RESUMO
Capirona (Calycophyllum spruceanum Benth.) belongs to subfamily Ixoroideae, one of the major lineages in the Rubiaceae family, and is an important timber tree. It originated in the Amazon Basin and has widespread distribution in Bolivia, Peru, Colombia, and Brazil. In this study, we obtained the first complete chloroplast (cp) genome of capirona from the department of Madre de Dios located in the Peruvian Amazon. High-quality genomic DNA was used to construct libraries. Pair-end clean reads were obtained by PE 150 library and the Illumina HiSeq 2500 platform. The complete cp genome of C. spruceanum has a 154,480 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (84,813 bp) and a small single-copy (SSC) region (18,101 bp), separated by two inverted repeat (IR) regions (25,783 bp). The annotation of C. spruceanum cp genome predicted 87 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, and one pseudogene. A total of 41 simple sequence repeats (SSR) of this cp genome were divided into mononucleotides (29), dinucleotides (5), trinucleotides (3), and tetranucleotides (4). Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with the other six Ixoroideae species revealed that the small single copy and large single copy regions showed more divergence than inverted regions. Finally, phylogenetic analyses resolved that C. spruceanum is a sister species to Emmenopterys henryi and confirms its position within the subfamily Ixoroideae. This study reports for the first time the genome organization, gene content, and structural features of the chloroplast genome of C. spruceanum, providing valuable information for genetic and evolutionary studies in the genus Calycophyllum and beyond.
Assuntos
Evolução Biológica , Proteínas de Cloroplastos/genética , Cloroplastos/genética , DNA de Cloroplastos/genética , Genoma de Cloroplastos , Polimorfismo de Nucleotídeo Único , Rubiaceae/genética , Proteínas de Cloroplastos/metabolismo , DNA de Cloroplastos/análise , Genômica , Anotação de Sequência Molecular , Filogenia , Rubiaceae/classificação , Rubiaceae/crescimento & desenvolvimentoRESUMO
KEY MESSAGE: The plastomes of E. edulis and E. oleracea revealed several molecular markers useful for genetic studies in natural populations and indicate specific evolutionary features determined by vicariant speciation. Arecaceae is a large and diverse family occurring in tropical and subtropical ecosystems worldwide. E. oleracea is a hyperdominant species of the Amazon forest, while E. edulis is a keystone species of the Atlantic forest. It has reported that E. edulis arose from vicariant speciation after the emergence of the belt barrier of dry environment (Cerrado and Caatinga biomes) between Amazon and Atlantic forests, isolating the E. edulis in the Atlantic forest. We sequenced the complete plastomes of E. edulis and E. oleracea and compared them concerning plastome structure, SSRs, tandem repeats, SNPs, indels, hotspots of nucleotide polymorphism, codon Ka/Ks ratios and RNA editing sites aiming to investigate evolutionary traits possibly affected by distinct environments. Our analyses revealed 303 SNPs, 91 indels, and 82 polymorphic SSRs among both species. Curiously, the narrow correlation among localization of repetitive sequences and indels strongly suggests that replication slippage is involved in plastid DNA mutations in Euterpe. Moreover, most non-synonymous substitutions represent amino acid variants in E. edulis that evolved specifically or in a convergent manner across the palm phylogeny. Amino acid variants observed in several plastid proteins in E. edulis were also identified as positive signatures across palm phylogeny. The higher incidence of specific amino acid changes in plastid genes of E. edulis in comparison with E. oleracea probably configures adaptive genetic variations determined by vicariant speciation. Our data indicate that the environment generates a selective pressure on the plastome making it more adapted to specific conditions.
Assuntos
Euterpe/genética , Evolução Molecular , Florestas , Genomas de Plastídeos/genética , Adaptação Fisiológica/genética , Arecaceae/classificação , Arecaceae/genética , Proteínas de Cloroplastos/genética , Proteínas de Cloroplastos/metabolismo , DNA de Cloroplastos/análise , DNA de Cloroplastos/genética , Ecossistema , Euterpe/classificação , Genes de Cloroplastos/genética , Repetições de Microssatélites/genética , Mutação , Filogenia , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA , Especificidade da EspécieRESUMO
Casearia grandiflora (Salicaceae) is a typical Cerrado species adapted to disturbed environments, making it useful for restoration projects. Knowledge of genetic diversity is important for establishing conservation strategies for this species. This study aimed to compare chloroplast haplotype diversity and structure of C. grandiflora, under the assumption that protected areas hold greater genetic diversity than disturbed areas. The populations studied are from Parque Nacional de Sete Cidades Conservation Unit and from the surroundings of the city of Cocal de Telha, both located in the State of Piauí. Molecular analyses were performed with seven chloroplast microsatellite loci. The number of private haplotypes and haplotype diversity were higher in the conservation unit, which reinforces the importance of these areas in maintaining biodiversity. Analysis of molecular variance showed that most of the genetic variation is found within populations, with a moderate divergence between them (FST = 0.14). The Bayesian analysis and discriminant analysis of principal components suggested that populations are not structured, revealing that a set of individuals from Parque Nacional de Sete Cidades were more divergent within populations than between them. Since literature has little information on C. grandiflora, the results of this study provide important contribution to a better understanding of the specie's genetic diversity.
