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1.
Zootaxa ; 4576(1): zootaxa.4576.1.5, 2019 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-31715776

RESUMO

The genus Orthopristis includes seven valid species, three from the western Atlantic and five from eastern Pacific, while the available identification guides and taxonomic keys incorrectly recognize Orthopristis ruber as the only valid species found on the Atlantic coast of South America. Efforts to expand the inventory of fish species from the northern coast of Brazil led to the identification of two distinct species of Orthopristis from Atlantic South America, based on the analysis of coloration patterns and meristic data, as well as DNA. In the present study, the limits of Orthopristis ruber are reviewed, while Orthopristis scapularis is recognized as a valid species for the northern and northeastern coasts of South America. Based on intermediate morphological characteristics and nuclear DNA markers, a hybrid zone was identified off the state of Espírito Santo, on the eastern Brazilian coast. Additionally, considerations are made on the diversity and biogeography of the coastal marine and estuarine fishes found on the Brazilian coast.


Assuntos
Perciformes , Animais , Brasil , Peixes , Hibridização Genética
2.
Zootaxa ; 4679(3): zootaxa.4679.3.11, 2019 Oct 03.
Artigo em Inglês | MEDLINE | ID: mdl-31715954

RESUMO

Andrew Brower recently published a long article in this journal that seeks to dismantle evidence for hybridization between species of Heliconius butterflies. The main evidence that Brower criticizes here is given in two papers published by my colleagues and myself in 2007. In this reply, I briefly defend our evidence, and at greater length provide additional background information to help establish the credibility of the evidence even more firmly than previously.


Assuntos
Borboletas , Animais , Hibridização Genética
3.
J Agric Food Chem ; 67(42): 11805-11814, 2019 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-31566383

RESUMO

The impact of cross-breeding two low phytic acid (lpa) rice mutants on the content of phytic acid and the metabolite profile of the resulting double mutant was investigated. Progenies resulting from the cross of Os-lpa-XS110-1, a rice mutant carrying the myo-inositol kinase (OsMIK) mutated gene, and Os-lpa-XS110-2, with the multidrug resistance-associated protein ABC transporter gene 5 (OsMRP5) as the mutation target, were subjected to high-pressure ion chromatography. The reduction of the phytic acid content in the double mutant (-63%) was much more pronounced than in the single mutants (-26 and -47%). Gas chromatography-based metabolite profiling revealed a superimposition of the metabolite profiles inherited from the lpa progenitors in the double mutant progenies; the resulting metabolite signature was predominated by the OsMIK mutation effect. The study demonstrated that cross-breeding of two single lpa mutants can be employed to generate double lpa rice mutants showing both a significant reduction in the content of phytic acid and the imprinting of a specific mutation-induced metabolite signature.


Assuntos
Transportadores de Cassetes de Ligação de ATP/genética , Hibridização Genética , Oryza/química , Fosfotransferases (Aceptor do Grupo Álcool)/genética , Ácido Fítico/análise , Proteínas de Plantas/genética , Transportadores de Cassetes de Ligação de ATP/metabolismo , Mutação , Oryza/genética , Oryza/metabolismo , Fosfotransferases (Aceptor do Grupo Álcool)/metabolismo , Ácido Fítico/metabolismo , Proteínas de Plantas/metabolismo , Sementes/química , Sementes/genética , Sementes/metabolismo
4.
Mol Plant Microbe Interact ; 32(12): 1623-1634, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31657673

RESUMO

Pathogenic fungi can have devastating effects on agriculture and health. One potential challenge in dealing with pathogens is the possibility of a host jump (i.e., when a pathogen infects a new host species). This can lead to the emergence of new diseases or complicate the management of existing threats. We studied host specificity by using a hybrid fungus formed by mating two closely related fungi: Ustilago bromivora, which normally infects Brachypodium spp., and U. hordei, which normally infects barley. Although U. hordei was unable to infect Brachypodium spp., the hybrid could. These hybrids also displayed the same mating-type bias that had been observed in U. bromivora and provide evidence of a dominant spore-killer-like system on the sex chromosome of U. bromivora. By analyzing the genomic composition of 109 hybrid strains, backcrossed with U. hordei over four generations, we identified three regions associated with infection on Brachypodium spp. and 75 potential virulence candidates. The most strongly associated region was located on chromosome 8, where seven genes encoding predicted secreted proteins were identified. The fact that we identified several regions relevant for pathogenicity on Brachypodium spp. but that none were essential suggests that host specificity, in the case of U. bromivora, is a multifactorial trait which can be achieved through different subsets of virulence factors.


