RESUMO
Chloroplast genomes (cpDNA) in angiosperms are usually highly conserved. Although rearrangements have been observed in some lineages, such as Passiflora, the mechanisms that lead to rearrangements are still poorly elucidated. In the present study, we obtained 20 new chloroplast genomes (18 species from the genus Passiflora, and Dilkea retusa and Mitostemma brevifilis from the family Passifloraceae) in order to investigate cpDNA evolutionary history in this group. Passiflora cpDNAs vary in size considerably, with â¼50 kb between shortest and longest. Large inverted repeat (IR) expansions were identified, and at the extreme opposite, the loss of an IR was detected for the first time in Passiflora, a rare event in angiosperms. The loss of an IR region was detected in Passiflora capsularis and Passiflora costaricensis, a species in which occasional biparental chloroplast inheritance has previously been reported. A repertory of rearrangements such as inversions and gene losses were detected, making Passiflora one of the few groups with complex chloroplast genome evolution. We also performed a phylogenomic study based on all the available cp genomes and our analysis implies that there is a need to reconsider the taxonomic classifications of some species in the group.
Assuntos
DNA de Cloroplastos/química , Rearranjo Gênico , Genoma de Cloroplastos , Passiflora/genética , Filogenia , Sequências Repetidas Invertidas , Passiflora/química , Passiflora/classificaçãoRESUMO
KEY MESSAGE: The plastome of Linum usitatissimum was completely sequenced allowing analyses of evolution of genome structure, RNA editing sites, molecular markers, and indicating the position of Linaceae within Malpighiales. Flax (Linum usitatissimum L.) is an economically important crop used as food, feed, and industrial feedstock. It belongs to the Linaceae family, which is noted by high morphological and ecological diversity. Here, we reported the complete sequence of flax plastome, the first species within Linaceae family to have the plastome sequenced, assembled and characterized in detail. The plastome of flax is a circular DNA molecule of 156,721 bp with a typical quadripartite structure including two IRs of 31,990 bp separating the LSC of 81,767 bp and the SSC of 10,974 bp. It shows two expansion events from IRB to LSC and from IRB to SSC, and a contraction event in the IRA-LSC junction, which changed significantly the size and the gene content of LSC, SSC and IRs. We identified 109 unique genes and 2 pseudogenes (rpl23 and ndhF). The plastome lost the conserved introns of clpP gene and the complete sequence of rps16 gene. The clpP, ycf1, and ycf2 genes show high nucleotide and aminoacid divergence, but they still possibly retain the functionality. Moreover, we also identified 176 SSRs, 20 tandem repeats, and 39 dispersed repeats. We predicted in 18 genes a total of 53 RNA editing sites of which 32 were not found before in other species. The phylogenetic inference based on 63 plastid protein-coding genes of 38 taxa supports three major clades within Malpighiales order. One of these clades has flax (Linaceae) sister to Chrysobalanaceae family, differing from earlier studies that included Linaceae into the euphorbioid clade.
Assuntos
Linho/genética , Genomas de Plastídeos/genética , Linaceae/genética , Plastídeos/genética , Edição de RNA , Sítios de Ligação/genética , Proteínas de Cloroplastos/genética , DNA de Cloroplastos/química , DNA de Cloroplastos/genética , Evolução Molecular , Genes de Cloroplastos/genética , Linaceae/classificação , Filogenia , Análise de Sequência de DNARESUMO
The genus Stevia comprises approximately 200 species, which are distributed in North and South America, and are representative of the species diversity of the Asteraceae in the New World. We reconstructed the phylogenetic relationships using sequences of ITS and cpDNA and estimated the divergence times of the major clade of this genus. Our results suggested that Stevia originated in Mexico 7.0-7.3 million years ago (Mya). Two large clades, one with shrub species and another with herb species, were separated at about 6.6 Mya. The phylogenetic reconstruction suggested that an ancestor of Stevia was a small shrub in temperate pine-oak forests and the evolutionary change from a shrub state to a herb state occurred only once. A Brazilian clade was nested in a Mexican herb clade, and its origin was estimated to be 5.2 Mya, suggesting that the migration from North America to South America occurred after the formation of the Isthmus of Panama. The species diversity in Mexico appears to reflect the habitat diversity within the temperate pine-oak forest zone. The presence of many conspecific diploid-polyploid clades in the phylogenetic tree reflects the high frequency of polyploidization among the perennial Stevia species.
