, a Solanum metabolic database (SMD) and a detailed biosynthetic pathway of Solanum metabolites were created. Results of analyses identified seven marker metabolites that distinguish four Solanum sections, and revealed species-specific chemical patterns. Combining LC-MS data with multivariate statistical analysis was proven effective in studying the metabolic network within the large genus Solanum, allowing for integration of complicated chemistry, morphology, and evolutionary relationships.
Eggplant and related Solanum species contain
abundant caffeoylquinic acid (CQA) derivatives. Frui... more Eggplant and related Solanum species contain abundant caffeoylquinic acid (CQA) derivatives. Fruit of the invasive species Solanum viarum Dunal contain numerous complex CQA derivatives, but only a few have been identified. The structures of two new compounds isolated from methanolic extracts of S. viarum fruit by C18-HPLC-DAD were determined using 2D NMR and MS data. Both include two 5-CQA molecules joined by glucose via ester and glycosidic linkages. The structures of compounds 1 and 2 (viarumacids A and B) are, respectively, 5-caffeoyl- and 3-malonyl-5-caffeoyl-[4-(1β-[6-(5- caffeoyl)quinate]glucopyranosyl)]quinic acid. The antioxidant activities determined by ABTS•+ and DPPH• assays were in the order 1 > 2 > 5-CQA.
Rafflesia is a genus of holoparasitic plants endemic to Southeast Asia that has lost the ability ... more Rafflesia is a genus of holoparasitic plants endemic to Southeast Asia that has lost the ability to undertake photosynthesis. With short-read sequencing technology, we assembled a draft sequence of the mitochondrial genome of Rafflesia lagascae Blanco, a species endemic to the Philippine island of Luzon, with ∼350x sequencing depth coverage. Using multiple approaches, however, we were only able to identify small fragments of plastid sequences at low coverage depth (< 2x) and could not recover any substantial portion of a chloroplast genome. The gene fragments we identified included photosynthesis and energy production genes (atp, ndh, pet, psa, psb, rbcL), ribosomal RNA genes (rrn16, rrn23), ribosomal protein genes (rps7, rps11, rps16), transfer RNA genes, as well as matK, accD, ycf2, and multiple non-genic regions from the inverted repeats. None of the identified plastid gene sequences had intact reading frames. Phylogenetic analysis suggests that ~33% of these remnant plastid genes may have been horizontally transferred from the host plant genus Tetrastigma with the rest having ambiguous phylogenetic positions (<50% bootstrap support), except for psaB which was strongly allied with the plastid homologue in Nicotiana. Our inability to identify substantial plastid genome sequences from R. lagascae using multiple approaches - despite success in identifying and developing a draft assembly of the much larger mitochondrial genome - suggests that the parasitic plant genus Rafflesia may be the first plant group for which there is no recognizable plastid genome, or if present is found in cryptic form at very low levels.
Plants rely on transcriptional dynamics to respond to multiple climatic fluctuations and contexts... more Plants rely on transcriptional dynamics to respond to multiple climatic fluctuations and contexts in nature. We analyzed the genome-wide gene expression patterns of rice (Oryza sativa) growing in rainfed and irrigated fields during two distinct tropical seasons and determined simple linear models that relate transcriptomic variation to climatic fluctuations. These models combine multiple environmental parameters to account for patterns of expression in the field of co-expressed gene clusters. We examined the similarities of our environmental models between tropical and temperate field conditions, using previously published data. We found that field type and macroclimate had broad impacts on transcriptional responses to environmental fluctuations, especially for genes involved in photosynthesis and development. Nevertheless, variation in solar radiation and temperature at the timescale of hours had reproducible effects across environmental contexts. These results provide a basis for ...
Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the M... more Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This anal...