Assuntos
Brachypodium , Ustilago , Brachypodium/microbiologia , Genômica , Hordeum/microbiologia , Hibridização Genética , Ustilago/genética , Ustilago/patogenicidade , Virulência/genética
5.
Int J Food Microbiol ; 310: 108331, 2019 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-31479829

RESUMO

Lack of the prezygotic barrier in the Saccharomyces genus facilitates the construction of artificial interspecific hybrids among different Saccharomyces species. Hybrids that maintain the interesting features of parental strains have been applied in industry for many beneficial purposes. Two of the most important problems faced by wine makers is nitrogen deficiency in grape must and low-temperature fermentation. In our study, hybrids were constructed by using selected low nitrogen-demanding cryotolerant S. eubayanus, S. uvarum strains and S. cerevisiae. The fermentation capacity of the hybrid strains was tested under four conditions by combining two temperatures, 12 °C and 28 °C, and two nitrogen concentrations, 60 mg/L and 300 mg/L. The hybrid strains obtained combined characters of both parental strains and conferred better fermentation rates under low-temperature or low-nitrogen conditions. The hybrid strains also produced larger amounts of acetate esters and higher alcohols, which increase aroma intensity and complexity in wine. Nitrogen sources were more rapidly consumed by the hybrid strains, which allows greater competition ability under nitrogen-deficiency conditions. Therefore, the interspecific hybridisation between low nitrogen-demanding cryotolerant strains and S. cerevisiae is a potential solution for low-temperature or low-nitrogen fermentations.


Assuntos
Temperatura Baixa , Fermentação , Microbiologia de Alimentos/métodos , Hibridização Genética , Nitrogênio , Saccharomyces , Vinho/microbiologia , Ácido Acético/metabolismo , Álcoois/metabolismo , Biotecnologia , Ésteres/metabolismo , Nitrogênio/metabolismo , Odorantes , Saccharomyces/classificação , Saccharomyces/genética , Saccharomyces/metabolismo , Vitis/microbiologia
6.
Yi Chuan ; 41(8): 703-715, 2019 Aug 20.
Artigo em Chinês | MEDLINE | ID: mdl-31447421

RESUMO

Hybrid rice has contributed greatly to global food security. Cytoplasmic male sterility (CMS) and photo/ thermo sensitive genic male sterility (P/TGMS) are genetic bases for three-line and two-line hybrid rice production, respectively. In contrast, (sub-) specific hybrid sterility (HS) is a major barrier for utilization of hybrid vigor of distant hybrid rice. Therefore, understanding the molecular regulatory mechanism of rice fertility is a key technical issue for hybrid rice industry, and a long-standing basic scientific issue for nuclear-cytoplasmic interaction and reproductive isolation. Chinese geneticists of plant sciences have made tremendous contributions on the molecular genetic basis of rice fertility related to hybrid rice production. Here, we review the development of hybrid rice production systems in China and summarize current advance on genetic basis and molecular mechanism of CMS, P/TGMS, and HS involved in hybrid rice. We also discuss problems of hybrid rice production in China and point out new direction for future utilization of heterosis in rice.