Assuntos
Casearia/genética , Cloroplastos/genética , DNA de Cloroplastos/análise , Variação Genética , Teorema de Bayes , Conservação dos Recursos Naturais , Análise Discriminante , Genética Populacional , Haplótipos , Repetições de MicrossatélitesRESUMO
UNLABELLED: ⢠PREMISE OF THE STUDY: Whole genome duplication (WGD) and specific polyploidy events marked turning points for angiosperm genome structure and evolution. Therefore, cytogenetic studies of polyploidy-prone groups such as the tropical Malvaceae and plant formations such as as the Brazilian Cerrado have gained further importance. We present new chromosome counts for Cerrado Bombacoideae and revised chromosome numbers for the Malvaceae s.l., compare these between subfamilies, and relate them to phylogenetic signal.⢠METHODS: We studied the chromosome number of Eriotheca candolleana, E. gracilipes, E. pubescens, Pachira glabra, Pseudobombax longiflorum, and P. tomentosum. We also compared Eriotheca species ploidy levels using flow cytometry. We compiled chromosome numbers for 557 species of Malvaceae s.l., including 37 Bombacoideae species. We included this information in a phylogenetic reconstruction based on chloroplast matK-trnK DNA to evaluate chromosome evolution of the Malvaceae s.l. and the Bombacoideae in particular.⢠KEY RESULTS: The Cerrado Bombacoideae presented consistently high chromosome numbers. Numbers for Eriotheca species were among the highest and varied among populations. Flow cytometry analyses showed similar 1Cx DNA for all cytotypes and indicated neopolyploidy. Chromosome numbers differed between subfamilies, with the lowest numbers in the Malvoideae and Byttnerioideae and the highest in Tilioideae. Chromosome numbers had significant phylogenetic signal for Bombacoideae but not for Malvoideae or Malvaceae s.l.⢠CONCLUSIONS: Clearly distinct chromosome numbers allied to monophyly provide some support for a circumscription of the Bombacoideae and distinction within the Malvaceae. The phylogenetic signal for chromosome number supports the idea of an ancient WGD and further neopolyploidy events as important evolutionary trends for the Bombacoideae.
Assuntos
Evolução Biológica , Cromossomos de Plantas , Malvaceae/genética , Filogenia , Poliploidia , Brasil , DNA de Cloroplastos/análiseRESUMO
Phylogeographic studies have made a significant contribution to the interpretation of genetic lineage distribution in response to climate changes, such as during glaciation events of the Neogene. However, the effects of ancient landscapes associated with global sea level rises, tectonic processes, and climatology driving lineage evolution have been largely overlooked. These effects can be tested in widespread lineages of cold-tolerant species that have endured cooling, and thus, phylogeographic patterns may reflect large-scale processes that were not reset by the ice ages. We hereby combine geological evidence from marine sedimentary basins, Andean orogeny, and climatology with molecular dating and statistical phylogeography to infer how geological and climatic processes affected the distribution of lineages in cold-tolerant Nothofagus species during the Cenozoic. A total of 239 populations along the entire range of all species within the genus Nothofagus (N. antarctica, N. betuloides, N. dombeyi, N. nitida, and N. pumilio) were sampled and analyzed by sequencing three non-coding regions of the chloroplast. We found 30 chloroplast DNA haplotypes that were geographically structured. Molecular dating calibrated with fossils revealed that ancestral lineages appeared in Eocene/Oligocene, whereas most divergences took place during the Miocene; in turn, Bayesian skyline plots showed that population expansion occurred in the Early Pleistocene (1.5-1 million years ago). Lineage divergence from all wide-ranging Nothofagus was spatially and temporally concordant with episodic marine transgressions and warmer times in Patagonia during Eocene/Miocene Epochs. Long-lasting stable raised areas preserved haplotype diversity throughout Patagonia, from where cold-tolerant taxa expanded their ranges during pre-Quaternary times. The detailed study of such ancient divergences is novel and allows us to infer the effects of geological processes on distribution patterns of ancient lineages, that is, phylogeology.
