RESUMEN
BACKGROUND: Ilex metabaptista is a woody tree species with strong waterlogging tolerance and is also admired as a landscape plant with high development prospects and scientific research value. Unfortunately, populations of this species have declined due to habitat loss. Thus, it is a great challenge for us to efficiently protect I. metabaptista resources from extinction. Molecular biology research can provide the scientific basis for the conservation of species. However, the study of I. metabaptista genetics is still in its infancy. To date, no mitochondrial genome (mitogenome) in the genus Ilex has been analysed in detail. RESULTS: The mitogenome of I. metabaptista was assembled based on the reads from Illumina and Nanopore sequencing platforms; it was a typical circular DNA molecule of 529,560 bp with a GC content of 45.61% and contained 67 genes, including 42 protein-coding genes, 22 tRNA genes, and 3 rRNA genes. Repeat sequence analysis and prediction of RNA editing sites revealed a total of 286 dispersed repeats, 140 simple repeats, 18 tandem repeats, and 543 RNA editing sites. Analysis of codon usage showed that codons ending in A/T were preferred. Gene migration was observed to occur between the mitogenome and chloroplast genome via the detection of homologous fragments. In addition, Ka/Ks analysis revealed that most of the protein-coding genes in the mitogenome had undergone negative selection, and only the ccmB gene had undergone potential positive selection in most asterids. Nucleotide polymorphism analysis revealed the variation in each gene, with atp9 being the most notable. Furthermore, comparative analysis showed that the GC contents were conserved, but the sizes and structure of mitogenomes varied greatly among asterids. Phylogenetic analysis based on the mitogenomes reflected the exact evolutionary and taxonomic status of I. metabaptista. CONCLUSION: In this study, we sequenced and annotated the mitogenome of I. metabaptista and compared it with the mitogenomes of other asterids, which provided essential background information for further understanding of the genetics of this plant and helped lay the foundation for future studies on molecular breeding of I. metabaptista.
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Aquifoliaceae , Genoma Mitocondrial , Ilex , Aquifoliaceae/genética , Genoma Mitocondrial/genética , Ilex/genética , Filogenia , ChinaRESUMEN
BACKGROUND: Ilex pubescens is an important traditional Chinese medicinal plant with many naturally occurring compounds and multiple pharmacological effects. However, the lack of reference genomic information has led to tardiness in molecular biology research and breeding programs of this plant. RESULTS: To obtain knowledge on the genomic information of I. pubescens, a genome survey was performed for the first time by next generation sequencing (NGS) together with genome size estimation using flow cytometry. The whole genome survey of I. pubescens generated 46.472 Gb of sequence data with approximately 82.2 × coverage. K-mer analysis indicated that I. pubescens has a small genome of approximately 553 Mb with 1.93% heterozygosity rate and 39.1% repeat rate. Meanwhile, the genome size was estimated to be 722 Mb using flow cytometry, which was possibly more precise for assessment of genome size than k-mer analysis. A total of 45.842 Gb clean reads were assembled into 808,938 scaffolds with a relatively short N50 of 760 bp. The average guanine and cytosine (GC) content was 37.52%. In total, 197,429 microsatellite motifs were detected with a frequency of 2.8 kb, among which mononucleotide motifs were the most abundant (up to 62.47% of the total microsatellite motifs), followed by dinucleotide and trinucleotide motifs. CONCLUSION: In summary, the genome of I. pubescens is small but complex with a high level of heterozygosity. Even though not successfully applied for estimation of genome size due to its complex genome, the survey sequences will help to design whole genome sequencing strategies and provide genetic information support for resource protection, genetic diversity analysis, genetic improvement and artificial breeding of I. pubescens.