Assuntos
Hibridização Genética , Oryza/genética , Oryza/fisiologia , Infertilidade das Plantas/genética , China , Fertilidade/genética , Vigor Híbrido
7.
Chemistry ; 25(53): 12298-12302, 2019 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-31386225

RESUMO

Oligonucleotide-based therapeutics have made rapid progress in clinical treatment of a variety of disease indications. Since most therapeutic oligonucleotides serve more than just one function and tend to have a prolonged lifetime, spatio-temporal control of these functions would be desirable. Photoswitches like azobenzene have proven themselves as useful tools in this matter. Upon irradiation, the photoisomerization of the azobenzene moiety causes destabilization in adjacent base pairs, leading to a decreased hybridization affinity. Since the way the azobenzene is incorporated in the oligonucleotide is of utmost importance, we synthesized locked azobenzene C-nucleosides and compared their photocontrol capabilities to established azobenzene C-nucleosides in oligonucleotide test-sequences by means of fluorescence-, UV/Vis-, and CD-spectroscopy.


Assuntos
Compostos Azo/química , Nucleosídeos/química , Oligonucleotídeos/química , Pareamento de Bases , Hibridização Genética , Hibridização de Ácido Nucleico , Análise Espectral
8.
BMC Evol Biol ; 19(1): 164, 2019 08 05.
Artigo em Inglês | MEDLINE | ID: mdl-31382876

RESUMO

BACKGROUND: Hybridogenesis can represent the first stage towards hybrid speciation where the hybrid taxon eventually weans off its parental species. In hybridogenetic water frogs, the hybrid Pelophylax kl. esculentus (genomes RL) usually eliminates one genome from its germline and relies on its parental species P. lessonae (genomes LL) or P. ridibundus (genomes RR) to perpetuate in so-called L-E and R-E systems. But not exclusively: some all-hybrid populations (E-E system) bypass the need for their parental species and fulfill their sexual cycle via triploid hybrid frogs. Genetic surveys are essential to understand the great diversity of these hybridogenetic dynamics and their evolution. Here we conducted such study using RAD-sequencing on Pelophylax from southern Switzerland (Ticino), a geographically-isolated region featuring different assemblages of parental P. lessonae and hybrid P. kl. esculentus. RESULTS: We found two types of hybridogenetic systems in Ticino: an L-E system in northern populations and a presumably all-hybrid E-E system in the closely-related southern populations, where P. lessonae was not detected. In the latter, we did not find evidence for triploid individuals from the population genomic data, but identified a few P. ridibundus (RR) as offspring from interhybrid crosses (LR × LR). CONCLUSIONS: Assuming P. lessonae is truly absent from southern Ticino, the putative maintenance of all-hybrid populations without triploid individuals would require an unusual lability of genome elimination, namely that P. kl. esculentus from both sexes are capable of producing gametes with either L or R genomes. This could be achieved by the co-existence of L- and R- eliminating lineages or by "hybrid amphigamy", i. e. males and females producing sperm and eggs among which both genomes are represented. These hypotheses imply that polyploidy is not the exclusive evolutionary pathway for hybrids to become reproductively independent, and challenge the classical view that hybridogenetic taxa are necessarily sexual parasites.


Assuntos
Hibridização Genética , Ranidae/genética , Animais , Feminino , Especiação Genética , Genoma , Células Germinativas , Heterozigoto , Masculino , Filogeografia , Ranidae/classificação , Reprodução , Isolamento Reprodutivo , Suíça , Triploidia
9.
J Insect Sci ; 19(4)2019 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-31422419

RESUMO

Torymus sinensis Kamijo (Hymenoptera: Torymidae) is an alien parasitoid that is used in many areas of the world for biological control the Asian chestnut gall wasp, Dryocosmus kuriphilus Yasumatsu (Hymenoptera: Cynipidae). In Italy, this parasitoid was imported from Japan in 2003 and subsequently multiplied and released throughout the country. In this study, a phylogenetic investigation was carried out on insects from three different sites in northern Tuscany (Italy). Moreover, the possible hybridization between T. sinensis and some native Torymus species was evaluated. The conserved region 18S rRNA gene and the hypervariable ITS2 (Internal Transcribed Spacer 2) region of the ribosomal cistrone were selected as molecular markers. Sequencing the amplified products, after cloning, ruled out any hybridization between T. sinensis and the native Torymus species, and also confirmed the presence of two haplotypes for the Tuscan population of T. sinensis both for the region of the 18S rRNA gene as well as for the ITS2 region. These results confirm that the environmental impact of the alien parasitoid T. sinensis in the study site is acceptable, although an extensive and repeated monitoring would be desirable.