Assuntos
Evolução Biológica , Magnoliopsida/classificação , Clima , DNA de Cloroplastos/análise , Haplótipos , Magnoliopsida/genética , Filogenia , FilogeografiaRESUMO
BACKGROUND: Podocarpus lambertii (Podocarpaceae) is a native conifer from the Brazilian Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots in the world. The advancement of next-generation sequencing technologies has enabled the rapid acquisition of whole chloroplast (cp) genome sequences at low cost. Several studies have proven the potential of cp genomes as tools to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as further probe the structural and functional evolution of plants. In this work, we present the complete cp genome sequence of P. lambertii. METHODOLOGY/PRINCIPAL FINDINGS: The P. lambertii cp genome is 133,734 bp in length, and similar to other sequenced cupressophytes, it lacks one of the large inverted repeat regions (IR). It contains 118 unique genes and one duplicated tRNA (trnN-GUU), which occurs as an inverted repeat sequence. The rps16 gene was not found, which was previously reported for the plastid genome of another Podocarpaceae (Nageia nagi) and Araucariaceae (Agathis dammara). Structurally, P. lambertii shows 4 inversions of a large DNA fragment â¼20,000 bp compared to the Podocarpus totara cp genome. These unexpected characteristics may be attributed to geographical distance and different adaptive needs. The P. lambertii cp genome presents a total of 28 tandem repeats and 156 SSRs, with homo- and dipolymers being the most common and tri-, tetra-, penta-, and hexapolymers occurring with less frequency. CONCLUSION: The complete cp genome sequence of P. lambertii revealed significant structural changes, even in species from the same genus. These results reinforce the apparently loss of rps16 gene in Podocarpaceae cp genome. In addition, several SSRs in the P. lambertii cp genome are likely intraspecific polymorphism sites, which may allow highly sensitive phylogeographic and population structure studies, as well as phylogenetic studies of species of this genus.
Assuntos
DNA de Cloroplastos/genética , DNA de Plantas/genética , Genoma de Cloroplastos , Traqueófitas/genética , DNA de Cloroplastos/análise , DNA de Plantas/análise , Genes de Plantas , Genoma de Planta , Sequências Repetitivas de Ácido Nucleico , Análise de Sequência de DNARESUMO
Environmental reservoirs of zooxanthellae are essential for coral larvae settlement; understanding where they occur and how they are maintained is important for coral reef ecology. This study investigated the dispersal of Symbiodinium spp. by the stoplight parrotfish Sparisoma viride, which had high mean densities of viable and cultivable Symbiodinium (3207-8900 cells ml(-1)) in faeces. Clades A, B and G were detected using amplified chloroplast ribosomal sequences (cp23S-HVR), and corresponded with diet preferences of fish and the environmental Symbiodinium diversity of the region. Cells are constantly dispersed in the water column and deposited in the substrate at a local level (86 ± 17.8 m(2)), demonstrating that parrotfishes are vectors for short-distance dispersal of zooxanthellae. Such dispersal could constitute a key role in the maintenance of environmental Symbiodinium reservoirs.
