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1.
Ecol Lett ; 23(4): 663-673, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32012420

RESUMO

Underpinnings of the distribution of allopolyploid species (hybrids with duplicated genome) along spatial and ecological gradients are elusive. As allopolyploid speciation combines the range of genetic and ecological characteristics of divergent diploids, allopolyploids initially show their additivity and are predicted to evolve differentiated ecological niches to establish in face of their competition. Here, we use four diploid wild wheats that differentially combined into four independent allopolyploid species to test for such additivity and assess the impact of ecological constraints on species ranges. Divergent genetic variation from diploids being fixed in heterozygote allopolyploids supports their genetic additivity. Spatial integration of comparative phylogeography and modelling of climatic niches supports ecological additivity of locally adapted diploid progenitors into allopolyploid species which subsequently colonised wide ranges. Allopolyploids fill suitable range to a larger extent than diploids and conservative evolution following the combination of divergent species appears to support their expansion under environmental changes.


Assuntos
Diploide , Triticum , Ecossistema , Humanos , Filogeografia , Poliploidia
2.
Nat Ecol Evol ; 4(3): 453-460, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32042122

RESUMO

Sex is common among eukaryotes, but entails considerable costs. The selective conditions that drive the evolutionary maintenance of sexual reproduction remain an open question. One long-standing explanation is that sex and recombination facilitate adaptation to fluctuating environmental conditions, although the genetic mechanisms that underlie such a benefit have not been empirically observed. In this study, we compare the dynamics and fitness effects of mutations in sexual and asexual diploid populations of the yeast Saccharomyces cerevisiae during adaptation to a fluctuating environment. While we find no detectable difference in the rate of adaptation between sexual and asexual populations, only the former evolve high fitness mutations in parallel, a genetic signature of adaptation. Using genetic reconstructions and fitness assays, we demonstrate that evolved, overdominant mutations can be beneficial in asexual populations, but maintained at lower frequencies in sexual populations due to segregation load. Overall these data show that sex alters the molecular basis of adaptation in diploids, and confers both costs and benefits.


Assuntos
Diploide , Saccharomyces cerevisiae , Evolução Biológica , Evolução Molecular , Seleção Genética
3.
Trends Ecol Evol ; 35(1): 34-42, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31703819

RESUMO

Hybridization has broad evolutionary consequences, from fueling or counteracting speciation to facilitating adaptation to novel environments. Hybridization and subsequent introgression appear widespread along the tree of life. However, our understanding of how distinct evolutionary forces shape admixed genomes and the fate of introgressed genetic variants remains scarce. Most admixture research in animals has focused on diploid organisms. We propose that haplodiploid organisms can help resolve open questions about the genomic consequences of hybridization in natural populations. The ploidy difference between haploid males and diploid females, the availability of genome-wide male haplotypes, and ongoing cases of admixture make haplodiploid organisms promising models to improve our knowledge with regards to the evolution of hybrid genomes.


Assuntos
Diploide , Hibridização Genética , Animais , Feminino , Genômica , Haploidia , Masculino
4.
Mol Genet Genomics ; 295(1): 209-219, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31642957

RESUMO

The objective of this study was to map the quantitative trait loci (QTLs) for chip color after harvest (AH), cold storage (CS) and after reconditioning (RC) in diploid potato and compare them with QTLs for starch-corrected chip color. Chip color traits AH, CS, and RC significantly correlated with tuber starch content (TSC). To limit the effect of starch content, the chip color was corrected for TSC. The QTLs for chip color (AH, CS, and RC) and the starch-corrected chip color determined with the starch content after harvest (SCAH), after cold storage (SCCS) and after reconditioning (SCRC) were compared to assess the extent of the effect of starch and the location of genetic factors underlying this effect on chip color. We detected QTLs for the AH, CS, RC and starch-corrected traits on ten potato chromosomes, confirming the polygenic nature of the traits. The QTLs with the strongest effects were detected on chromosomes I (AH, 0 cM, 11.5% of variance explained), IV (CS, 43.9 cM, 12.7%) and I (RC, 49.7 cM, 14.1%). When starch correction was applied, the QTLs with the strongest effects were revealed on chromosomes VIII (SCAH, 39.3 cM, 10.8% of variance explained), XI (SCCS, 79.5 cM, 10.9%) and IV (SCRC, 43.9 cM, 10.8%). Applying the starch correction changed the landscape of QTLs for chip color, as some QTLs became statistically insignificant, shifted or were refined, and new QTLs were detected for SCAH. The QTLs on chromosomes I and IV were significant for all traits with and without starch correction.