Assuntos
DNA Espaçador Ribossômico/análise , DNA Ribossômico/análise , Genótipo , Controle Biológico de Vetores , Vespas/genética , Animais , Sequência de Bases , Hibridização Genética , Espécies Introduzidas , Itália , Filogenia , Alinhamento de Sequência , Vespas/classificação
10.
Science ; 365(6454): 640-641, 2019 08 16.
Artigo em Inglês | MEDLINE | ID: mdl-31416949
11.
Genet Sel Evol ; 51(1): 45, 2019 Aug 19.
Artigo em Inglês | MEDLINE | ID: mdl-31426753

RESUMO

BACKGROUND: Crossbreeding is widely used in pig production because of the benefits of heterosis effects and breed complementarity. Commonly, sire lines are bred for traits such as feed efficiency, growth and meat content, whereas maternal lines are also bred for reproduction and longevity traits, and the resulting three-way crossbred pigs are used for production of meat. The most important genetic basis for heterosis is dominance effects, e.g. removal of inbreeding depression. The aims of this study were to (1) present a modification of a previously developed model with additive, dominance and inbreeding depression genetic effects for analysis of data from a purebred sire line and three-way crossbred pigs; (2) based on this model, present equations for additive genetic variances, additive genetic covariance, and estimated breeding values (EBV) with associated accuracies for purebred and crossbred performances; (3) use the model to analyse four production traits, i.e. ultra-sound recorded backfat thickness (BF), conformation score (CONF), average daily gain (ADG), and feed conversion ratio (FCR), recorded on Danbred Duroc and Danbred Duroc-Landrace-Yorkshire crossbred pigs reared in the same environment; and (4) obtain estimates of genetic parameters, additive genetic correlations between purebred and crossbred performances, and EBV with associated accuracies for purebred and crossbred performances for this data set. RESULTS: Additive genetic correlations (with associated standard errors) between purebred and crossbred performances were equal to 0.96 (0.07), 0.83 (0.16), 0.75 (0.17), and 0.87 (0.18) for BF, CONF, ADG, and FCR, respectively. For BF, ADG, and FCR, the additive genetic variance was smaller for purebred performance than for crossbred performance, but for CONF the reverse was observed. EBV on Duroc boars were more accurate for purebred performance than for crossbred performance for BF, CONF and FCR, but not for ADG. CONCLUSIONS: Methodological developments led to equations for genetic (co)variances and EBV with associated accuracies for purebred and crossbred performances in a three-way crossbreeding system. As illustrated by the data analysis, these equations may be useful for implementation of genomic selection in this system.


Assuntos
Cruzamento , Depressão por Endogamia , Modelos Genéticos , Modelos Estatísticos , Suínos/genética , Animais , Cruzamentos Genéticos , Feminino , Variação Genética , Hibridização Genética , Masculino
12.
An Acad Bras Cienc ; 91(suppl 3): e20190325, 2019 Aug 26.
Artigo em Inglês | MEDLINE | ID: mdl-31460594

RESUMO

The West Indian (Trichechus manatus) and Amazonian (T. inunguis) manatees have a sympatric occurrence at the mouth of the Amazon River. A result of this interspecific encounter is the occurrence of hybrids, which are frequently found along the coasts of Amapá state in Brazil, French Guiana and Guyana. Here we present new genetic evidence indicating the occurrence of a hybrid swarm along the Guianas Shield coastline, which is an interspecific hybrid zone that also separates T. manatus populations located east (Brazil) and west (Caribbean, Gulf of Mexico, Florida and Antilles). In addition, we suggest that this hybrid population occupies a peculiar mangrove-rich environment under strong influence of the Amazon River plume, which requires an independent management and should be considered a special conservation area.