The purpose of the study &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp... more The purpose of the study &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot;Phylogeographic relationships among Asian eggplants and new perspectives on eggplant domestication&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot; by Meyer et al. (2012) was to use new and expanded accession sets coupled with molecular data to evaluate possible scenarios of eggplant domestication with as little influence as possible from any previously published nomenclatural scheme, and taking into consideration multiple sources of evidence regarding the history of eggplant in Asia. Samuels (2013) disfavored this system and in his Letter to the Editor attempted to re-evaluate the results according to his system. However, Samuels appears to have misread Meyer et al. and also makes several claims without the support of evidence. We stand by the results of Meyer et al., which are in agreement with the recent and much needed new taxonomic treatment for wild relatives of eggplant.
Fruit of the cultivated eggplant species Solanum melongena, Solanum aethiopicum, and Solanum macr... more Fruit of the cultivated eggplant species Solanum melongena, Solanum aethiopicum, and Solanum macrocarpon, and wild relatives including Solanum anguivi and Solanum incanum, have a high content of hydroxycinnamic acid conjugates with potential human health benefits. Typically, caffeoylquinic acid esters predominate, and in particular 5-O-(E)-caffeoylquinic acid. By contrast, fruit from accession PI 319855 in the USDA eggplant core collection, unambiguously identified as Solanum viarum by morphological characters, were found to include several major, closely related hydroxycinnamic acid conjugates with much longer C18-HPLC retention times than those of 5-O-(E)-caffeoylquinic acid and other monocaffeoylquinic acid isomers. Four of these compounds were isolated from methanolic extracts of lyophilized fruit tissues by C18-HPLC, and structurally elucidated using (1)H and (13)C NMR techniques and HR-TOF-MS. Isomeric compounds 1 and 2 are composed of 5-O-(E)-caffeoylquinic acid with a malonyl group on the 3- or 4-hydroxyl of quinic acid, respectively, plus a 6-O-sinapoylglucose group 1-O-β-D linked with the 4-hydroxyl on the phenyl ring of the caffeoyl moiety (1β,4β-dihydroxy-3β-carboxyacetoxy- and 1β,3β-dihydroxy-4β-carboxyacetoxy-5α-[[3-[4-[1β-(6-O-(E)-sinapoyl-β-D-glucopyranosyl)oxy]-3-hydroxyphenyl]-(E)-1-oxo-2-propenyl]oxy]cyclohexanecarboxylic acid). Compound 3 has the same structure as 1 and 2 without malonation of quinic acid (1β,3β,4β-trihydroxy-5α-[[3-[4-[1β-(6-O-(E)-sinapoyl-β-d-glucopyranosyl)oxy]-3-hydroxyphenyl]-(E)-1-oxo-2-propenyl]oxy]cyclohexanecarboxylic acid). Compound 4 differs from 3 by methylation of the carboxyl group on quinic acid (methyl 1β,3β,4β-trihydroxy-5α-[[3-[4-[1β-(6-O-(E)-sinapoyl-β-D-glucopyranosyl)oxy]-3-hydroxyphenyl]-(E)-1-oxo-2-propenyl]oxy]cyclohexanecarboxylate). Some features of these four new compounds, such as malonation and the specific linkages between caffeoyl, glucosyl, and sinapoyl moieties, are common in acylated and glycosylated phenylpropanoids, but have not previously been reported in complex derivatives of 5-O-(E)-caffeoylquinic acid.
Domestication is a good model for the study of evolutionary processes because of the recent evolu... more Domestication is a good model for the study of evolutionary processes because of the recent evolution of crop species (<12,000 years ago), the key role of selection in their origins, and good archaeological and historical data on their spread and diversification. Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops. Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations that occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations and that are associated with geographical adaptation of crop species.
