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1.
Mol Phylogenet Evol ; 142: 106642, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31605812

RESUMO

Hybridization and introgression between species in contact/hybrid zones provide important insight into the genetic and ecological mechanisms of speciation. Cactaceae represents the most important radiation of true succulent angiosperms in the New World. This diversification continues to date, with species experiencing few intrinsic barriers to gene flow and the frequent occurrence of natural hybridization. Here, we used RAD-Seq single-nucleotide polymorphism (SNP) data to investigate the genetic architecture of hybridization in four hybrid zones hosting Melocactus concinnus and four congeneric species (M. ernestii, M. glaucescens, M. paucispinus, and M. zehntneri). Our results revealed that M. concinnus is highly promiscuous in sympatric areas and hybridizes with various species distributed in Morro do Chapéu (Diamantina Plateau, Bahia), eastern Brazil. However, the contemporary genomic introgression among the investigated species is very low (c. 2-5%), confirming that even in the face of hybridization, Melocactus species maintain their genetic integrity. The genomic cline approach showed a large fraction of loci deviating from a model of neutral introgression, where most of the loci are consistent with selection favoring parental genotypes. Our results suggest the occurrence of weak premating but strong postmating reproductive isolation in the analyzed cactus species. Furthermore, as most of the Melocactus species are restricted in distribution, hybridization might negatively affect their integrity if hybrids replace the parental species.


Assuntos
Cactaceae/genética , Hibridização Genética , Brasil , Fluxo Gênico , Introgressão Genética , Polimorfismo de Nucleotídeo Único , Isolamento Reprodutivo , Simpatria
2.
PLoS One ; 14(11): e0220676, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31697700

RESUMO

The Drosophila repleta group is an array of more than 100 species endemic to the "New World", many of which are cactophilic. The ability to utilize decaying cactus tissues as breeding and feeding sites is a key aspect that allowed the successful diversification of the repleta group in American deserts and arid lands. Within this group, the Drosophila buzzatii cluster is a South American clade of seven closely related species in different stages of divergence, making them a valuable model system for evolutionary research. Substantial effort has been devoted to elucidating the phylogenetic relationships among members of the D. buzzatii cluster, including molecular phylogenetic studies that have generated ambiguous results where different tree topologies have resulted dependent on the kinds of molecular marker used. Even though mitochondrial DNA regions have become useful markers in evolutionary biology and population genetics, none of the more than twenty Drosophila mitogenomes assembled so far includes this cluster. Here, we report the assembly of six complete mitogenomes of five species: D. antonietae, D. borborema, D. buzzatii, two strains of D. koepferae and D. seriema, with the aim of revisiting phylogenetic relationships and divergence times by means of mitogenomic analyses. Our recovered topology using complete mitogenomes supports the hypothesis of monophyly of the D. buzzatii cluster and shows two main clades, one including D. buzzatii and D. koepferae (both strains), and the other containing the remaining species. These results are in agreement with previous reports based on a few mitochondrial and/or nuclear genes, but conflict with the results of a recent large-scale nuclear phylogeny, indicating that nuclear and mitochondrial genomes depict different evolutionary histories.


Assuntos
Drosophila/genética , Genoma Mitocondrial/genética , Animais , Evolução Biológica , Cactaceae/genética , Núcleo Celular/genética , DNA Mitocondrial/genética , Marcadores Genéticos/genética , Genômica/métodos , Filogenia
3.
Food Funct ; 10(12): 8116-8128, 2019 Dec 11.
Artigo em Inglês | MEDLINE | ID: mdl-31746888

RESUMO

It has been revealed in our previous studies that trypsin scavenges superoxide anions. In the current study, the mechanisms of storage quality improvement by trypsin were evaluated in H. undatus. Strikingly, the improvement is due not to its antibacterial or antifungal activity but to its superoxide scavenging activity. Moreover, trypsin significantly decreased the levels of ROS, cell permeability and membrane lipid peroxidation. The activities of major antioxidant enzymes were significantly improved by trypsin treatment. Transcriptome profiles of H. undatus treated with trypsin revealed the pathways and regulatory mechanisms of antioxidant genes up or down-regulated following trypsin treatment by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses. The results of protein-protein interaction networks indicated that CAT is the key among the enzymes of the complicated antioxidant system. In addition, the current results showed that the synergistic effect of trypsin with antioxidant enzymes can regulate the levels of endogenous active oxygen species, reduce malondialdehyde content, improve cell membrane integrity, alleviate cell damage and delay fruit ageing.