Assuntos
DNA de Cloroplastos/genética , DNA Ribossômico/genética , Dinoflagellida/fisiologia , Comportamento Alimentar , Perciformes/fisiologia , Animais , Colômbia , Recifes de Corais , DNA de Cloroplastos/análise , DNA Ribossômico/análise , Dinoflagellida/genética , Fezes/química , Dados de Sequência Molecular , Filogenia , Densidade Demográfica , Análise de Sequência de DNA , SimbioseRESUMO
PREMISE OF THE STUDY: The South American genus Gymnocalycium (Cactoideae-Trichocereae) demonstrates how the sole use of morphological data in Cactaceae results in conflicts in assessing phylogeny, constructing a taxonomic system, and analyzing trends in the evolution of the genus. METHODS: Molecular phylogenetic analysis was performed using parsimony and Bayesian methods on a 6195-bp data matrix of plastid DNA sequences (atpI-atpH, petL-psbE, trnK-matK, trnT-trnL-trnF) of 78 samples, including 52 species and infraspecific taxa representing all the subgenera of Gymnocalycium. We assessed morphological character evolution using likelihood methods to optimize characters on a Bayesian tree and to reconstruct possible ancestral states. KEY RESULTS: The results of the phylogenetic study confirm the monophyly of the genus, while supporting overall the available infrageneric classification based on seed morphology. Analysis showed the subgenera Microsemineum and Macrosemineum to be polyphyletic and paraphyletic. Analysis of morphological characters showed a tendency toward reduction of stem size, reduction in quantity and hardiness of spines, increment of seed size, development of napiform roots, and change from juicy and colorful fruits to dry and green fruits. CONCLUSIONS: Gymnocalycium saglionis is the only species of Microsemineum and a new name is required to identify the clade including the remaining species of Microsemineum; we propose the name Scabrosemineum in agreement with seed morphology. Identifying morphological trends and environmental features allows for a better understanding of the events that might have influenced the diversification of the genus.
Assuntos
Cactaceae/classificação , Cactaceae/genética , Evolução Molecular , Filogenia , Análise de Sequência de DNA , Teorema de Bayes , Evolução Biológica , Cactaceae/anatomia & histologia , DNA de Cloroplastos/análise , Frutas/anatomia & histologia , Geografia , Dados de Sequência Molecular , Raízes de Plantas/anatomia & histologia , Caules de Planta/anatomia & histologia , Sementes/anatomia & histologia , América do SulRESUMO
Andigena potatoes (Solanum tuberosum L. subsp. andigena Hawkes) (2n = 4x = 48) are important, native-farmer-selected cultivars in the Andes, which form a primary gene pool for improving a worldwide grown potato (S. tuberosum subsp. tuberosum). To elucidate the origin of Andigena, 196 Andigena accessions were compared with 301 accessions of 33 closely related cultivated and wild species using several types of chloroplast DNA (ctDNA) markers and nuclear DNA (nDNA) restriction fragment length polymorphism (RFLP) markers. Fourteen ctDNA types (haplotypes) and 115 RFLP bands were detected in Andigena, of which the main haplotypes and frequent RFLP bands were mostly shared with a cultivated diploid species, S. stenotomum Juz. et Buk. Principal component analysis of nDNA polymorphisms revealed a progressive and continuous variation from Peruvian wild species with C-type ctDNA to a group of wild species having S-type ctDNA in its variation range (S. bukasovii, S. canasense, S. candolleanum, and S. multidissectum), to cultivated diploid potatoes (S. phureja and S. stenotomum), and to cultivated tetraploid potatoes (Andigena and Chilean S. tuberosum subsp. tuberosum). These results suggest that the initial Andigena population arose with multiple origins exclusively from S. stenotomum. The overall evolutionary process toward the present-day Andigena was discussed.
Assuntos
Nucléolo Celular/genética , DNA de Cloroplastos/análise , Evolução Molecular , Marcadores Genéticos , Solanum tuberosum/genética , Argentina , Bolívia , DNA de Plantas/análise , Equador , Geografia , México , Peru , Filogenia , Polimorfismo GenéticoRESUMO
The geographical distribution of chloroplast DNA (cpDNA) variation in 39 populations of two hybridizing Mexican red oaks, Quercus affinis and Q. laurina, was investigated using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Six haplotypes were identified. Of these, two (H1 and H4), separated by four mutations, had high frequencies (58 and 23% of the individuals, respectively) and were present across the whole geographical range of both species, often co occurring in the same populations. The other four haplotypes were rare, geographically restricted, and are probably derived from the two frequent haplotypes. Latitudinal or other clinal patterns in diversity levels or haplotype composition of populations were not apparent. The pattern of haplotype distribution was characterized by some mosaicism, with contrasting populations often situated in proximity. Average within-population diversity (hS=0.299) and population differentiation (GST=0.499) were, respectively, higher and lower than values reported in previous studies of oak species. There was evidence for phylogeographical structure, as indicated by NST (0.566) being significantly higher than GST. Haplotypic variation was largely species-independent, although some very weak associations were detected between haplotypes H1 and H4 and morphological and nuclear molecular variation correspondingly characterizing Q. affinis and Q. laurina. These oaks probably did not experience a marked restriction to one or a few particular subregions of their present range during the last glacial cycle. It is more likely that substantial populations persisted throughout several episodes of climatic change, but experienced recurrent latitudinal and altitudinal migrations which may have caused the widespread distribution of haplotypes H1 and H4 and frequent intermixing of populations.