Domesticated food crops are derived from a phylogenetically diverse assemblage of wild ancestors ... more Domesticated food crops are derived from a phylogenetically diverse assemblage of wild ancestors through artificial selection for different traits. Our understanding of domestication, however, is based upon a subset of well-studied ‘model’ crops, many of them from the Poaceae family. Here, we investigate domestication traits and theories using a broader range of crops. We reviewed domestication information (e.g. center of domestication, plant traits, wild ancestors, domestication dates, domestication traits, early and current uses) for 203 major and minor food crops. Compiled data were used to test classic and contemporary theories in crop domestication. Many typical features of domestication associated with model crops, including changes in ploidy level, loss of shattering, multiple origins, and domestication outside the native range, are less common within this broader dataset. In addition, there are strong spatial and temporal trends in our dataset. The overall time required to domesticate a species has decreased since the earliest domestication events. The frequencies of some domestication syndrome traits (e.g. nonshattering) have decreased over time, while others (e.g. changes to secondary metabolites) have increased. We discuss the influences of the ecological, evolutionary, cultural and technological factors that make domestication a dynamic and ongoing process.
The ways in which geographically separate communities use crops reflect the agricultural and cult... more The ways in which geographically separate communities use crops reflect the agricultural and cultural influences on each community. The eggplant (Solanum melongena L.; Solanaceae), which was domesticated in South and Southeast Asia, has long been used in a variety of medicinal and culinary preparations across many different Asian ethnolinguistic groups. Here, we report the total uses for eggplant and sixteen related species in three regions, India, southern China, and Malesia, and conduct a comparative analysis in order to form hypotheses about how influences on plant use in one region could have affected use and evolutionary trajectories in other regions. Results from literature review and 101 interviews show a total of 77 medicinal attributes for eggplant, with few similar attributes mentioned in different regions, leading us to hypothesize that largely pristine (i.e., without influence from other regions) development of uses, which could serve as selection pressures, occurred for eggplant in India, southern China, and Malesia. Results also show that many Solanum species have been fluidly adopted into uses developed for other species in a single region.
Cross-species comparative genomics approaches have been
employed to map and clone many important ... more Cross-species comparative genomics approaches have been employed to map and clone many important disease resistance (R) genes from Solanum species—especially wild relatives of potato and tomato. These efforts will increase with the recent release of potato genome sequence and the impending release of tomato genome sequence. Most R genes belong to the prominent nucleotide binding site-leucine rich repeat (NBS-LRR) class and conserved NBS-LRR protein motifs enable survey of the R gene space of a plant genome by generation of resistance gene analogs (RGA), polymerase chain reaction fragments derived from R genes. We generated a collection of 97 RGA from the disease-resistant wild potato S. bulbocastanum, complementing smaller collections from other Solanum species. To further comparative genomics approaches, we combined all known Solanum RGA and cloned solanaceous NBS-LRR gene sequences, nearly 800 sequences in total, into a single meta-analysis. We defined R gene diversity bins that reflect both evolutionary relationships and DNA cross-hybridization results. The resulting framework is amendable and expandable, providing the research community with a common vocabulary for present and future study of R gene lineages. Through a series of sequence and hybridization experiments, we demonstrate that all tested R gene lineages are of ancient origin, are shared between Solanum species, and can be successfully accessed via comparative genomics approaches.
The domestication history of eggplant (Solanum melongena L.) has long been debated, with studies ... more The domestication history of eggplant (Solanum melongena L.) has long been debated, with studies unable to narrow down where domestication occurred within a broad region of tropical Asia. The most commonly hypothesized region is India, however China has an equally old written record of eggplant use dating ca. 2000 years before present. Both regions have a high diversity of landraces and populations of putatively wild eggplant: Solanum incanum L. in India and Solanum undatum Lam. in SE Asia. An additional complication is that there is taxonomic confusion regarding the two candidate progenitors. Here, we synthesize historic, morphologic, and molecular data (nrITS sequence and AFLP) to interpret the phylogeographic relationships among candidate progenitors and Asian eggplant landraces in order to test theories of domestication. A minimum of two domestication events is supported: one in India and one in southern China/SE Asia. Results also support separate domestication of S. melongena subsp. ovigerum, a group of morphologically distinct eggplants found in SE Asia, and suggest Asian S. incanum and S. undatum may not be genetically distinct. Routes of the spread of eggplant cultivation throughout Asia are proposed, and evolutionary relationships among allied species are discussed.