Assuntos
Locos de Características Quantitativas/genética , Solanum tuberosum/genética , Amido/genética , Mapeamento Cromossômico/métodos , Cor , Diploide , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Tubérculos/genética
5.
Ecol Lett ; 23(1): 68-78, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31637845

RESUMO

Polyploid speciation entails substantial and rapid postzygotic reproductive isolation of nascent species that are initially sympatric with one or both parents. Despite strong postzygotic isolation, ecological niche differentiation has long been thought to be important for polyploid success. Using biogeographic data from across vascular plants, we tested whether the climatic niches of polyploid species are more differentiated than their diploid relatives and if the climatic niches of polyploid species differentiated faster than those of related diploids. We found that polyploids are often more climatically differentiated from their diploid parents than the diploids are from each other. Consistent with this pattern, we estimated that polyploid species generally have higher rates of multivariate niche differentiation than their diploid relatives. In contrast to recent analyses, our results confirm that ecological niche differentiation is an important component of polyploid speciation and that niche differentiation is often significantly faster in polyploids.


Assuntos
Diploide , Poliploidia , Ecossistema , Família , Humanos , Plantas
6.
Syst Biol ; 69(1): 91-109, 2020 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-31127939

RESUMO

Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situation. Dactylorhiza (Orchidaceae: Orchidinae) is a genus much affected by allopolyploid speciation and reticulate phylogenetic relationships. Here, we use genetic variation at tens of thousands of genomic positions to unravel the convoluted evolutionary history of Dactylorhiza. We first investigate circumscription and relationships of diploid species in the genus using coalescent and maximum likelihood methods, and then group 16 allotetraploids by maximum affiliation to their putative parental diploids, implementing a method based on genotype likelihoods. The direction of hybrid crosses is inferred for each allotetraploid using information from maternally inherited plastid RADseq loci. Starting from age estimates of parental taxa, the relative ages of these allotetraploid entities are inferred by quantifying their genetic similarity to the diploids and numbers of private alleles compared with sibling allotetraploids. Whereas northwestern Europe is dominated by young allotetraploids of postglacial origins, comparatively older allotetraploids are distributed further south, where climatic conditions remained relatively stable during the Pleistocene glaciations. Our bioinformatics approach should prove effective for the study of other naturally occurring, nonmodel, polyploid plant complexes.


Assuntos
Orchidaceae/classificação , Orchidaceae/genética , Filogenia , Diploide , Europa (Continente) , Tetraploidia
7.
Cytogenet Genome Res ; 159(4): 208-214, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31846969

RESUMO

The karyotypes and other chromosomal markers of 4 catfish species, namely Lasiancistrus schomburgkii, Lasiancistrus sp., Araichthysloro, and Megalancistrus sp., members of a taxonomically complex and speciose tribe of catfishes Ancistrini, Hypostominae, were examined using conventional (Giemsa staining, Ag-NOR, and C-banding) and molecular cytogenetic protocols (FISH) and DNA barcoding. In L. schomburgkii, Lasiancistrus sp., and A.loro a diploid number 2n = 54 was observed, with karyotypes composed of 28m + 16sm + 10st, 36m + 12sm + 6st chromosomes, while Megalancistrus sp. had 2n = 52, with the karyotype composed of 28m + 16sm + 8st chromosomes. The Ag-NOR phenotypes were simple in all 4 species, which was confirmed by FISH with an 18S rDNA probe. However, the positive 5S rDNA sites varied among species: 2 chromosome pairs in L. schomburgkii, Lasiancistrus sp., and A. loro, and only 1 pair in Megalancistrus sp. The blocks of constitutive heterochromatin were poorly visible in the pericentromeric and telomeric regions of most chromosomes of the examined species by C-banding. The genetic distance analysis, based on mtDNA COI gene sequences (DNA barcoding), confirmed the species as 4 taxonomic units. Ours and other published data indicate that karyotype differentiation among Ancistrini is complex and divergent and indicates the occurrence of common chromosomal rearrangements, such as pericentric inversions conserving the diploid number, and other rearrangements that are more frequent in some genera, such as centric fusions in Ancistrus.