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Ilex , Ilex/genética , Aquifoliaceae/genética , Genoma de Planta , Citometría de Flujo , Fitomejoramiento , Genómica , Repeticiones de MicrosatéliteRESUMEN
Ilex dabieshanensis K. Yao & M. B. Deng is not only a highly valued tree species for landscaping, it is also a good material for making kuding tea due to its anti-inflammatory and lipid-lowering medicinal properties. Utilizing next-generation and long-read sequencing technologies, we assembled the whole chloroplast genome of I. dabieshanensis. The genome was 157,218 bp in length, exhibiting a typical quadripartite structure with a large single copy (LSC: 86,607 bp), a small single copy (SSC: 18,427 bp) and a pair of inverted repeat regions (IRA and IRB: each of 26,092 bp). A total of 121 predicted genes were encoded, including 113 distinctive (79 protein-coding genes, 30 tRNAs, and 4 rRNAs) and 8 duplicated (8 protein-coding genes) located in the IR regions. Overall, 132 SSRs and 43 long repeats were detected and could be used as potential molecular markers. Comparative analyses of four traditional Ilex tea species (I. dabieshanensis, I. paraguariensis, I. latifolia and I. cornuta) revealed seven divergent regions: matK-rps16, trnS-psbZ, trnT-trnL, atpB-rbcL, petB-petD, rpl14-rpl16, and rpl32-trnL. These variations might be applicable for distinguishing different species within the genus Ilex. Phylogenetic reconstruction strongly suggested that I. dabieshanensis formed a sister clade to I. cornuta and also showed a close relationship to I. latifolia. The generated chloroplast genome information in our study is significant for Ilex tea germplasm identification, phylogeny and genetic improvement.
Asunto(s)
Genoma del Cloroplasto , Ilex , Aquifoliaceae/genética , Ilex/genética , Filogenia , TéRESUMEN
Ilex asprella is a widely used herbs in Traditional Chinese Medicine for treating viral infection and relieving inflammation. Due to the earlier fruiting period of I. asprella, it is the major food source for frugivores in summer. Despite its pharmacological and ecological importance, a reference genome for I. asprella is lacking. By using Illumina, stLFR and Omni-C sequencing data, we present the first chromosomal-level assembly for I. asprella. The genome assembly size is 804 Mbp, with Benchmarking Universal Single-Copy Orthologs (BUSCO) score 94.4% for eudicotyledon single copy genes. Transcriptomes of leaves, stems, flowers, premature fruits and roots were analyzed, providing 39,215 gene models. The complete set of genes involved in the triterpenoids production is disclosed for the first time. We have also found the oxidosqualene cyclases (OSCs), CYP716s and UDP-glycosyltransferases (UGTs), which are responsible for the modification of triterpenoid backbones, resulting in the high variety of triterpenoid saponins.
Asunto(s)
Ilex , Saponinas , Triterpenos , Triterpenos/metabolismo , Ilex/genética , Ilex/metabolismo , Antivirales/farmacología , Transcriptoma , Raíces de Plantas/metabolismo , Saponinas/metabolismoRESUMEN
BACKGROUND: Ilex (Aquifoliaceae) are of great horticultural importance throughout the world for their foliage and decorative berries, yet a dearth of genetic information has hampered our understanding of phylogenetic relationships and evolutionary history. Here, we compare chloroplast genomes from across Ilex and estimate phylogenetic relationships. RESULTS: We sequenced the chloroplast genomes of seven Ilex species and compared them with 34 previously published Ilex plastomes. The length of the seven newly sequenced Ilex chloroplast genomes ranged from 157,182 bp to 158,009 bp, and contained a total of 118 genes, including 83 protein-coding, 31 rRNA, and four tRNA genes. GC content ranged from 37.6 to 37.69%. Comparative analysis showed shared genomic structures and gene rearrangements. Expansion and contraction of the inverted repeat regions at the LSC/IRa and IRa/SSC junctions were observed in 22 and 26 taxa, respectively; in contrast, the IRb boundary was largely invariant. A total of 2146 simple sequence repeats and 2843 large repeats were detected in the 41 Ilex plastomes. Additionally, six genes (psaC, rbcL, trnQ, trnR, trnT, and ycf1) and two intergenic spacer regions (ndhC-trnV and petN-psbM) were identified as hypervariable, and thus potentially useful for future phylogenetic studies and DNA barcoding. We recovered consistent phylogenetic relationships regardless of inference methodology or choice of loci. We recovered five distinct, major clades, which were inconsistent with traditional taxonomic systems. CONCLUSION: Our findings challenge traditional circumscriptions of the genus Ilex and provide new insights into the evolutionary history of this important clade. Furthermore, we detail hypervariable and repetitive regions that will be useful for future phylogenetic and population genetic studies.