Assuntos
Variação Genética/genética , Hibridização Genética , Especificidade da Espécie , Trichechus inunguis/genética , Trichechus manatus/genética , Animais , Teorema de Bayes , Brasil , Região do Caribe , Guiana , Filogenia , Dinâmica Populacional , Rios , Trichechus inunguis/fisiologia , Trichechus manatus/fisiologia
13.
BMC Plant Biol ; 19(1): 319, 2019 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-31311507

RESUMO

BACKGROUND: Non-host resistance (NHR) presents a compelling long-term plant protection strategy for global food security, yet the genetic basis of NHR remains poorly understood. For many diseases, including stem rust of wheat [causal organism Puccinia graminis (Pg)], NHR is largely unexplored due to the inherent challenge of developing a genetically tractable system within which the resistance segregates. The present study turns to the pathogen's alternate host, barberry (Berberis spp.), to overcome this challenge. RESULTS: In this study, an interspecific mapping population derived from a cross between Pg-resistant Berberis thunbergii (Bt) and Pg-susceptible B. vulgaris was developed to investigate the Pg-NHR exhibited by Bt. To facilitate QTL analysis and subsequent trait dissection, the first genetic linkage maps for the two parental species were constructed and a chromosome-scale reference genome for Bt was assembled (PacBio + Hi-C). QTL analysis resulted in the identification of a single 13 cM region (~ 5.1 Mbp spanning 13 physical contigs) on the short arm of Bt chromosome 3. Differential gene expression analysis, combined with sequence variation analysis between the two parental species, led to the prioritization of several candidate genes within the QTL region, some of which belong to gene families previously implicated in disease resistance. CONCLUSIONS: Foundational genetic and genomic resources developed for Berberis spp. enabled the identification and annotation of a QTL associated with Pg-NHR. Although subsequent validation and fine mapping studies are needed, this study demonstrates the feasibility of and lays the groundwork for dissecting Pg-NHR in the alternate host of one of agriculture's most devastating pathogens.


Assuntos
Basidiomycota/fisiologia , Berberis/genética , Berberis/microbiologia , Doenças das Plantas/genética , Mapeamento Cromossômico , Cromossomos de Plantas , Resistência à Doença/genética , Perfilação da Expressão Gênica , Genoma de Planta , Hibridização Genética , Padrões de Herança , Fenótipo , Doenças das Plantas/microbiologia , Caules de Planta/microbiologia , Locos de Características Quantitativas
14.
BMC Plant Biol ; 19(1): 303, 2019 Jul 10.
Artigo em Inglês | MEDLINE | ID: mdl-31291892

RESUMO

BACKGROUND: Polyploidy and hybridization are ubiquitous in Rubus L., a large and taxonomically challenging genus. Chinese Rubus are mainly concentrated into two major sections, the diploid Idaeobatus and the polyploid Malachobatus. However, it remains unclear to be auto- or allo- polyploid origin of polyploids in Rubus. We investigated the homoeologs and the structure of the GBSSI-1 (granule-bound starch synthase I) gene in 140 Rubus individuals representing 102 taxa in 17 (out of the total 24) subsections of 7 (total of 12) sections at different ploidy levels. RESULTS: Based on the gene structure and sequence divergence, we defined three gene variants, GBSSI-1a, GBSSI-1b, and GBSSI-1c. When compared with GBSSI-1a, both GBSSI-1b and GBSSI-1c have a shorter fourth intron, and GBSSI-1c had an additional deletion in the fifth intron. For diploids, either GBSSI-1a or GBSSI-1b was detected in 56 taxa consisting of 82 individuals from sect. Idaeobatus, while both alleles existed in R. pentagonus and R. peltatus. Both homoeologs GBSSI-1a and GBSSI-1b were identified in 39 taxa (48 individuals) of Malachobatus polyploids. They were also observed in two sect. Dalibardastrum taxa, in one sect. Chamaebatus taxon, and in three taxa from sect. Cylactis. Interestingly, all three homoeologs were observed in the three tetraploid taxa. Phylogenetic trees and networks suggested two clades (I and II), corresponding to GBSSI-1a, and GBSSI-1b/1c sequences, respectively. GBSSI-1 homoeologs from the same polyploid individual were resolved in different well-supported clades, and some of these homoelogs were more closely related to homoelogs in other species than they were to each other. This implied that the homoeologs of these polyploids were donated by different ancestral taxa, indicating their allopolyploid origin. Two kinds of diploids hybridized to form most allotetraploid species. The early-divergent diploid species with GBSSI-1a or -1b emerged before polyploid formation in the evolutionary history of Rubus. CONCLUSION: This study provided new insights into allopolyploid origin and evolution from diploid to polyploid within the genus Rubus at the molecular phylogenetic level, consistent with the taxonomic treatment by Yü et al. and Lu.