Assuntos
Peixes-Gato/genética , Animais , Inversão Cromossômica/genética , Cromossomos/genética , Citogenética/métodos , DNA Ribossômico/genética , Diploide , Feminino , Heterocromatina/genética , Cariótipo , Masculino , Filogenia , Telômero/genética
8.
BMC Bioinformatics ; 20(1): 548, 2019 Nov 05.
Artigo em Inglês | MEDLINE | ID: mdl-31690272

RESUMO

BACKGROUND: Genome graph is an emerging approach for representing structural variants on genomes with branches. For example, representing structural variants of cancer genomes as a genome graph is more natural than representing such genomes as differences from the linear reference genome. While more and more structural variants are being identified by long-read sequencing, many of them are difficult to visualize using existing structural variants visualization tools. To this end, visualization method for large genome graphs such as human cancer genome graphs is demanded. RESULTS: We developed MOdular Multi-scale Integrated Genome graph browser, MoMI-G, a web-based genome graph browser that can visualize genome graphs with structural variants and supporting evidences such as read alignments, read depth, and annotations. This browser allows more intuitive recognition of large, nested, and potentially more complex structural variations. MoMI-G has view modules for different scales, which allow users to view the whole genome down to nucleotide-level alignments of long reads. Alignments spanning reference alleles and those spanning alternative alleles are shown in the same view. Users can customize the view, if they are not satisfied with the preset views. In addition, MoMI-G has Interval Card Deck, a feature for rapid manual inspection of hundreds of structural variants. Herein, we describe the utility of MoMI-G by using representative examples of large and nested structural variations found in two cell lines, LC-2/ad and CHM1. CONCLUSIONS: Users can inspect complex and large structural variations found by long-read analysis in large genomes such as human genomes more smoothly and more intuitively. In addition, users can easily filter out false positives by manually inspecting hundreds of identified structural variants with supporting long-read alignments and annotations in a short time. SOFTWARE AVAILABILITY: MoMI-G is freely available at https://github.com/MoMI-G/MoMI-G under the MIT license.


Assuntos
Genoma Humano , Software , Navegador , Alelos , Linhagem Celular , Diploide , Variação Estrutural do Genoma , Humanos , Interface Usuário-Computador
9.
BMC Plant Biol ; 19(1): 503, 2019 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-31729948

RESUMO

BACKGROUND: Dicer-like proteins (DCLs) are essential players in RNA-silencing mechanisms, acting in gene regulation via miRNAs and in antiviral protection in plants and have also been associated to other biotic and abiotic stresses. To the best of our knowledge, despite being identified in some crops, cotton DCLs haven't been characterized until now. In this work, we characterized the DCLs of three cotton species and analyzed their expression profiles during biotic stress. RESULTS: As main results, 11 DCLs in the allotetraploid cotton Gossypium hirsutum, 7 and 6 in the diploid G. arboreum and G. raimondii, were identified, respectively. Among some DCLs duplications observed in these genomes, the presence of an extra DCL3 in the three cotton species were detected, which haven't been found in others eudicots. All the DCL types identified by in silico analysis in the allotetraploid cotton genome were able to generate transcripts, as observed by gene expression analysis in distinct tissues. Based on the importance of DCLs for plant defense against virus, responses of cotton DCLs to virus infection and/or herbivore attack using two commercial cotton cultivars (cv.), one susceptible (FM966) and another resistant (DO) to polerovirus CLRDV infection, were analyzed. Both cvs. Responded differently to virus infection. At the inoculation site, the resistant cv. showed strong induction of DCL2a and b, while the susceptible cv. showed a down-regulation of these genes, wherever DCL4 expression was highly induced. A time course of DCL expression in aerial parts far from inoculation site along infection showed that DCL2b and DCL4 were repressed 24 h after infection in the susceptible cotton. As CLRDV is aphid-transmitted, herbivore attack was also checked. Opposite expression pattern of DCL2a and b and DCL4 was observed for R and S cottons, showing that aphid feeding alone may induce DCL modulation. CONCLUSIONS: Almost all the DCLs of the allotetraploide G. hirsutum cotton were found in their relative diploids. Duplications of DCL2 and DCL3 were found in the three species. All four classes of DCL responded to aphid attack and virus infection in G. hirsutum. DCLs initial responses against the virus itself and/or herbivore attack may be contributing towards virus resistance.