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Genoma del Cloroplasto , Ilex , Aquifoliaceae/genética , Cloroplastos/genética , Ilex/genética , FilogeniaRESUMEN
Ilex is a monogeneric plant group (containing approximately 600 species) in the Aquifoliaceae family and one of the most commonly used medicinal herbs. However, its taxonomy and phylogenetic relationships at the species level are debatable. Herein, we obtained the complete chloroplast genomes of all 19 Ilex types that are native to Hong Kong. The genomes are conserved in structure, gene content and arrangement. The chloroplast genomes range in size from 157,119 bp in Ilex graciliflora to 158,020 bp in Ilex kwangtungensis. All these genomes contain 125 genes, of which 88 are protein-coding and 37 are tRNA genes. Four highly varied sequences (rps16-trnQ, rpl32-trnL, ndhD-psaC and ycf1) were found. The number of repeats in the Ilex genomes is mostly conserved, but the number of repeating motifs varies. The phylogenetic relationship among the 19 Ilex genomes, together with eight other available genomes in other studies, was investigated. Most of the species could be correctly assigned to the section or even series level, consistent with previous taxonomy, except Ilex rotunda var. microcarpa, Ilex asprella var. tapuensis and Ilex chapaensis. These species were reclassified; I. rotunda was placed in the section Micrococca, while the other two were grouped with the section Pseudoaquifolium. These studies provide a better understanding of Ilex phylogeny and refine its classification.
Asunto(s)
Cloroplastos/genética , Evolución Molecular , Ilex/genética , Filogenia , Genoma del Cloroplasto/genética , Genómica , Hong Kong , Repeticiones de Microsatélite/genéticaRESUMEN
BACKGROUND: Understanding the origin of genetic variation is the key to predict how species will respond to future climate change. The genus Quercus is a species-rich and ecologically diverse woody genus that dominates a wide range of forests and woodland communities of the Northern Hemisphere. Quercus thus offers a unique opportunity to investigate how adaptation to environmental changes has shaped the spatial genetic structure of closely related lineages. Furthermore, Quercus provides a deep insight into how tree species will respond to future climate change. This study investigated whether closely related Quercus lineages have similar spatial genetic structures and moreover, what roles have their geographic distribution, ecological tolerance, and historical environmental changes played in the similar or distinct genetic structures. RESULTS: Despite their close relationships, the three main oak lineages (Quercus sections Cyclobalanopsis, Ilex, and Quercus) have different spatial genetic patterns and occupy different climatic niches. The lowest level and most homogeneous pattern of genetic diversity was found in section Cyclobalanopsis, which is restricted to warm and humid climates. The highest genetic diversity and strongest geographic genetic structure were found in section Ilex, which is due to their long-term isolation and strong local adaptation. The widespread section Quercus is distributed across the most heterogeneous range of environments; however, it exhibited moderate haplotype diversity. This is likely due to regional extinction during Quaternary climatic fluctuation in Europe and North America. CONCLUSIONS: Genetic variations of sections Ilex and Quercus were significantly predicted by geographic and climate variations, while those of section Cyclobalanopsis were poorly predictable by geographic or climatic diversity. Apart from the different historical environmental changes experienced by different sections, variation of their ecological or climatic tolerances and physiological traits induced varying responses to similar environment changes, resulting in distinct spatial genetic patterns.
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Cloroplastos/genética , Ilex/genética , Quercus/genética , Cambio Climático , Ecología , Europa (Continente) , Bosques , Estructuras Genéticas , Variación Genética , Haplotipos , Ilex/citología , Ilex/crecimiento & desarrollo , América del Norte , Filogenia , Quercus/citología , Quercus/crecimiento & desarrolloRESUMEN
BACKGROUND: The genus Ilex (Aquifoliaceae) has a near-cosmopolitan distribution in mesic habitats from tropical to temperate lowlands and in alpine forests. It has a high rate of hybridization and plastid capture, and comprises four geographically structured plastid groups. A previous study showed that the plastid rbcL gene, coding for the large subunit of Rubisco, has a particularly high rate of non-synonymous substitutions in Ilex, when compared with other plant lineages. This suggests a strong positive selection on rbcL, involved in yet unknown adaptations. We therefore investigated positive selection on rbcL in 240 Ilex sequences from across the global range. RESULTS: The rbcL gene shows a much higher rate of positive selection in Ilex than in any other plant lineage studied so far (> 3000 species) by tests in both PAML and SLR. Most positively selected residues are on the surface of the folded large subunit, suggesting interaction with other subunits and associated chaperones, and coevolution between positively selected residues is prevalent, indicating compensatory mutations to recover molecular stability. Coevolution between positively selected sites to restore global stability is common. CONCLUSIONS: This study has confirmed the predicted high incidence of positively selected residues in rbcL in Ilex, and shown that this is higher than in any other plant lineage studied so far. The causes and consequences of this high incidence are unclear, but it is probably associated with the similarly high incidence of hybridization and introgression in Ilex, even between distantly related lineages, resulting in large cytonuclear discordance in the phylogenies.