Assuntos
Rubus/genética , Sintase do Amido/genética , Núcleo Celular/enzimologia , Diploide , Evolução Molecular , Hibridização Genética , Filogenia , Poliploidia , Rubus/enzimologia , Tetraploidia
15.
Zool Res ; 40(4): 293-304, 2019 Jul 18.
Artigo em Inglês | MEDLINE | ID: mdl-31271004

RESUMO

Divergence of gene expression and alternative splicing is a crucial driving force in the evolution of species; to date, however the molecular mechanism remains unclear. Hybrids of closely related species provide a suitable model to analyze allele-specific expression (ASE) and allele-specific alternative splicing (ASS). Analysis of ASE and ASS can uncover the differences in cis-regulatory elements between closely related species, while eliminating interference of trans-regulatory elements. Here, we provide a detailed characterization of ASE and ASS from 19 and 10 transcriptome datasets across five tissues from reciprocal-cross hybrids of horse×donkey (mule/hinny) and cattle×yak (dzo), respectively. Results showed that 4.8%-8.7% and 10.8%-16.7% of genes exhibited ASE and ASS, respectively. Notably, lncRNAs and pseudogenes were more likely to show ASE than protein-coding genes. In addition, genes showing ASE and ASS in mule/hinny were found to be involved in the regulation of muscle strength, whereas those of dzo were involved in high-altitude adaptation. In conclusion, our study demonstrated that exploration of genes showing ASE and ASS in hybrids of closely related species is feasible for species evolution research.


Assuntos
Alelos , Processamento Alternativo , Bovinos/genética , Equidae/genética , Hibridização Genética/genética , Animais , Sequência de Bases , Regulação da Expressão Gênica , RNA/genética , RNA/metabolismo
16.
Sci Total Environ ; 689: 980-990, 2019 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-31280179

RESUMO

The study aims to analyse the stability of the narrow crowned Norway spruce (pendula form) compared to the normal spruce form (pyramidalis form) and the hybrids of the two forms, in 5 field trials (Comandau, Lepsa 1&2, Ilva Mica and Voineasa) located in the Romanian Carpathians. Trees height (Th), breast height diameter (Dbh), height growth of the last year, crown diameter (Cd), number of branches per whorl (Nbw) and dominant branch diameter (Dbd) traits were measured and survival rate (Sr) was determined, at 20 years old. Also, branches finesse (Bf), trees volume (Tv) and trees slenderness (Ts) were calculated. In order to compare the wood density (Cwd) there were collected cores. In all trials ANOVA revealed significant (p < 0.05) differences between the two forms of spruce and the hybrids (mainly between those that have a different crown form mother), especially for the stability and quality traits. Factorial ANOVA revealed a high influence (p < 0.001) of the locality and also a significant influence (p < 0.05) of the locality × spruce form interaction. The factor "form" was significant for some traits involved in Norway spruce stability (Ts, Cd, Nbw). The pendula trees present higher values for Sr, Dbh and Tv, and lower values for Ts, Cd, Nbw, Dbd and Bf, compared to pyramidalis spruce form, which showed a higher stability. Heritability was in generally low (h2 < 0.4), with exceptions of Ts which presents a medium rate of heritage. For the same trait, different heritability was registered in different environmental conditions. The Cwd was higher only with 2% for the pendula form in Lepsa trial, while in Comandau trial the pyramidalis registered a higher value (7%). In the new breeding programme, the selection strategy may be pursued with the pendula trees selection based on Ts and branches traits.