Assuntos
Regulação da Expressão Gênica de Plantas , Genoma de Planta/genética , Gossypium/genética , Ribonuclease III/genética , Estresse Fisiológico , Diploide , Perfilação da Expressão Gênica , Gossypium/fisiologia , MicroRNAs/genética , Proteínas de Plantas/genética , Poliploidia , RNA de Plantas/genética
10.
BMC Plant Biol ; 19(1): 439, 2019 Oct 22.
Artigo em Inglês | MEDLINE | ID: mdl-31640550

RESUMO

BACKGROUND: The Hessian fly (Mayetiola destructor), belonging to the gall midge family (Cecidomyiidae), is a devastating pest of wheat (Triticum aestivum) causing significant yield losses. Despite identification and characterization of numerous Hessian fly-responsive genes and associated biological pathways involved in wheat defense against this dipteran pest, their functional validation has been challenging. This is largely attributed to the large genome, polyploidy, repetitive DNA, and limited genetic resources in hexaploid wheat. The diploid progenitor Aegilops tauschii, D-genome donor of modern-day hexaploid wheat, offers an ideal surrogate eliminating the need to target all three homeologous chromosomes (A, B and D) individually, and thereby making the functional validation of candidate Hessian fly-responsive genes plausible. Furthermore, the well-annotated sequence of Ae. tauschii genome and availability of genetic resources amenable to manipulations makes the functional assays less tedious and time-consuming. However, prior to utilization of this diploid genome for downstream studies, it is imperative to characterize its physical and molecular responses to Hessian fly. RESULTS: In this study we screened five Ae. tauschii accessions for their response to the Hessian fly biotypes L and vH13. Two lines were identified that exhibited a homozygous resistance response to feeding by both Hessian fly biotypes. Studies using physical measurements and neutral red staining showed that the resistant Ae. tauschii accessions resembled hexaploid wheat in their phenotypic responses to Hessian fly, that included similarities in larval developmental stages, leaf and plant growth, and cell wall permeability. Furthermore, molecular responses, characterized by gene expression profiling using quantitative real-time PCR, in select resistant Ae. tauschii lines also revealed similarities with resistant hexaploid wheat. CONCLUSIONS: Phenotypic and molecular characterization of Ae. tauschii to Hessian fly infestation revealed resistant accessions that shared similarities to hexaploid wheat. Resembling the resistant hexaploid wheat, the Ae. tauschii accessions mount an early defense strategy involving defense proteins including lectins, secondary metabolites and reactive oxygen species (ROS) radicals. Our results reveal the suitability of the diploid progenitor for use as an ideal tool for functional genomics research in deciphering the wheat-Hessian fly molecular interactions.


Assuntos
Aegilops/genética , Dípteros/fisiologia , Genoma de Planta/genética , Doenças das Plantas/imunologia , Triticum/genética , Aegilops/imunologia , Aegilops/parasitologia , Animais , Diploide , Genômica , Fenótipo , Doenças das Plantas/parasitologia , Poliploidia , Espécies Reativas de Oxigênio/metabolismo , Triticum/imunologia , Triticum/parasitologia
11.
Nat Commun ; 10(1): 4660, 2019 10 11.
Artigo em Inglês | MEDLINE | ID: mdl-31604920

RESUMO

Whole-genome sequencing using sequencing technologies such as Illumina enables the accurate detection of small-scale variants but provides limited information about haplotypes and variants in repetitive regions of the human genome. Single-molecule sequencing (SMS) technologies such as Pacific Biosciences and Oxford Nanopore generate long reads that can potentially address the limitations of short-read sequencing. However, the high error rate of SMS reads makes it challenging to detect small-scale variants in diploid genomes. We introduce a variant calling method, Longshot, which leverages the haplotype information present in SMS reads to accurately detect and phase single-nucleotide variants (SNVs) in diploid genomes. We demonstrate that Longshot achieves very high accuracy for SNV detection using whole-genome Pacific Biosciences data, outperforms existing variant calling methods, and enables variant detection in duplicated regions of the genome that cannot be mapped using short reads.