Assuntos
Antioxidantes/metabolismo , Cactaceae/química , Cactaceae/genética , Frutas/química , Proteínas de Plantas/genética , Tripsina/química , Antioxidantes/análise , Cactaceae/metabolismo , Conservação de Alimentos/métodos , Armazenamento de Alimentos , Frutas/genética , Frutas/metabolismo , Perfilação da Expressão Gênica , Ontologia Genética , Malondialdeído/análise , Malondialdeído/metabolismo , Proteínas de Plantas/metabolismo , Espécies Reativas de Oxigênio/análise , Espécies Reativas de Oxigênio/metabolismo , Transcriptoma
4.
Int J Mol Sci ; 20(10)2019 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-31117184

RESUMO

MicroRNA396 (miR396) is a conserved microRNA family that targets growth-regulating factors (GRFs), which play significant roles in plant growth and stress responses. Available evidence justifies the idea that miR396-targeted GRFs have important functions in many plant species; however, no genome-wide analysis of the pitaya (Hylocereus polyrhizus) miR396 gene has yet been reported. Further, its biological functions remain elusive. To uncover the regulatory roles of miR396 and its targets, the hairpin sequence of pitaya miR396b and the open reading frame (ORF) of its target, HpGRF6, were isolated from pitaya. Phylogenetic analysis showed that the precursor miR396b (MIR396b) gene of plants might be clustered into three major groups, and, generally, a more recent evolutionary relationship in the intra-family has been demonstrated. The sequence analysis indicated that the binding site of hpo-miR396b in HpGRF6 is located at the conserved motif which codes the conserved "RSRKPVE" amino acid in the Trp-Arg-Cys (WRC) region. In addition, degradome sequencing analysis confirmed that four GRFs (GRF1, c56908.graph_c0; GRF4, c52862.graph_c0; GRF6, c39378.graph_c0 and GRF9, c54658.graph_c0) are hpo-miR396b targets that are regulated by specific cleavage at the binding site between the 10th and 11th nucleotides from the 5' terminus of hpo-miR396b. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that hpo-miR396b is down-regulated when confronted with drought stress (15% polyethylene glycol, PEG), and its expression fluctuates under other abiotic stresses, i.e., low temperature (4 ± 1 °C), high temperature (42 ± 1 °C), NaCl (100 mM), and abscisic acid (ABA; 0.38 mM). Conversely, the expression of HpGRF6 showed the opposite trend to exposure to these abiotic stresses. Taken together, hpo-miR396b plays a regulatory role in the control of HpGRF6, which might influence the abiotic stress response of pitaya. This is the first documentation of this role in pitaya and improves the understanding of the molecular mechanisms underlying the tolerance to drought stress in this fruit.


Assuntos
Cactaceae/genética , Regulação da Expressão Gênica de Plantas , MicroRNAs/metabolismo , Estresse Fisiológico , Cactaceae/metabolismo , Cactaceae/fisiologia , MicroRNAs/fisiologia , Proteínas de Plantas/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA de Plantas
5.
FEBS Open Bio ; 9(8): 1403-1412, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31127874

RESUMO

Reverse-transcription quantitative real-time PCR (RT-qPCR) is a primary tool for measuring gene expression levels, and selection of appropriate reference genes is crucial for accurate and reproducible results of gene expression under various experimental conditions. However, no systematic evaluation of reference genes in pitaya (Hylocereus undatus Britt.) has been performed. Here, we examined the expression of five candidate reference genes, namely elongation factor 1-alpha (HuEF1-α), 18S ribosomal RNA (Hu18S rRNA), ubiquitin (HuUBQ), actin (HuACT), and ubiquitin-conjugating enzyme (HuUQT), under different conditions in pitaya. The expression stabilities of these five genes were evaluated using two computation programs: geNorm and NormFinder. The results were further validated by normalizing the expression of the phosphoglycerate kinase (HuPGK) and ethylene-responsive transcription factor (HuERF) genes. Our results indicate that combined use of HuUBQ and HuUQT is the most stable reference under all of the experimental conditions examined. HuEF1-α, HuUBQ, and HuUQT are the top three most stable reference genes under salt stress, drought stress, and heat stress, and across different cultivars. HuEF1-α, HuACT, and HuUQT exhibited the most stable expression patterns across different tissues. Our results will allow researchers to select the most appropriate reference genes for gene expression studies of pitaya under different conditions.