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Ilex/genética , Ribulosa-Bifosfato Carboxilasa/genética , Selección Genética , Secuencia de Bases , Codón/genética , Evolución Molecular , Hibridación Genética , Modelos Moleculares , Filogenia , Ribulosa-Bifosfato Carboxilasa/químicaRESUMEN
Eleven previously undescribed compounds including two triterpenes, ilexchinenin A and ilexchinenin B, and nine triterpenoid saponins, ilexchinenosides A-I, along with twelve known triterpenoids were isolated from the leaves of Ilex chinensis Sims (Aquifoliaceae). Their structures were elucidated by spectroscopic analysis and comparison with known compounds. Furthermore, eight compounds exhibited significant inhibitory effects on NO production of lipopolysaccharide (LPS)-induced murine macrophages, while nine compounds exhibited potent hepatoprotective activity against N-acetyl-p-aminophenol (APAP)-induced HepG2 cell damage in in vitro assays.
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Ilex/química , Triterpenos/aislamiento & purificación , Animales , Ilex/genética , Ilex/metabolismo , Lipopolisacáridos/farmacología , Macrófagos/efectos de los fármacos , Estructura Molecular , Hojas de la Planta/química , Raíces de Plantas/química , Saponinas/química , Triterpenos/químicaRESUMEN
Aquifoliaceae is the largest family in the campanulid order Aquifoliales. It consists of a single genus, Ilex, the hollies, which is the largest woody dioecious genus in the angiosperms. Most species are in East Asia or South America. The taxonomy and evolutionary history remain unclear due to the lack of a robust species-level phylogeny. We produced the first complete chloroplast genomes in this family, including seven Ilex species, by Illumina sequencing of long-range PCR products and subsequent reference-guided de novo assembly. These genomes have a typical bicyclic structure with a conserved genome arrangement and moderate divergence. The total length is 157,741 bp and there is one large single-copy region (LSC) with 87,109 bp, one small single-copy with 18,436 bp, and a pair of inverted repeat regions (IR) with 52,196 bp. A total of 144 genes were identified, including 96 protein-coding genes, 40 tRNA and 8 rRNA. Thirty-four repetitive sequences were identified in Ilex pubescens, with lengths >14 bp and identity >90%, and 11 divergence hotspot regions that could be targeted for phylogenetic markers. This study will contribute to improved resolution of deep branches of the Ilex phylogeny and facilitate identification of Ilex species.
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Genoma del Cloroplasto/fisiología , Ilex/genética , Filogenia , Ilex/clasificaciónRESUMEN
Ilex, the largest genus of dioecious woody plants, is a good study system to assess the role of hybridization in speciation and evolution. Ilex dabieshanensis, a tree endemic to Dabieshan Mountains region, was initially described as a new species. Based on morphological intermediacy and sympatric distribution with its putative parental species, I. cornuta and I. latifolia, we proposed it as a natural hybrid between them. In this study, we sequenced one chloroplast intergenic spacer (trnH-psbA) and two nuclear genes (gapC and nepGS) in I. dabieshanensis and its putative parental species to test the hybrid origin hypothesis. Our results showed that there were one to two differentially fixed sequence differences between I. cornuta and I. latifolia at the two nuclear genes. Twelve of the 14 individuals of I. dabieshanensis exhibited additivity in chromatograms on these differentially fixed sites at both nuclear genes, and the remaining two exhibited additivity in chromatograms on the fixed site at only the nepGS gene. Except one haplotype of I. cornuta at the nepGS gene, all of the haplotypes of I. cornuta at the two nuclear genes were well separated from those of I. latifolia, and most haplotypes of I. dabieshanensis were shared with those of I. cornuta and I. latifolia. Phylogenetic analysis of these haplotypes was largely consistent with haplotype network analysis. I. cornuta and I. latifolia differed by two nucleotide substitutions in the chloroplast intergenic spacer, and 12 individuals of I. dabieshanensis had the same sequences as I. latifolia, while the remaining two were identical with I. cornuta. The molecular data provide convincing evidence for the hybrid origin of I. dabieshanensis and asymmetrical direction of hybridization. One haplotype of I. cornuta at the nepGS gene was nested with those of I. latifolia, indicating introgression to I. cornuta.