Assuntos
Polimorfismo de Nucleotídeo Único , Software , Sequenciamento Completo do Genoma/métodos , Algoritmos , Diploide , Genoma Humano , Haplótipos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Sequências Repetitivas de Ácido Nucleico , Análise de Sequência de DNA/métodos
12.
Enzyme Microb Technol ; 131: 109382, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31615681

RESUMO

In an effort to find a suitable genetic background for efficient cellulolytic secretion, genetically diverse strains were transformed to produce core fungal cellulases namely, ß-glucosidase (BGLI), endoglucanase (EGII) and cellobiohydrolase (CBHI) in various combinations and expression configurations. The secreted enzyme activity levels, gene copy number, substrate specificities, as well as hydrolysis and fermentation yields of the transformants were analysed. The effectiveness of the partially cellulolytic yeast transformants to convert two different pre-treated corn residues, namely corn cob and corn husk was then explored. Higher secretion titers were achieved by cellulolytic strains with the YI13 genetic background and cellulolytic transformants produced up to 1.34 fold higher glucose concentrations (g/L) than a control composed of equal amounts of each enzyme type. The transformant co-producing BGLI and EGII in a secreted ratio of 1:15 (cellulase activity unit per gram dry cell weight) converted 56.5% of the cellulose present in corn cob to glucose in hydrolysis experiments and yielded 4.05 g/L ethanol in fermentations. We demonstrate that the choice of optimal genetic background and cellulase activity secretion ratio can improve cellulosic ethanol production by consolidated bioprocessing yeast strains.


Assuntos
Celulase/metabolismo , Expressão Gênica , Leveduras/enzimologia , Leveduras/metabolismo , Zea mays/metabolismo , Biotransformação , Celulase/genética , Diploide , Fermentação , Dosagem de Genes , Hidrólise , Leveduras/genética
13.
Plant Cell ; 31(11): 2550-2551, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31562214
14.
Cytogenet Genome Res ; 159(1): 32-38, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31542782

RESUMO

Despite the variation observed in the diploid chromosome number of storks (Ciconiiformes, Ciconiidae), from 2n = 52 to 2n = 78, most reports have relied solely on analyses by conventional staining. As most species have similar macrochromosomes, some authors propose that karyotype evolution involves mainly fusions between microchromosomes, which are highly variable in species with different diploid numbers. In order to verify this hypothesis, in this study, the karyotypes of 2 species of storks from South America with different diploid numbers, the jabiru (Jabiru mycteria, 2n = 56) and the maguary stork (Ciconia maguary, 2n = 72), were analyzed by chromosome painting using whole chromosome probes from the macrochromosomes of Gallus gallus (GGA) and Leucopternis albicollis (LAL). The results revealed that J. mycteria and C. maguary share synteny within chromosome pairs 1-9 and Z. The syntenies to the macrochromosomes of G. gallus are conserved, except for GGA4, which is homologous to 2 different pairs, as in most species of birds. A fusion of GGA8 and GGA9 was observed in both species. Additionally, chromosomes corresponding to GGA4p and GGA6 are fused to other segments that did not hybridize to any of the macrochromosome probes used, suggesting that these segments correspond to microchromosomes. Hence, our data corroborate the proposed hypothesis that karyotype evolution is based on fusions involving microchromosomes. In view of the morphological constancy of the macrochromosome pairs in most Ciconiidae, we propose a putative ancestral karyotype for the family, including the GGA8/GGA9 fusion, and a diploid number of 2n = 78. The use of probes for microchromosome pairs should be the next step in identifying other synapomorphies that may help to clarify the phylogeny of this family.