Assuntos
Sequência de Bases/genética , Cactaceae/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa/normas , Actinas/genética , Expressão Gênica/genética , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica de Plantas/genética , Genes de Plantas/genética , Fator 1 de Elongação de Peptídeos/genética , RNA Ribossômico 18S/genética , Padrões de Referência , Análise de Sequência de RNA/métodos , Ubiquitina/genética , Enzimas de Conjugação de Ubiquitina/genética , Sequenciamento Completo do Exoma/métodos
6.
Int J Mol Sci ; 20(8)2019 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-30999552

RESUMO

Sugar level is an important determinant of fruit taste and consumer preferences. However, upstream regulators that control sugar accumulation during fruit maturation are poorly understood. In the present work, we found that glucose is the main sugar in mature pitaya (Hylocereus) fruit, followed by fructose and sucrose. Expression levels of two sucrose-hydrolyzing enzyme genes HpINV2 and HpSuSy1 obviously increased during fruit maturation, which were correlated well with the elevated accumulation of glucose and fructose. A WRKY transcription factor HpWRKY3 was further identified as the putative binding protein of the HpINV2 and HpSuSy1 promoters by yeast one-hybrid and gel mobility shift assays. HpWRKY3 was localized exclusively in the nucleus and possessed trans-activation ability. HpWRKY3 exhibited the similar expression pattern with HpINV2 and HpSuSy1. Finally, transient expression assays in tobacco leaves showed that HpWRKY3 activated the expressions of HpINV2 and HpSuSy1. Taken together, we propose that HpWRKY3 is associated with pitaya fruit sugar accumulation by activating the transcriptions of sucrose metabolic genes. Our findings thus shed light on the transcriptional mechanism that regulates the sugar accumulation during pitaya fruit quality formation.


Assuntos
Cactaceae/metabolismo , Frutas/metabolismo , Proteínas de Plantas/metabolismo , Sacarose/metabolismo , Fatores de Transcrição/metabolismo , Cactaceae/genética , Frutas/genética , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Hidrólise , Proteínas de Plantas/genética , Fatores de Transcrição/genética , Ativação Transcricional
7.
Protoplasma ; 256(3): 805-814, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30604246

RESUMO

The clade ACPT (Anacampserotaceae, Cactaceae, Portulacaceae, and Talinaceae) is the most diverse lineage of the subordem Cactineae. The relationships between these families are still uncertain, with different topologies suggested by phylogenetic analyses with several combinations of markers. Different basic numbers (x) have been suggested for each family and for the subord, often in a contestable way. Comparative cytogenetic has helped to understand the evolutionary relationships of phylogenetically poorly resolved groups, as well as their mechanisms of karyotype evolution. The karyotype evolution in representatives of Cactineae was analyzed, focusing on the ACPT clade, through the analysis of chromosome number in a phylogenetic bias. The phylogeny obtained showed a well-resolved topology with support for the monophyly of the five families. Although a chromosomal number is known for less than 30% of the Cactineae species, the analyses revealed a high karyotype variability, from 2n = 8 to 2n = 110. The analysis of character reconstruction of the ancestral haploid numbers (p) suggested p = 12 for Cactineae, with distinct basic numbers for the clade family ACPT: Cactaceae and Montiaceae (p = 11), Talinaceae (p = 12), and Anacampserotaceae and Portulacaceae (p = 9). Talinaceae, Anacampserotaceae, and Cactaceae were stable, while Portulaca and Montiaceae were karyotypically variable. The chromosome evolution of this group was mainly due to events of descending disploidy and poliploidy. Our data confirm that the low phylogenetic resolution among the families of the ACPT clade is due to a divergence of this clade in a short period of time. However, each of these families can be characterized by basic chromosome numbers and unique karyotype evolution events.