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Ilex/genética , Núcleo Celular/genética , Cloroplastos/genética , Genes de Plantas , Haplotipos , Ilex/clasificación , FilogeniaRESUMEN
OBJECTIVE: To establish molecular method for identification of Ilex plants using the internal transcribed spacer(ITS) bar- code. METHODS: DNA was extracted using centrifugal columnar kits. The ITS sequences of all experimental samples were amplified and sequenced using a pair of universal primers. The alignment and the phylogenetic tree were performed in MEGA5. 0. RESULTS: The length of ITS sequence in each species was 759 bp,in which there were 216 sites discrepancy. CONCLUSION: DNA barcoding technology based on ITS sequence can be used to identify plants of Ilex genus.
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Ilex/genética , Código de Barras del ADN Taxonómico , Cartilla de ADN , ADN de Plantas/genética , Filogenia , Análisis de Secuencia de ADNRESUMEN
Ilex asprella, which contains abundant α-amyrin type triterpenoid saponins, is an anti-influenza herbal drug widely used in south China. In this work, we first analysed the transcriptome of the I. asprella root using RNA-Seq, which provided a dataset for functional gene mining. mRNA was isolated from the total RNA of the I. asprella root and reverse-transcribed into cDNA. Then, the cDNA library was sequenced using an Illumina HiSeq™ 2000, which generated 55,028,452 clean reads. De novo assembly of these reads generated 51,865 unigenes, in which 39,269 unigenes were annotated (75.71% yield). According to the structures of the triterpenoid saponins of I. asprella, a putative biosynthetic pathway downstream of 2,3-oxidosqualene was proposed and candidate unigenes in the transcriptome data that were potentially involved in the pathway were screened using homology-based BLAST and phylogenetic analysis. Further amplification and functional analysis of these putative unigenes will provide insight into the biosynthesis of Ilex triterpenoid saponins.
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Ilex/genética , Ácido Oleanólico/análogos & derivados , Raíces de Plantas/metabolismo , Saponinas/metabolismo , Triterpenos/metabolismo , Secuencia de Bases , Vías Biosintéticas , Minería de Datos , Bases de Datos Genéticas , Medicamentos Herbarios Chinos , Eritritol/análogos & derivados , Eritritol/metabolismo , Expresión Génica , Perfilación de la Expresión Génica , Genes de Plantas , Ácido Mevalónico/metabolismo , Ácido Oleanólico/biosíntesis , Filogenia , Extractos Vegetales/química , Saponinas/biosíntesis , Saponinas/genética , Análisis de Secuencia de ADN , Análisis de Secuencia de ARN , Escualeno/análogos & derivados , Transcriptoma/genéticaRESUMEN
The history and diversification of the genus Ilex (Aquifoliaceae), based on 108 different species (116 specimens), are inferred from the analysis of two nuclear (ITS and nepGS) and three plastid (rbcL, trnL-F and atpB-rbcL) sequences. Nuclear and plastid trees are highly incongruent and the nuclear tree is more compatible with current taxonomic classifications than the plastid one. The most recent common ancestor (MRCA) of extant species is dated from the Miocene, although the Ilex stem lineage can be traced back to the late Cretaceous, according to fossil records. This suggests extensive lineage extinctions between the Cretaceous and Miocene and may also explain the difficulties encountered in defining the relationships between Ilex and its closest relatives. The MRCA ancestral area was identified as being in the North Hemisphere (North America and/or East Asia). Several bidirectional North America/East Asia and North America/South America dispersal events are proposed to explain observed geographic and phylogenetic patterns. Hybridization and introgression events between distantly related lineages are also inferred, indicating weak reproductive barriers between species in Ilex.