This study presents a strategy based on repeatable reversed-phase LC-TOF-MS methods and statistic... more This study presents a strategy based on repeatable reversed-phase LC-TOF-MS methods and statistical tools, including untargeted PCA and targeted PLS/OPLS-DA models, to analyze 31 accessions representing 24 species in the eggplant genus Solanum (Solanaceae), including eight species whose metabolic profiles were studied for the first time. Sixty-two Solanum metabolites were identified after detailed analysis of UV absorbance spectra, mass spectral fragmentation patterns, NMR spectra, and/or co-injection experiments with authentic standards. Among these were two new 5-O-caffeoylquinic acid derivatives that were identified by analyzing their MS/MS fragmentation. Based on these results, a Solanum metabolic database (SMD) and a detailed biosynthetic pathway of Solanum metabolites were created. Results of analyses identified seven marker metabolites that distinguish four Solanum sections, and revealed species-specific chemical patterns. Combining LC-MS data with multivariate statistical analysis was proven effective in studying the metabolic network within the large genus Solanum, allowing for integration of complicated chemistry, morphology, and evolutionary relationships.
Eggplant and related Solanum species contain
abundant caffeoylquinic acid (CQA) derivatives. Frui... more Eggplant and related Solanum species contain abundant caffeoylquinic acid (CQA) derivatives. Fruit of the invasive species Solanum viarum Dunal contain numerous complex CQA derivatives, but only a few have been identified. The structures of two new compounds isolated from methanolic extracts of S. viarum fruit by C18-HPLC-DAD were determined using 2D NMR and MS data. Both include two 5-CQA molecules joined by glucose via ester and glycosidic linkages. The structures of compounds 1 and 2 (viarumacids A and B) are, respectively, 5-caffeoyl- and 3-malonyl-5-caffeoyl-[4-(1β-[6-(5- caffeoyl)quinate]glucopyranosyl)]quinic acid. The antioxidant activities determined by ABTS•+ and DPPH• assays were in the order 1 > 2 > 5-CQA.
Rafflesia is a genus of holoparasitic plants endemic to Southeast Asia that has lost the ability ... more Rafflesia is a genus of holoparasitic plants endemic to Southeast Asia that has lost the ability to undertake photosynthesis. With short-read sequencing technology, we assembled a draft sequence of the mitochondrial genome of Rafflesia lagascae Blanco, a species endemic to the Philippine island of Luzon, with ∼350x sequencing depth coverage. Using multiple approaches, however, we were only able to identify small fragments of plastid sequences at low coverage depth (< 2x) and could not recover any substantial portion of a chloroplast genome. The gene fragments we identified included photosynthesis and energy production genes (atp, ndh, pet, psa, psb, rbcL), ribosomal RNA genes (rrn16, rrn23), ribosomal protein genes (rps7, rps11, rps16), transfer RNA genes, as well as matK, accD, ycf2, and multiple non-genic regions from the inverted repeats. None of the identified plastid gene sequences had intact reading frames. Phylogenetic analysis suggests that ~33% of these remnant plastid genes may have been horizontally transferred from the host plant genus Tetrastigma with the rest having ambiguous phylogenetic positions (<50% bootstrap support), except for psaB which was strongly allied with the plastid homologue in Nicotiana. Our inability to identify substantial plastid genome sequences from R. lagascae using multiple approaches - despite success in identifying and developing a draft assembly of the much larger mitochondrial genome - suggests that the parasitic plant genus Rafflesia may be the first plant group for which there is no recognizable plastid genome, or if present is found in cryptic form at very low levels.