Assuntos
Cactaceae/classificação , Cactaceae/genética , Caryophyllales/classificação , Caryophyllales/genética , Citogenética , Filogenia , Portulacaceae/classificação , Portulacaceae/genética , Cromossomos de Plantas/genética , Modelos Biológicos
8.
Molecules ; 24(3)2019 Jan 27.
Artigo em Inglês | MEDLINE | ID: mdl-30691184

RESUMO

The red flesh trait gives red pitayas more healthful components and a higher price, while the genetic mechanism behind this trait is unknown. In this manuscript, transcriptome analysis was employed to discover the genetic differences between white and red flesh in pitayas. A total of 27.99 Gb clean data were obtained for four samples. Unigenes, 79,049 in number, were generated with an average length of 1333 bp, and 52,618 Unigenes were annotated. Compared with white flesh, the expression of 10,215 Unigenes was up-regulated, and 4853 Unigenes were down-regulated in red flesh. The metabolic pathways accounted for 64.6% of all differentially expressed Unigenes in KEGG pathways. The group with high betalain content in red flesh and all structural genes, related to betalain biosynthesis, had a higher expression in red flesh than white flesh. The expression of the key gene, tyrosine hydroxylase CYP76AD1, was up-regulated 245.08 times, while 4,5-DOPA dioxygenase DODA was up-regulated 6.46 times. Moreover, the special isomers CYP76AD1α and DODAα were only expressed in red flesh. The competitive anthocyanin biosynthesis pathway had a lower expression in red flesh. Two MYB transcription factors were of the same branch as BvMYB1, regulating betalain biosynthesis in beet, and those transcription factors had expression differences in two kinds of pitayas, which indicated that they should be candidate genes controlling betalain accumulation in red pitayas. This research would benefit from identifying the major gene controlling red flesh trait and breed new cultivars with the red flesh trait. Future research should aim to prove the role of each candidate gene in betalain biosynthesis in red pitayas.


Assuntos
Betalaínas/biossíntese , Cactaceae/genética , Cactaceae/metabolismo , Frutas/genética , Frutas/metabolismo , Regulação da Expressão Gênica de Plantas , Transcriptoma , Antocianinas/biossíntese , Vias Biossintéticas/genética , Cactaceae/classificação , Biologia Computacional/métodos , Perfilação da Expressão Gênica , Genes de Plantas , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia
9.
Plant Physiol Biochem ; 135: 460-468, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30497974

RESUMO

Frequent somatic variations exist in pitaya (Hylocereus undatus) plants grown under abiotic stress conditions. Long terminal repeat (LTR) retrotransposons can be activated under stressful conditions and play key roles in plant genetic variation and evolution. However, whether LTR retrotransposons promotes pitaya somatic variations by regulating abiotic stress responses is still uncertain. In this study, transcriptionally active LTR retrotransposons were identified in pitaya after exposure to a number of stress factors, including in vitro culturing, osmotic changes, extreme temperatures and hormone treatments. In total, 26 LTR retrotransposon reverse transcriptase (RT) cDNA sequences were isolated and identified as belonging to 9 Ty1-copia and 4 Ty3-gypsy families. Several RT cDNA sequences had differing similarity levels with RTs from pitaya genomic DNA and other plant species, and were differentially expressed in pitaya under various stress conditions. LTR retrotransposons accounted for at least 13.07% of the pitaya genome. HuTy1P4 had a high copy number and low expression level in young stems of pitaya, and its expression level increased after exposure to hormones and abiotic stresses, including in vitro culturing, osmotic changes, cold and heat. HuTy1P4 may have been subjected to diverse transposon events in 13 pitaya plantlets successively subcultured for four cycles. Thus, the expression levels of these retrotransposons in pitaya were associated with stress responses and may be involved in the occurrence of the somaclonal variation in pitaya.