Assuntos
Aves/genética , Coloração Cromossômica/veterinária , Cromossomos/genética , Variação Genética/genética , Cariótipo , Animais , Brasil , Diploide , Evolução Molecular , Feminino , Filogenia
15.
Nat Commun ; 10(1): 4388, 2019 09 26.
Artigo em Inglês | MEDLINE | ID: mdl-31558727

RESUMO

Meiosis is a conserved tenet of sexual reproduction in eukaryotes, yet this program is seemingly absent from many extant species. In the human fungal pathogen Candida albicans, mating of diploid cells generates tetraploid products that return to the diploid state via a non-meiotic process of depolyploidization known as concerted chromosome loss (CCL). Here, we report that recombination rates are more than three orders of magnitude higher during CCL than during normal mitotic growth. Furthermore, two conserved 'meiosis-specific' factors play central roles in CCL as SPO11 mediates DNA double-strand break formation while both SPO11 and REC8 regulate chromosome stability and promote inter-homolog recombination. Unexpectedly, SPO11 also promotes DNA repair and recombination during normal mitotic divisions. These results indicate that C. albicans CCL represents a 'parameiosis' that blurs the conventional boundaries between mitosis and meiosis. They also reveal parallels with depolyploidization in mammalian cells and provide potential insights into the evolution of meiosis.


Assuntos
Candida albicans/genética , Diploide , Recombinação Homóloga/genética , Meiose/genética , Tetraploidia , Candidíase/microbiologia , Cromossomos Fúngicos/genética , Dano ao DNA , Endodesoxirribonucleases/genética , Endodesoxirribonucleases/metabolismo , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Humanos , Mitose/genética , Recombinases Rec A/genética , Recombinases Rec A/metabolismo , Reparo de DNA por Recombinação
16.
Plant Sci ; 287: 110174, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31481216

RESUMO

Asteraceae is the largest family of angiosperms, comprising approximately 24,000 species. Molecular genetic studies of Asteraceae are essential for understanding plant diversity. Chrysanthemum morifolium is the most industrially important ornamental species in Asteraceae. Most cultivars of C. morifolium are autohexaploid and self-incompatible. These properties are major obstacles to the genetic analysis and modern breeding of C. morifolium. Furthermore, high genome heterogeneity complicates molecular biological analyses. In this study, we developed a model strain in the genus Chrysanthemum. C. seticuspe is a diploid species with a similar flowering property and morphology to C. morifolium and can be subjected to Agrobacterium-mediated transformation. We isolated a natural self-compatible mutant of C. seticuspe and established a pure line through repeated selfing and selection. The resultant strain, named Gojo-0, was favorable for genetic analyses, including isolation of natural and induced mutants, and facilitated molecular biological analysis, including whole genome sequencing, owing to the simplicity and homogeneity of its genome. Interspecific hybridization with Chrysanthemum species was possible, enabling molecular genetic analysis of natural interspecific variations. The accumulation of research results and resources using Gojo-0 as a platform is expected to promote molecular genetic studies on the genus Chrysanthemum and the genetic improvement of chrysanthemum cultivars.


Assuntos
Chrysanthemum/genética , Chrysanthemum/ultraestrutura , DNA de Plantas/genética , Diploide , Flores/ultraestrutura , Hibridização Genética , Microscopia Eletrônica de Varredura , Modelos Biológicos , Mutação , Filogenia , Melhoramento Vegetal/métodos , Polinização , Autofertilização
17.
Plant Physiol Biochem ; 143: 154-164, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31505448

RESUMO

Stevia rebaudiana is an important medical plant for producing steviol glycosides (SGs) or stevioside. Autotetraploids (4x = 44) show an increasing level of morphology, physiology and tolerances comparing to diploids (2x = 22). However, little information regarded on the comparative transcriptome analysis between diploid and autotetraploid S. rebaudiana was found. In this study, synthetic autotetraploid was induced and morphological features were confirmed. A comprehensive transcriptome of stevia leaf, stem and root from the diploids and autotetraploids was constructed based on RNA-seq, yielded 1,000,892,422 raw reads and subsequently assembled into 251,455 transcripts, corresponded to 146,130 genes. Pairwise comparisons of the six leaf libraries between the diploids and autotetraploids revealed 4114 differentially expression genes (DEGs), in which 2105 (51.17%) were up-regulated in autotetraploids and associated with SGs biosynthesis, plant growth and secondary metabolism. Moreover, weighted gene co-expression network analysis showed co-expressed genes of fifteen genes of SG biosynthesis pathway were enriched in photosynthesis, flavonoid and secondary metabolic process, plant growth and morphogenesis. A hundred of DEGs related to plant resistance were identified by interviewing PlantPReS database. This study has highlighted molecular changes related to SGs metabolism of polyploidy, and advanced our understanding in plant resistance responsible for phenotypic change of autotetraploids.