Assuntos
Asteraceae/genética , Biodiversidade , Filogenia , Stevia/genética , Asteraceae/classificação , Evolução Biológica , Brasil , DNA de Cloroplastos/química , DNA de Cloroplastos/genética , DNA Intergênico/química , DNA Intergênico/genética , DNA de Plantas/química , DNA de Plantas/genética , Ecossistema , México , Filogeografia , Poliploidia , Alinhamento de Sequência , Análise de Sequência de DNA , Stevia/classificaçãoRESUMO
PREMISE OF THE STUDY: Bignoniaceae is an important component of neotropical forests and a model for evolutionary and biogeographical studies. A previous combination of molecular markers and morphological traits improved the phylogeny of the group. Here we demonstrate the value of next-generation sequencing (NGS) to assemble the chloroplast genome of eight Anemopaegma species and solve taxonomic problems. METHODS: Three NGS platforms were used to sequence total DNA of Anemopaegma species. After genome assembly and annotation, we compared chloroplast genomes within Anemopaegma, with other Lamiales species, and the evolutionary rates of protein-coding genes using Tanaecium tetragonolobum as the outgroup. Phylogenetic analyses of Anemopaegma with different data sets were performed. KEY RESULTS: Chloroplast genomes of Anemopaegma species ranged from 167,413 bp in A. foetidum to 168,987 bp in A. acutifolium ("typical" form). They exhibited a characteristic quadripartite structure with a large single-copy region (75,070-75,761 bp), a small single-copy region (12,766-12,817 bp) and a pair of inverted repeat regions (IRs) (39,480-40,481) encoding an identical set of 112 genes. An inversion of a fragment with ca. 8 kb, located in the IRs and containing the genes trnI-AAU, ycf2, and trnL-CAA, was observed in these chloroplast genomes when compared with those of other Lamiales. CONCLUSIONS: Anemopaegma species have the largest genomes within the Lamiales possibly due to the large amount of repetitive sequences and IR expansion. Variation was higher in coding regions than in noncoding regions, and some genes were identified as markers for differentiation between species. The use of the entire chloroplast genome gave better phylogenetic resolution of the taxonomic groups. We found that two forms of A. acutifolium result from different maternal lineages.
Assuntos
Bignoniaceae/classificação , Genoma de Cloroplastos/genética , Genoma de Planta/genética , Bignoniaceae/genética , Cloroplastos/genética , Inversão Cromossômica , DNA de Cloroplastos/química , DNA de Cloroplastos/genética , Sequenciamento de Nucleotídeos em Larga Escala , Fases de Leitura Aberta/genética , Filogenia , Sequências Repetitivas de Ácido Nucleico/genética , Análise de Sequência de DNARESUMO
The aims of this study were to establish a random amplified polymorphic DNA (RAPD) fingerprint database of chloroplast DNA (cpDNA) from different cultivars of Cornus officinalis and to convert RAPD markers to sequence characterized amplified regions (SCAR) markers. A method of extraction was established that was suitable for obtaining cpDNA from samples rapidly dried in silicone; an RAPD fingerprint database was built; and the genetic distance between samples was used as statistical clustering variables for calculating DICE genetic similarity coefficients and for building a kinship tree chart. RAPD markers were converted to SCAR markers to design specific primers, and samples from C. officinalis cultivars, plants of the same family, and its adulterants, were used for amplification and identification. Fifteen amplified primers with stable polymorphisms were screened for amplification of 130 copies of materials. In total, 57 sites were achieved, 40 of which were polymorphic, and the polymorphic rate was up to 70.18%. A genetic tree was built based on seven cultivars. SCAR markers of C. officinalis cpDNA were successfully converted into RAPD markers. cpDNA samples from hawthorn, C. officinalis, Cornus wood, and grape were used for SCAR amplification, and their bands were distinctly different. In conclusion, SCAR markers and cpDNA may be used for research on C. officinalis and its adulterants, and the results may provide a basis for identifying germplasm and screening fine varieties at a molecular level.