Assuntos
Cactaceae/genética , Regulação da Expressão Gênica de Plantas/fisiologia , Retroelementos/genética , Sequências Repetidas Terminais/genética , Cactaceae/fisiologia , Clonagem Molecular , DNA de Plantas/genética , Genoma de Planta/genética , Genoma de Planta/fisiologia , Retroelementos/fisiologia , Análise de Sequência de DNA , Estresse Fisiológico/genética , Estresse Fisiológico/fisiologia , Sequências Repetidas Terminais/fisiologia
10.
J Hered ; 110(1): 4-21, 2019 01 07.
Artigo em Inglês | MEDLINE | ID: mdl-30476167

RESUMO

Members of the cactus family are keystone species of arid and semiarid biomes in the Americas, as they provide shelter and resources to support other members of ecosystems. Extraordinary examples are the several species of flies of the genus Drosophila that lay eggs and feed in their rotting stems, which provide a model system for studying evolutionary processes. Although there is significant progress in understanding the evolution of Drosophila species, there are gaps in our knowledge about the cactus lineages hosting them. Here, we review the current knowledge about the evolution of Cactaceae, focusing on phylogenetic relationships and trends revealed by the study of DNA sequence data. During the last several decades, the availability of molecular phylogenies has considerably increased our understanding of the relationships, biogeography, and evolution of traits in the family. Remarkably, although succulent cacti have very low growth rates and long generation times, they underwent some of the fastest diversifications observed in the plant kingdom, possibly fostered by strong ecological interactions. We have a better understanding of the reproductive biology, population structure and speciation mechanisms in different clades. The recent publication of complete genomes for some species has revealed the importance of phenomena such as incomplete lineage sorting. Hybridization and polyploidization are common in the family, and have been studied using a variety of phylogenetic methods. We discuss potential future avenues for research in Cactaceae, emphasizing the need of a concerted effort among scientists in the Americas, together with the analyses of data from novel sequencing techniques.


Assuntos
Evolução Biológica , Cactaceae/genética , Animais , DNA de Plantas , Genômica , Filogenia , Filogeografia
11.
J Hered ; 110(1): 46-57, 2019 01 07.
Artigo em Inglês | MEDLINE | ID: mdl-30107510

RESUMO

Host plant shifts in herbivorous insects often involve facing new environments that may speed up the evolution of oviposition behavior, performance-related traits, morphology, and, incidentally, reproductive isolation. In the genus Drosophila, cactophilic species of the repleta group include emblematic species in the study of the evolution of host plant utilization. The South American D. buzzatii and its sibling D. koepferae are a model system for the study of differential host plant use. Although these species exhibit a certain degree of niche overlap, the former breeds primarily on decaying cladodes of Opuntia cacti while D. koepferae main hosts are columnar cacti of the genus Trichocereus. Opuntia sulphurea and Trichocereus terscheckii are among the main hosts in nature. These cacti differ in ecological (spatial and temporal predictability) and chemical characteristics. Particularly relevant is the presence of toxic alkaloids in T. terscheckii. Studies of the effects of these cacti and alkaloids revealed the remarkable impact on oviposition behavior, viability, developmental time, wing morphology, mating success, and developmental stability in both species. Recent whole-genome expression studies showed that expression profiles are massively affected by the rearing cactus, and that the presence of alkaloids is the main factor modulating gene expression in D. buzzatii. Functional enrichment analysis indicated that differentially expressed genes are related to detoxification processes and stress response-though genes involved in development are an important part of the transcriptomic response. The implications of our studies in the evolution of host plant use in the repleta group are discussed.


Assuntos
Adaptação Biológica , Cactaceae/fisiologia , Drosophila/fisiologia , Transcriptoma , Alcaloides/metabolismo , Animais , Evolução Biológica , Cactaceae/genética , Cactaceae/parasitologia , Drosophila/genética , Ecossistema , Feminino , Masculino , Modelos Biológicos , Oviposição , Reprodução
12.
Genetica ; 146(3): 329-340, 2018 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-29779125

RESUMO

Endemic, obligate outcrossing plant species with narrow geographic distributions and disjunct populations are prone to loss of genetic diversity. Simultaneously, delineating clear species boundaries is important for targeted conservation efforts. The rare and endemic cactus, Sclerocactus brevihamatus subsp. tobuschii (SBT), has a parapatric relationship with Sclerocactus brevihamatus subsp. brevihamatus (SBB) but genetic distance between the two taxa is unknown. We: (1) developed taxon-specific polymorphic microsatellites, (2) assessed genetic diversity within and among nine populations of SBT, and within one population of SBB, and (3) estimated the genetic relationship between the two subspecies. Within-population genetic diversity of SBT was moderate to high (mean Ho = 0.37; mean He = 0.59). Indirect estimate of inbreeding corrected for null alleles (Fis-INEst) was low for SBT, ranging from 0.03 to 0.14 (mean Fis-INEst = 0.07). Genetic differentiation among populations of SBT was low based on Fst (0.08) and AMOVA (ФPT = 0.10). Lack of genetic and spatial correlation in SBT populations coupled with the presence of private alleles and bottleneck events in several populations suggests that reproductive isolation is occurring but that sufficient time may not have yet passed to manifest strong differentiation. Cluster analyses segregated the 10 populations into three distinct groups, and separated SBB genotypes clearly. Results suggest that while hybridization between the two subspecies may occur, SBT is clearly differentiated genetically from SBB to retain its current taxonomic status.