Assuntos
Hibridização Genética , Picea/metabolismo , Melhoramento Vegetal , Picea/anatomia & histologia , Picea/genética , Romênia , Especificidade da Espécie , Madeira/análise
17.
Plant Dis ; 103(9): 2295-2304, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31355734

RESUMO

Phytophthora species hybrids have been repeatedly reported as causing damaging diseases to cultivated and wild plants. Two known hybrids, P. andina and P. × pelgrandis, are pathogens of Solanaceae and ornamentals, respectively, although the extent of their host ranges are unknown. P. andina emerged from hybridization of P. infestans and an unidentified related species, whereas P. × pelgrandis emerged from P. nicotianae and P. cactorum. Considering that hybrids and parental species can coexist in the same regions and to distinguish them usually requires cloning or whole genome sequencing, we aimed to develop a rapid tool to distinguish them. Specifically, we used high-resolution melting (HRM) assays to differentiate genotypes based on their amplicon melting profiles. We designed primers for P. × pelgrandis and parental species based on available sequences of P. nicotianae and P. cactorum nuclear genes containing polymorphisms between species. For P. andina, heterozygous sites from Illumina short reads were used for the same purpose. We identified multiple amplicons exhibiting differences in melting curves between parental species and hybrids. We propose HRM as a rapid method for differentiation of P. andina and P. × pelgrandis hybrids from parental species that could be employed to advance research on these pathogens.


Assuntos
Hibridização Genética , Tipagem Molecular , Phytophthora , Primers do DNA , Hibridização Genética/genética , Tipagem Molecular/métodos , Tipagem Molecular/normas , Phytophthora/classificação , Phytophthora/genética , Solanaceae/parasitologia , Temperatura de Transição
18.
Genome Biol ; 20(1): 136, 2019 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-31300020

RESUMO

BACKGROUND: Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive. RESULTS: By investigating the whole-genome resequencing data of 93 accessions from worldwide populations of bread wheat and its diploid and tetraploid progenitors, together with 90 published exome-capture data, we find that the B subgenome has more variations than A and D subgenomes, including SNPs and deletions. Population genetics analyses support a monophyletic origin of domesticated wheat from wild emmer in northern Levant, with substantial introgressed genomic fragments from southern Levant. Southern Levant contributes more than 676 Mb in AB subgenomes and enriched in the pericentromeric regions. The AB subgenome introgression happens at the early stage of wheat speciation and partially contributes to their greater genetic diversity. Furthermore, we detect massive alien introgressions that originated from distant species through natural and artificial hybridizations, resulting in the reintroduction of ~ 709 Mb and ~ 1577 Mb sequences into bread wheat landraces and varieties, respectively. A large fraction of these intra- and inter-introgression fragments are associated with quantitative trait loci of important traits, and selection events are also identified. CONCLUSION: We reveal the significance of multiple introgressions from distant wild populations and alien species in shaping the genetic components of bread wheat, and provide important resources and new perspectives for future wheat breeding.