Assuntos
Cornus/genética , DNA de Cloroplastos/genética , Marcadores Genéticos , Polimorfismo Genético , Sequência de Bases , Análise por Conglomerados , Cornus/classificação , DNA de Cloroplastos/química , Dados de Sequência Molecular , Técnica de Amplificação ao Acaso de DNA Polimórfico , Análise de Sequência de DNA , Transformação GenéticaRESUMO
PREMISE OF STUDY: Flowering traits can sometimes be overemphasized in taxonomic classifications. The fused and completely differentiated papilionate floral organs in the neotropical legume trees Vatairea and Vataireopsis were traditionally used in part to ascribe these genera to the tribe Dalbergieae. In contrast, the free and mostly undifferentiated floral parts of Luetzelburgia and Sweetia fit the circumscription of the "primitive" Sophoreae. Such divergent floral morphologies thought to divide deep phylogenetic lineages indeed may be prone to episodic transformation among close papilionoid relatives. METHODS: We sampled 26 of 27 known species of Luetzelburgia, Sweetia, Vatairea, and Vataireopsis in parsimony and Bayesian phylogenetic analyses of nuclear ribosomal ITS/5.8S and six plastid (matK, 3'-trnK, psbA-trnH, trnL intron, rps16 intron, and trnD-T) DNA sequence loci. KEY RESULTS: The analyses of individual and combined data sets strongly resolved the monophyly of each of Luetzelburgia, Sweetia, Vatairea, and Vataireopsis. Vataireopsis was resolved as sister to the rest and the morphologically divergent Luetzelburgia and Vatairea were strongly resolved as sister clades. Floral morphology was generally not a good predictor of phylogenetic relatedness. CONCLUSIONS: Luetzelburgia, Sweetia, Vatairea, and Vataireopsis are unequivocally resolved as the "vataireoid" clade. Fruit and vegetative traits are found to be more phylogenetically conserved than many floral traits. This explains why the identity of the vataireoids has been overlooked or confused. The evolvability of floral traits may also be a general condition among many of the early-branching papilionoid lineages.
Assuntos
DNA de Cloroplastos/química , Fabaceae/genética , Flores/anatomia & histologia , Filogenia , Evolução Biológica , DNA Intergênico/química , Fabaceae/anatomia & histologia , Fabaceae/químicaRESUMO
Salvia subgenus Calosphace (Lamiaceae) is economically and ethnomedicinally significant and comprised of more than 500 species. Although strongly supported as monophyletic, it has received no comprehensive systematic research since the initial establishment of 91 taxonomic sections in 1939. Representative taxa of 73 sections of Calosphace were sampled to investigate the phylogenetic relationships and identify major lineages using chloroplast (intergenic spacer psbA-trnH) and nuclear ribosomal DNA (internal transcribed spacer). Phylogenetic analysis of the combined data sets established monophyly of seven sections (Blakea, Corrugatae, Erythrostachys, Hastatae, Incarnatae, Microsphace, and Sigmoideae) and four major lineages (S. axillaris, "Hastatae clade", "Uliginosae clade", and "core Calosphace"). Sections spanning two or more centers of diversity are not supported by our results; rather, supported relationships exhibit significant geographic structure. Mexico is supported as the geographic origin of Calosphace, and no more than seven dispersal events to South America are required to account for current disjunct distributions.
Assuntos
DNA de Plantas/química , Filogenia , Salvia/classificação , DNA de Cloroplastos/química , DNA de Cloroplastos/genética , DNA Intergênico/química , DNA Intergênico/genética , DNA de Plantas/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Geografia , Mutação INDEL , México , Salvia/genética , Análise de Sequência de DNA , América do SulRESUMO
BACKGROUND: Mangroves are ecologically important and highly threatened forest communities. Observational and genetic evidence has confirmed the long distance dispersal capacity of water-dispersed mangrove seeds, but less is known about the relative importance of pollen vs. seed gene flow in connecting populations. We analyzed 980 Avicennia germinans for 11 microsatellite loci and 940 Rhizophora mangle for six microsatellite loci and subsampled two non-coding cpDNA regions in order to understand population structure, and gene flow within and among four major estuaries on the Caribbean and Pacific coasts of Panama. RESULTS: Both species showed similar rates of outcrossing (t= 0.7 in A. germinans and 0.8 in R. mangle) and strong patterns of spatial genetic structure within estuaries, although A. germinans had greater genetic structure in nuclear and cpDNA markers (7 demes > 4 demes and Sp= 0.02 > 0.002), and much greater cpDNA diversity (H(d)= 0.8 > 0.2) than R. mangle. The Central American Isthmus serves as an exceptionally strong barrier to gene flow, with high levels nuclear (F(ST)= 0.3-0.5) and plastid (F(ST)= 0.5-0.8) genetic differentiation observed within each species between coasts and no shared cpDNA haplotypes between species on each coast. Finally, evidence of low ratios of pollen to seed dispersal (r = -0.6 in A. germinans and 7.7 in R. mangle), coupled with the strong observed structure in nuclear and plastid DNA among most estuaries, suggests low levels of gene flow in these mangrove species. CONCLUSIONS: We conclude that gene dispersal in mangroves is usually limited within estuaries and that coastal geomorphology and rare long distance dispersal events could also influence levels of structure.