Assuntos
Cactaceae/classificação , Cactaceae/genética , Variação Genética , Genética Populacional , Alelos , DNA de Plantas , Evolução Molecular , Repetições de Microssatélites , Texas
13.
Am J Bot ; 105(3): 446-462, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29738076

RESUMO

PREMISE OF THE STUDY: The Caryophyllales contain ~12,500 species and are known for their cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear, and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. METHODS: We generated 84 transcriptomes and combined these with 224 publicly available transcriptomes to perform a phylogenomic analysis of Caryophyllales. To overcome the computational challenge of ortholog detection in such a large data set, we developed an approach for clustering gene families that allowed us to analyze >300 transcriptomes and genomes. We then inferred the species relationships using multiple methods and performed gene-tree conflict analyses. KEY RESULTS: Our phylogenetic analyses resolved many clades with strong support, but also showed significant gene-tree discordance. This discordance is not only a common feature of phylogenomic studies, but also represents an opportunity to understand processes that have structured phylogenies. We also found taxon sampling influences species-tree inference, highlighting the importance of more focused studies with additional taxon sampling. CONCLUSIONS: Transcriptomes are useful both for species-tree inference and for uncovering evolutionary complexity within lineages. Through analyses of gene-tree conflict and multiple methods of species-tree inference, we demonstrate that phylogenomic data can provide unparalleled insight into the evolutionary history of Caryophyllales. We also discuss a method for overcoming computational challenges associated with homolog clustering in large data sets.


Assuntos
Evolução Biológica , Caryophyllales/genética , Genes de Plantas , Genômica/métodos , Modelos Genéticos , Filogenia , Transcriptoma , Cactaceae/genética , Carnivoridade , Análise por Conglomerados , Evolução Molecular , Genoma de Planta , Análise de Sequência de DNA , Homologia de Sequência , Especificidade da Espécie
14.
PLoS One ; 13(4): e0195475, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29630653

RESUMO

Succulent cacti (Cactaceae) are among the most threatened taxonomic groups assessed to date. Here we evaluated the genetic diversity and population structure of a narrow endemic columnar cactus Pilosocereus aureispinus. This species is only found in a small area of c. 300 km2 of rocky savanna from eastern Brazil and it is currently classified as vulnerable (VU) on the International Union for Conservation of Nature (IUCN) red list. Eight microsatellite loci were genotyped for 91 individuals from four localities of the known P. aureispinus range. In contrast with expectations for narrow endemic species, we found relatively high levels of genetic diversity (e.g., HE = 0.390 to 0.525; HO = 0.394 to 0.572) and very low population structure based on the variation of six loci. All the analyzed individuals were clustered in one unique genetic group in assignment tests. We also generated the sequences of two plastid markers (trnT-trnL and psbD-trnT) and found no variation on a subsample of 39 individuals. We used Landsat 8 images and Normalized Difference Vegetation Index to estimate a potential extent of occurrence of c. 750 km2 for this species. Our results showed that P. aureispinus is not suffering from erosion of nuclear genetic variability due to its narrow distribution. However, we advocate that because of the extremely limited extent of occurrence, the ongoing anthropogenic disturbances in its habitat, and phylogenetic distinctiveness of P. aureispinus, this species should be classified as endangered (EN) on the IUCN Red List.