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Evolución Molecular , Hibridación Genética , Ilex/genética , Filogenia , Teorema de Bayes , Núcleo Celular/genética , ADN de Plantas/genética , Geografía , Modelos Genéticos , Plastidios/genética , Análisis de Secuencia de ADNRESUMEN
A total of seven Kudingcha genotypes from three plant species (Ilex kudingcha, Ilex cornuta, and Ligustrum robustum) with different geographic origins in China were investigated for their major phenolic compounds, individual and total phenolics contents, and in vitro antioxidant properties (ABTS, DPPH, FRAP, and OH assays). LC-PDA-APCI-MS analysis showed that Kudingcha genotypes from Ilex and Ligustrum had entirely different phenolic profiles. Major phenolics in Kudingcha genotypes from two Ilex species were mono- and dicaffeoylquinic acids, whereas those in a Kudingcha genotype from Ligustrum were phenylethanoid and monoterpenoid glycosides. All Kudingcha genotypes of Ilex exhibited significantly stronger antioxidant capacities than that of Ligustrum. Within six Ilex genotypes, great variation existed in their composition of individual phenolic compounds and their antioxidant properties. The comparative data and LC fingerprints obtained in this study may provide useful information for screening and breeding of better Kudingcha genotypes and also for their authentication and quality control.
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Antioxidantes/farmacología , Genotipo , Ilex/química , Ligustrum/química , Fenoles/análisis , Fenoles/farmacología , China , Cromatografía Liquida , Ilex/genética , Ligustrum/genética , Espectrometría de Masas , Extractos Vegetales/química , Hojas de la Planta/químicaRESUMEN
The techniques of random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphisms (AFLPs) were used to amplify the genomic DNA of 10 species of Ilex, so as to reveal the polymorphism in different species of Ilex. In RAPD analysis, a total of 301 lines were amplified with 11 kinds of primers selected from 100 kinds of 10 bp random primers, and the polymorphism was 98.63%. In AFLPs analysis,a huge diversity was showed by 3 primers combinations carried out on these species. Both RAPD and AFLPs analysis were clustered by UPGMA and the results showed that the genetic distances were the closest between I. purpurea and I. vomitoria Ait, I. Litseaefolia and I. zhejiangensis, I. hylonoma var. glabra and I. triflora var. kanehirai.
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Variación Genética , Ilex/genética , Polimorfismo Genético , Análisis del Polimorfismo de Longitud de Fragmentos Amplificados , Ilex/clasificación , Filogenia , Técnica del ADN Polimorfo Amplificado AleatorioRESUMEN
Details of the recently elucidated biosynthetic pathways of caffeine and related purine alkaloids are reviewed. The main caffeine biosynthetic pathway is a sequence consisting of xanthosine-->7-methylxanthosine-->7-methylxanthine-->theobromine-->caffeine. Genes encoding N-methyltransferases involved in three of these four reactions have been isolated and the molecular structure of N-methyltransferases investigated. Pathways for the catabolism of caffeine have also been studied, although there are currently no reports of enzymatic and genetic studies having been successfully carried out. Metabolism of purine alkaloids in species including Camellia, Coffea, Theobroma and Ilex plants is summarised, and evidence for the involvement of caffeine in chemical defense and allelopathy is discussed. Finally, information is presented on metabolic engineering that has produced coffee seedlings with reduced caffeine content, and transgenic caffeine-producing tobacco plants with enhanced disease resistance.
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Alcaloides/biosíntesis , Cafeína/biosíntesis , Plantas Modificadas Genéticamente/metabolismo , Purinas/biosíntesis , Alcaloides/metabolismo , Cacao/genética , Cacao/metabolismo , Cafeína/metabolismo , Camellia/genética , Camellia/metabolismo , Coffea/genética , Coffea/metabolismo , Ilex/genética , Ilex/metabolismo , Plantas Modificadas Genéticamente/genética , Purinas/metabolismoRESUMEN
Host races play a central part in understanding the role of host plant mediated divergence and speciation of phytophagous insects. Of greatest interest are host-associated populations that have recently diverged; however, finding genetic evidence for very recent divergences is difficult because initially only a few loci are expected to evolve diagnostic differences. The holly leafminer Phytomyza glabricola feeds on two hollies, Ilex glabra and I. coriacea, that are broadly sympatric throughout most of their ranges. The leafminer is often present on both host plants and exhibits a dramatic life history difference on the two hosts, suggesting that host races may be present. We collected 1393 bp of mitochondrial cytochrome oxidase I (COI) sequence and amplified fragment length polymorphism (AFLP) data (45 polymorphic bands) from sympatric populations of flies reared from the two hosts. Phylogenetic and frequency analysis of mitochondrial COI sequence data uncovered considerable variation but no structuring by the host plant, and only limited differentiation among geographical locations. In contrast, analysis of AFLP frequency data found a significant effect with host plant, and a much smaller effect with geographical location. Likewise, neighbour-joining analysis of AFLP data resulted in clustering by host plant. The AFLP data indicate that P. glabricola is most likely comprised of two host races. Because there were no fixed differences in mitochondrial or AFLP data, this host-associated divergence is likely to have occurred very recently. P. glabricola therefore provides a new sympatric system for exploring the role of geography and ecological specialization in the speciation of phytophagous insects.