Assuntos
DNA de Cloroplastos/análise , Variação Genética , Quercus/genética , Meio Ambiente , Marcadores Genéticos , Haplótipos , Humanos , México , Mosaicismo , Filogenia , Polimorfismo de Fragmento de Restrição , Quercus/classificaçãoRESUMO
Assessing the impact of farmer management of maize landraces in the Central Valleys of Oaxaca, Mexico is crucial to an understanding of maize evolution, as it was first domesticated there. In this paper, we report on the impact of traditional farmer management of maize populations in this region in structuring molecular diversity and on the population dynamics of maize landraces. These populations, from a sample of local landraces cultivated by farmers in six villages, show little among-population differentiation (Fst=0.011). Most surprisingly, there is no isolation by distance and small among-village differentiation (Fst=0.003). For an outbreeding plant such as maize, one would expect populations to fit Hardy-Weinberg equilibrium, but significant homozygote excess (Fis=0.13) was found. This homozygote excess shows remarkable interpopulation and interlocus differences. We show that this pattern is related to variation in the mean anthesis-silking interval as well as to the flowering range or heterogeneity in flowering of a given population. A short anthesis-silking interval and high level of heterogeneity in flowering precocity will favor assortative mating. This leads to a locus-dependent population substructure giving an unusual case of Wahlund effect and inbreeding while high levels of seed exchange among farmers prevent population differentiation at both village and regional levels.
Assuntos
Agricultura , Genética Populacional , Zea mays/genética , DNA de Cloroplastos/análise , Genótipo , México , Análise de Sequência de DNA , Zea mays/crescimento & desenvolvimentoRESUMO
To conserve the long-term selection potential of maize, it is necessary to investigate past and present evolutionary processes that have shaped quantitative trait variation. Understanding the dynamics of quantitative trait evolution is crucial to future crop breeding. We characterized population differentiation of maize landraces from the State of Oaxaca, Mexico for quantitative traits and molecular markers. Qst values were much higher than Fst values obtained for molecular markers. While low values of Fst (0.011 within-village and 0.003 among-villages) suggest that considerable gene flow occurred among the studied populations, high levels of population differentiation for quantitative traits were observed (ie an among-village Qst value of 0.535 for kernel weight). Our results suggest that although quantitative traits appear to be under strong divergent selection, a considerable amount of gene flow occurs among populations. Furthermore, we characterized nonproportional changes in the G matrix structure both within and among villages that are consequences of farmer selection. As a consequence of these differences in the G matrix structure, the response to multivariate selection will be different from one population to another. Large changes in the G matrix structure could indicate that farmers select for genes of major and pleiotropic effect. Farmers' decision and selection strategies have a great impact on phenotypic diversification in maize landraces.
Assuntos
Agricultura , Variação Genética , Genética Populacional , Seleção Genética , Zea mays/genética , DNA de Cloroplastos/análise , México , Fenótipo , Análise de Sequência de DNA , Zea mays/classificaçãoRESUMO
In this work we report on the phylogeography of the endangered tree species Caryocar brasiliense based on variability in two classes of maternally inherited chloroplast DNA sequences with different rates of molecular evolution. Eleven sequence haplotypes of a noncoding region between the genes trnT and trnF and 21 distinct 10-locus microsatellite haplotypes could be identified in a total of 160 individuals, collected in 10 widespread populations of C. brasiliense. An amova indicated that most of the variation can be attributed to differences among populations, both for DNA sequence (87.51%) and microsatellites (84.38%). Phylogeography based on a median-joining network analysis of the noncoding region showed a sharp difference from the analysis of microsatellite haplotypes. Nevertheless, both analyses indicated that multiple lineages may have contributed to the origin of C. brasiliense populations in Brazilian Cerrado. Incongruences in the microsatellite haplotypes network suggest that homoplasy, which emerged from recurrent and independent mutations, greatly influenced the evolution of the C. brasiliense chloroplast genome. We hypothesize that our results may show the outcome of the restriction of ancient relic populations to moist refugias during extended droughts coinciding with glaciation in the northern hemisphere. The subsequent spread to favourable areas throughout Central Brazil may have caused contact between different lineages during the interglacial periods. The extinction of megafauna dispersers in the last glaciation may have caused a restriction in seed movement and currently, gene flow has been occurring mainly by pollen movement.