Assuntos
Avicennia/genética , Estuários , Variação Genética , Rhizophoraceae/genética , Região do Caribe , Núcleo Celular/genética , Cruzamentos Genéticos , DNA de Cloroplastos/química , DNA de Cloroplastos/genética , Ecossistema , Fluxo Gênico , Geografia , Haplótipos , Endogamia , Modelos Lineares , Repetições de Microssatélites/genética , Dados de Sequência Molecular , Oceano Pacífico , Panamá , Pólen/genética , Sementes/genética , Análise de Sequência de DNARESUMO
PREMISE OF THE STUDY: The temperate forests of southern South America were greatly affected by glaciations. Previous studies have indicated that some cold-tolerant tree species were able to survive glacial periods in small, ice-free patches within glaciated areas in the Andes and in southern Patagonia. Here we asked whether populations of the mesothermic species Eucryphia cordifolia also were able to survive glaciations in these areas or only in unglaciated coastal areas. METHODS: The chloroplast intergenic spacer trnV-ndhC was sequenced for 150 individuals from 22 locations. Genetic data were analyzed (standard indexes of genetic diversity, a haplotype network, and genetic differentiation) in a geographical context. KEY RESULTS: Two of the nine haplotypes detected were widespread in high frequency across the entire range of the species. The highest levels of genetic diversity were found around 40°S, decreasing sharply northward and more moderately southward. No differences in genetic diversity were found between Andean and coastal populations. Notably, seven haplotypes were found in a small area of the Coast Range known as the Cordillera Pelada (40°S). The differentiation coefficients G(ST) and N(ST) revealed that most of the genetic variation detected was due to variation within populations. CONCLUSIONS: The low levels of population differentiation and the high genetic diversity found in the Cordillera Pelada suggest that this area was the main refugium for E. cordifolia during glaciations. Nevertheless, given the high levels of genetic diversity found in some Andean populations, we cannot discount that some local populations also survived the glaciation in the Andes.
Assuntos
Genética Populacional , Magnoliopsida/genética , Polimorfismo Genético , Alelos , DNA de Cloroplastos/química , DNA de Cloroplastos/genética , DNA Intergênico/química , DNA Intergênico/genética , DNA de Plantas/química , DNA de Plantas/genética , Variação Genética , Geografia , Haplótipos , Camada de Gelo , Filogeografia , Análise de Sequência de DNA , América do Sul , Especificidade da Espécie , ÁrvoresRESUMO
PREMISE OF THE STUDY: Intraspecific variation among 20 populations of Podostemum ceratophyllum Michx. was investigated to test the hypothesis of range expansion from southern refugia since the last glacial maximum. METHODS: Six noncoding regions of chloroplast DNA were sequenced in 60 individuals. Populations were divided into two groups, north and south of the glacial boundary, in addition to isolated populations in Arkansas and Honduras. Variation in populations north of the boundary was compared with variation in populations to the south and in the isolated populations. KEY RESULTS: Nucleotide diversity was an order of magnitude lower in populations north of the glacial boundary than in those to the south. The Arkansas and Honduras populations showed no variation. The predominant haplotype in northern populations was also found in a Virginia population. CONCLUSIONS: Reduced variation north of the glacial boundary suggests a founder event associated with range expansion since the last glacial maximum. Colonization probably occurred from populations in refugia located several hundred kilometers south of the glacial boundary. The results provide insight into the effects of past and current climate change on patterns of geographic distribution and genetic variation in aquatic plants.