Assuntos
Evolução Biológica , Variação Genética , Genoma de Planta , Hibridização Genética , Triticum/genética , Cromossomos de Plantas , Domesticação , Sequenciamento Completo do Genoma
19.
BMC Plant Biol ; 19(1): 230, 2019 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-31151385

RESUMO

BACKGROUND: Interspecific hybridisation resulting in polyploidy is one of the major driving forces in plant evolution. Here, we present data from the molecular cytogenetic analysis of three cytotypes of Elytrigia ×mucronata using sequential fluorescence (5S rDNA, 18S rDNA and pSc119.2 probes) and genomic in situ hybridisation (four genomic probes of diploid taxa, i.e., Aegilops, Dasypyrum, Hordeum and Pseudoroegneria). RESULTS: The concurrent presence of Hordeum (descended from E. repens) and Dasypyrum + Aegilops (descended from E. intermedia) chromosome sets in all cytotypes of E. ×mucronata confirmed the assumed hybrid origin of the analysed plants. The following different genomic constitutions were observed for E. ×mucronata. Hexaploid plants exhibited three chromosome sets from Pseudoroegneria and one chromosome set each from Aegilops, Hordeum and Dasypyrum. Heptaploid plants harboured the six chromosome sets of the hexaploid plants and an additional Pseudoroegneria chromosome set. Nonaploid cytotypes differed in their genomic constitutions, reflecting different origins through the fusion of reduced and unreduced gametes. The hybridisation patterns of repetitive sequences (5S rDNA, 18S rDNA, and pSc119.2) in E. ×mucronata varied between and within cytotypes. Chromosome alterations that were not identified in the parental species were found in both heptaploid and some nonaploid plants. CONCLUSIONS: The results confirmed that both homoploid hybridisation and heteroploid hybridisation that lead to the coexistence of four different haplomes within single hybrid genomes occur in Elytrigia allopolyploids. The chromosomal alterations observed in both heptaploid and some nonaploid plants indicated that genome restructuring occurs during and/or after the hybrids arose. Moreover, a specific chromosomal translocation detected in one of the nonaploids indicated that it was not a primary hybrid. Therefore, at least some of the hybrids are fertile. Hybridisation in Triticeae allopolyploids clearly and significantly contributes to genomic diversity. Different combinations of parental haplomes coupled with chromosomal alterations may result in the establishment of unique lineages, thus providing raw material for selection.


Assuntos
Genótipo , Hibridização Genética , Poaceae/genética , Poliploidia , Análise Citogenética , República Tcheca , DNA de Plantas/análise , Hibridização In Situ , Hibridização in Situ Fluorescente , RNA Ribossômico 18S/análise , RNA Ribossômico 5S/análise
20.
BMC Evol Biol ; 19(1): 112, 2019 05 30.
Artigo em Inglês | MEDLINE | ID: mdl-31146685

RESUMO

BACKGROUND: Coalescent-based species tree inference has become widely used in the analysis of genome-scale multilocus and SNP datasets when the goal is inference of a species-level phylogeny. However, numerous evolutionary processes are known to violate the assumptions of a coalescence-only model and complicate inference of the species tree. One such process is hybrid speciation, in which a species shares its ancestry with two distinct species. Although many methods have been proposed to detect hybrid speciation, only a few have considered both hybridization and coalescence in a unified framework, and these are generally limited to the setting in which putative hybrid species must be identified in advance. RESULTS: Here we propose a method that can examine genome-scale data for a large number of taxa and detect those taxa that may have arisen via hybridization, as well as their potential "parental" taxa. The method is based on a model that considers both coalescence and hybridization together, and uses phylogenetic invariants to construct a test that scales well in terms of computational time for both the number of taxa and the amount of sequence data. We test the method using simulated data for up 20 taxa and 100,000bp, and find that the method accurately identifies both recent and ancient hybrid species in less than 30 s. We apply the method to two empirical datasets, one composed of Sistrurus rattlesnakes for which hybrid speciation is not supported by previous work, and one consisting of several species of Heliconius butterflies for which some evidence of hybrid speciation has been previously found. CONCLUSIONS: The proposed method is powerful for detecting hybridization for both recent and ancient hybridization events. The computations required can be carried out rapidly for a large number of sequences using genome-scale data, and the method is appropriate for both SNP and multilocus data.


Assuntos
Bases de Dados Genéticas , Genômica , Hibridização Genética , Modelos Genéticos , Animais , Borboletas/genética , Simulação por Computador , Crotalus/genética , Especiação Genética , Filogenia , Especificidade da Espécie
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