Assuntos
Cactaceae/genética , Espécies em Perigo de Extinção , Brasil , Cactaceae/classificação , Conservação dos Recursos Naturais , DNA de Plantas/genética , Marcadores Genéticos , Variação Genética , Genética Populacional , Pradaria , Repetições de Microssatélites , Filogenia , Filogeografia , Plastídeos/genética
15.
PLoS One ; 13(1): e0190385, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29342184

RESUMO

The Stenocereus griseus species complex (SGSC) has long been considered taxonomically challenging because the number of taxa belonging to the complex and their geographical boundaries remain poorly understood. Bayesian clustering and genetic distance-based methods were used based on nine microsatellite loci in 377 individuals of three main putative species of the complex. The resulting genetic clusters were assessed for ecological niche divergence and areolar morphology, particularly spination patterns. We based our species boundaries on concordance between genetic, ecological, and morphological data, and were able to resolve four species, three of them corresponding to S. pruinosus from central Mexico, S. laevigatus from southern Mexico, and S. griseus from northern South America. A fourth species, previously considered to be S. griseus and commonly misidentified as S. pruinosus in northern Mexico showed significant genetic, ecological, and morphological differentiation suggesting that it should be considered a new species, S. huastecorum, which we describe here. We show that population genetic analyses, ecological niche modeling, and morphological studies are complementary approaches for delimiting species in taxonomically challenging plant groups such as the SGSC.


Assuntos
Cactaceae/classificação , Teorema de Bayes , Cactaceae/genética , Genes de Plantas , Modelos Teóricos , Especificidade da Espécie
16.
Proc Natl Acad Sci U S A ; 114(45): 12003-12008, 2017 11 07.
Artigo em Inglês | MEDLINE | ID: mdl-29078296

RESUMO

Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae (Pachycereus, Lophocereus, and Stenocereus) and a more distant outgroup cactus, Pereskia We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting (ILS). In the best supported gene trees, 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves, a phenomenon termed "hemiplasy." The high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits, which could confound understanding of species relationships and character evolution in cacti.


Assuntos
Cactaceae/genética , Genoma de Planta/genética , Sequência de Bases , Evolução Molecular , Genômica/métodos , México , Modelos Genéticos , América do Norte , Filogenia
17.
J Hered ; 108(5): 469-478, 2017 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-28369439

RESUMO

Species inhabiting drylands commonly depend on the surrounding vegetation for recruitment under stress, while competition may affect populations in moister environments. Our objective was to analyze how different climates and vegetation affect the fine-scale spatial genetic structure (SGS) of the columnar cactus Echinopsis terscheckii. At 4 sites, we estimated vegetation cover by digitized patches and the normalized difference vegetation index (NDVI). We mapped 30 individuals per population and collected tissue for isozyme electrophoresis using 15 putative loci. Spatial autocorrelation between all possible genotype pairs and the number of genetically homogeneous groups and families were calculated for each population. Greater cover (66%) and average NDVI values were detected in the most humid habitat that consisted of fewer, larger, and more dispersed vegetation patches. All populations were genetically diverse and showed significant SGS. Positive correlations were found between the distance at which maximum autocorrelation and kinship values were reached and vegetation area and patch size. Also higher NDVI values were associated with lower number of patches. Populations exposed to higher precipitation and vegetation cover consisted of sparse individuals that clustered at larger distances whereas vegetation patches in arid climates produced groups of closely related genotypes at small distances. These results support the stress-gradient genetic hypothesis. Under water stress, facilitation promotes establishment underneath patchy vegetation resulting in fine-scale family structure. In moister xerophilous forests, competition for resources, that is, light, results in sparse individuals and thus coarse-scale neighborhoods. This information can guide conservation and/or restoration efforts, such as the spatial scale to be considered in germplasm collection.


Assuntos
Cactaceae/genética , Ecossistema , Genética Populacional , Argentina
18.
PLoS One ; 12(4): e0175905, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28426818