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employed to map and clone many important disease resistance
(R) genes from Solanum species—especially wild relatives
of potato and tomato. These efforts will increase with
the recent release of potato genome sequence and the impending
release of tomato genome sequence. Most R genes
belong to the prominent nucleotide binding site-leucine rich
repeat (NBS-LRR) class and conserved NBS-LRR protein
motifs enable survey of the R gene space of a plant genome
by generation of resistance gene analogs (RGA), polymerase
chain reaction fragments derived from R genes. We generated
a collection of 97 RGA from the disease-resistant wild
potato S. bulbocastanum, complementing smaller collections
from other Solanum species. To further comparative genomics
approaches, we combined all known Solanum RGA
and cloned solanaceous NBS-LRR gene sequences, nearly
800 sequences in total, into a single meta-analysis. We defined
R gene diversity bins that reflect both evolutionary
relationships and DNA cross-hybridization results. The resulting
framework is amendable and expandable, providing
the research community with a common vocabulary for
present and future study of R gene lineages. Through a
series of sequence and hybridization experiments, we demonstrate
that all tested R gene lineages are of ancient origin,
are shared between Solanum species, and can be successfully
accessed via comparative genomics approaches.
abundant caffeoylquinic acid (CQA) derivatives. Fruit of the
invasive species Solanum viarum Dunal contain numerous complex
CQA derivatives, but only a few have been identified. The
structures of two new compounds isolated from methanolic
extracts of S. viarum fruit by C18-HPLC-DAD were determined
using 2D NMR and MS data. Both include two 5-CQA molecules
joined by glucose via ester and glycosidic linkages. The
structures of compounds 1 and 2 (viarumacids A and B) are,
respectively, 5-caffeoyl- and 3-malonyl-5-caffeoyl-[4-(1β-[6-(5-
caffeoyl)quinate]glucopyranosyl)]quinic acid. The antioxidant
activities determined by ABTS•+ and DPPH• assays were in
the order 1 > 2 > 5-CQA.
employed to map and clone many important disease resistance
(R) genes from Solanum species—especially wild relatives
of potato and tomato. These efforts will increase with
the recent release of potato genome sequence and the impending
release of tomato genome sequence. Most R genes
belong to the prominent nucleotide binding site-leucine rich
repeat (NBS-LRR) class and conserved NBS-LRR protein
motifs enable survey of the R gene space of a plant genome
by generation of resistance gene analogs (RGA), polymerase
chain reaction fragments derived from R genes. We generated
a collection of 97 RGA from the disease-resistant wild
potato S. bulbocastanum, complementing smaller collections
from other Solanum species. To further comparative genomics
approaches, we combined all known Solanum RGA
and cloned solanaceous NBS-LRR gene sequences, nearly
800 sequences in total, into a single meta-analysis. We defined
R gene diversity bins that reflect both evolutionary
relationships and DNA cross-hybridization results. The resulting
framework is amendable and expandable, providing
the research community with a common vocabulary for
present and future study of R gene lineages. Through a
series of sequence and hybridization experiments, we demonstrate
that all tested R gene lineages are of ancient origin,
are shared between Solanum species, and can be successfully
accessed via comparative genomics approaches.
abundant caffeoylquinic acid (CQA) derivatives. Fruit of the
invasive species Solanum viarum Dunal contain numerous complex
CQA derivatives, but only a few have been identified. The
structures of two new compounds isolated from methanolic
extracts of S. viarum fruit by C18-HPLC-DAD were determined
using 2D NMR and MS data. Both include two 5-CQA molecules
joined by glucose via ester and glycosidic linkages. The
structures of compounds 1 and 2 (viarumacids A and B) are,
respectively, 5-caffeoyl- and 3-malonyl-5-caffeoyl-[4-(1β-[6-(5-
caffeoyl)quinate]glucopyranosyl)]quinic acid. The antioxidant
activities determined by ABTS•+ and DPPH• assays were in
the order 1 > 2 > 5-CQA.