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Variación Genética , Ilex/genética , Hojas de la Planta/parasitología , Plantas/parasitología , Animales , ADN Mitocondrial/genética , Complejo IV de Transporte de Electrones/genética , Ilex/clasificación , Ilex/enzimología , Mitocondrias/enzimología , North Carolina , Filogenia , South CarolinaRESUMEN
Nonrandom patterns of gene dispersal have been identified as possible causes of genetic structuring within populations. Attempts to model these patterns have generally focused solely on the effects of isolation by distance, but the processes involved are more complex than such modeling suggests. Here, we extend considerations of gene dispersal processes beyond simple isolation by distance effects by directly evaluating the effects of kin-structured gene dispersal mediated by the group dispersal of related seeds within fruits (i.e., kin-structured seed dispersal) by birds on genetic structure in Ilex leucoclada, a clonal dioecious shrub. To examine the genetic structure patterns, we established two 30x30 m plots (one with immature soils in old-growth forest and one in secondary forest, designated IM and SC, respectively) with different I. leucoclada stem densities. In these two plots 145 and 510 stems were found, representing 78 and 85 genets, respectively, identified by analyzing their genotypes at eight microsatellite loci. The clonal structure was stronger in the SC plot than in the IM plot. Correlograms of coancestry for genets in both plots exhibited significant, positive, high values in the shortest distance class, indicating the presence of strong genetic structure. However, Sp statistics revealed that the pattern of the genetic structure differed between the plots. In addition, to estimate the family structure within fruits, we sampled forty fruits, in total, from 15 randomly selected plants in the area around the IM and SC plots, and found that 80% of the fruits were multiseeded and 42-100% of the multiseeded fruits contained at least one pair of full sibs. Simulations based on these estimates demonstrated that the group dispersal of related seeds produced through correlated mating both within and across fruits, but not unstructured half-sib dispersal, could generate the observed magnitude and trends of genetic structure found in the IM plot. Furthermore, in addition to kin-structured seed dispersal, isolation by distance processes is also likely to promote genetic substructuring in the SC plot. After discussing possible ecological factors that may have contributed to the observed genetic structure, we contrast our results with those predicted by general isolation by distance models, and propose that kin-structured seed dispersal should promote some evolutionary phenomena, and thus should be incorporated, where appropriate, in models of gene dispersal in natural plant populations.
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Ilex/genética , Semillas/genética , Simulación por Computador , Frutas/genética , Genotipo , Ilex/embriología , Ilex/fisiología , Repeticiones de Microsatélite , Modelos Genéticos , Densidad de Población , Reproducción/genética , Reproducción/fisiología , Semillas/fisiologíaRESUMEN
BACKGROUND AND AIMS: The mode of reproduction (sexual vs. asexual) is likely to have important effects on genetic variation and its spatial distribution within plant populations. An investigation was undertaken of fine-scale clonal structure and diversity within patches of Ilex leucoclada (a clone-forming dioecious shrub). METHODS: Six patches were selected in a 1-ha plot previously established in an old-growth beech forest. Two of the selected patches were composed predominantly of stems with male flowers (male patch), and two contained stems with predominantly female flowers (female patch). The remaining two patches contained stems with male flowers and stems with female flowers in more or less equal proportions (mixed patch). Different genets were distinguished using random amplified polymorphic DNA (RAPD) markers. KEY RESULTS: One hundred and fifty-six genets with different RAPD phenotypes were identified among 1928 stems from the six patches. Among the six patches, the male patches had the lowest clonal diversity, and the mixed patches had the highest. Distribution maps of the genets showed that they extended downhill, reflecting natural layering that occurred when stems were pressed to the ground by heavy snow. In every patch, there were a few large genets with many stems and many small genets with a few stems. CONCLUSION: The differences in clonal diversity among patches may be due to differences in seedling recruitment frequencies. The skewed distribution of genet size (defined as the number of stems per genet) within patches may be due to differences in the timing of germination, or age (with early-establishing genets having clear advantages for acquiring resources) and/or intraspecific competition.