RESUMO

Historic demography changes of plant species adapted to New World arid environments could be consistent with either the Glacial Refugium Hypothesis (GRH), which posits that populations contracted to refuges during the cold-dry glacial and expanded in warm-humid interglacial periods, or with the Interglacial Refugium Hypothesis (IRH), which suggests that populations contracted during interglacials and expanded in glacial times. These contrasting hypotheses are developed in the present study for the giant columnar cactus Cephalocereus columna-trajani in the intertropical Mexican drylands where the effects of Late Quaternary climatic changes on phylogeography of cacti remain largely unknown. In order to determine if the historic demography and phylogeographic structure of the species are consistent with either hypothesis, sequences of the chloroplast regions psbA-trnH and trnT-trnL from 110 individuals from 10 populations comprising the full distribution range of this species were analysed. Standard estimators of genetic diversity and structure were calculated. The historic demography was analysed using a Bayesian approach and the palaeodistribution was derived from ecological niche modelling to determine if, in the arid environments of south-central Mexico, glacial-interglacial cycles drove the genetic divergence and diversification of this species. Results reveal low but statistically significant population differentiation (FST = 0.124, P < 0.001), although very clear geographic clusters are not formed. Genetic diversity, haplotype network and Approximate Bayesian Computation (ABC) demographic analyses suggest a population expansion estimated to have taken place in the Last Interglacial (123.04 kya, 95% CI 115.3-130.03). The species palaeodistribution is consistent with the ABC analyses and indicates that the potential area of palaedistribution and climatic suitability were larger during the Last Interglacial and Holocene than in the Last Glacial Maximum. Overall, these results suggest that C. columna-trajani experienced an expansion following the warm conditions of interglacials, in accordance with the GRH.


Assuntos
Cactaceae/classificação , Ecossistema , Cactaceae/genética , Cactaceae/fisiologia , DNA de Plantas/genética , DNA de Plantas/isolamento & purificação , Genes de Plantas , Haplótipos , México , Modelos Teóricos , Fotossíntese , Clima Tropical
19.
Mol Biol Rep ; 43(12): 1315-1320, 2016 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-27631640

RESUMO

The aim of this study was to develop microsatellite markers as a tool to study population structure, genetic diversity and effective population size of Echinopsis chiloensis, an endemic cactus from arid and semiarid regions of Central Chile. We developed 12 polymorphic microsatellite markers for E. chiloensis using next-generation sequencing and tested them in 60 individuals from six sites, covering all the latitudinal range of this species. The number of alleles per locus ranged from 3 to 8, while the observed (Ho) and expected (He) heterozygosity ranged from 0.0 to 0.80 and from 0.10 to 0.76, respectively. We also detected significant differences between sites, with FST values ranging from 0.05 to 0.29. Microsatellite markers will enable us to estimate genetic diversity and population structure of E. chiloensis in future ecological and phylogeographic studies.


Assuntos
Cactaceae/genética , Sequenciamento de Nucleotídeos em Larga Escala/normas , Análise de Sequência de DNA/normas , DNA de Plantas/genética , Genes de Plantas , Repetições de Microssatélites , Filogenia , Padrões de Referência
20.
Heredity (Edinb) ; 116(6): 550-7, 2016 06.
Artigo em Inglês | MEDLINE | ID: mdl-27071846

RESUMO

Pilosocereus machrisii and P. aurisetus are cactus species within the P. aurisetus complex, a group of eight cacti that are restricted to rocky habitats within the Neotropical savannas of eastern South America. Previous studies have suggested that diversification within this complex was driven by distributional fragmentation, isolation leading to allopatric differentiation, and secondary contact among divergent lineages. These events have been associated with Quaternary climatic cycles, leading to the hypothesis that the xerophytic vegetation patches which presently harbor these populations operate as refugia during the current interglacial. However, owing to limitations of the standard phylogeographic approaches used in these studies, this hypothesis was not explicitly tested. Here we use Approximate Bayesian Computation to refine the previous inferences and test the role of different events in the diversification of two species within P. aurisetus group. We used molecular data from chloroplast DNA and simple sequence repeats loci of P. machrisii and P. aurisetus, the two species with broadest distribution in the complex, in order to test if the diversification in each species was driven mostly by vicariance or by long-dispersal events. We found that both species were affected primarily by vicariance, with a refuge model as the most likely scenario for P. aurisetus and a soft vicariance scenario most probable for P. machrisii. These results emphasize the importance of distributional fragmentation in these species, and add support to the hypothesis of long-term isolation in interglacial refugia previously proposed for the P. aurisetus species complex diversification.


Assuntos
Evolução Biológica , Cactaceae/genética , Genética Populacional , Filogeografia , Refúgio de Vida Selvagem , Teorema de Bayes , Cactaceae/classificação , Simulação por Computador , DNA de Cloroplastos/genética , DNA de Plantas/genética , Ecossistema , Repetições de Microssatélites , Modelos Genéticos , Dispersão Vegetal , Análise de Sequência de DNA , América do Sul
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