Assuntos
Stevia/genética , Transcriptoma/genética , Diploide , Diterpenos de Caurano/metabolismo , Regulação da Expressão Gênica de Plantas/genética , Glucosídeos/metabolismo , Folhas de Planta/genética , Folhas de Planta/metabolismo , Raízes de Plantas/genética , Raízes de Plantas/metabolismo , Stevia/metabolismo
18.
Int J Mol Sci ; 20(18)2019 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-31510061

RESUMO

The involvement of chromosome changes in the initial steps of speciation is controversial. Here we examine diversification trends within the mole voles Ellobius, a group of subterranean rodents. The first description of their chromosome variability was published almost 40 years ago. Studying the G-band structure of chromosomes in numerous individuals revealed subsequent homologous, step-by-step, Robertsonian translocations, which changed diploid numbers from 54 to 30. Here we used a molecular cytogenetic strategy which demonstrates that chromosomal translocations are not always homologous; consequently, karyotypes with the same diploid number can carry different combinations of metacentrics. We further showed that at least three chromosomal forms with 2n = 34 and distinct metacentrics inhabit the Pamir-Alay mountains. Each of these forms independently hybridized with E. tancrei, 2n = 54, forming separate hybrid zones. The chromosomal variations correlate slightly with geographic barriers. Additionally, we confirmed that the emergence of partial or monobrachial homology appeared to be a strong barrier for hybridization in nature, in contradistinction to experiments which we reported earlier. We discuss the possibility of whole arm reciprocal translocations for mole voles. Our findings suggest that chromosomal translocations lead to diversification and speciation.


Assuntos
Arvicolinae/genética , Cromossomos de Mamíferos/genética , Especiação Genética , Variação Genética , Translocação Genética/genética , Animais , Arvicolinae/classificação , Bandeamento Cromossômico , Diploide , Geografia , Hibridização Genética , Cariótipo , Tadjiquistão
19.
Nat Commun ; 10(1): 4061, 2019 09 06.
Artigo em Inglês | MEDLINE | ID: mdl-31492891

RESUMO

Tiny marine green algae issued from two deep branches of the Chlorophyta, the Mamiellophyceae and Chloropicophyceae, dominate different regions of the oceans and play key roles in planktonic communities. Considering that the Mamiellophyceae is the sole lineage of prasinophyte algae that has been intensively investigated, the extent to which these two algal groups differ in their metabolic capacities and cellular processes is currently unknown. To address this gap of knowledge, we investigate here the nuclear genome sequence of a member of the Chloropicophyceae, Chloropicon primus. Among the main biological insights that emerge from this 17.4 Mb genome, we find an unexpected diploid structure for most chromosomes and a propionate detoxification pathway in green algae. Our results support the notion that separate events of genome minimization, which entailed differential losses of genes/pathways, have occurred in the Chloropicophyceae and Mamiellophyceae, suggesting different strategies of adaptation to oceanic environments.


Assuntos
Proteínas de Algas/genética , Clorófitas/genética , Diploide , Genoma , Água do Mar/microbiologia , Transdução de Sinais/genética , Adaptação Fisiológica/genética , Clorófitas/classificação , Evolução Molecular , Mutação INDEL , Oceanos e Mares , Filogenia , Polimorfismo de Nucleotídeo Único
20.
Genetics ; 213(2): 665-683, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31371407

RESUMO

Loss of heterozygosity (LOH) is observed during vegetative growth and reproduction of diploid genotypes through mitotic crossovers, aneuploidy caused by nondisjunction, and gene conversion. We aimed to test the role that LOH plays during adaptation of two highly heterozygous Saccharomyces cerevisiae genotypes to multiple environments over a short time span in the laboratory. We hypothesized that adaptation would be observed through parallel LOH events across replicate populations. Using genome resequencing of 70 clones, we found that LOH was widespread with 5.2 LOH events per clone after ∼500 generations. The most common mode of LOH was gene conversion (51%) followed by crossing over consistent with either break-induced replication or double Holliday junction resolution. There was no evidence that LOH involved nondisjunction of whole chromosomes. We observed parallel LOH in both an environment-specific and environment-independent manner. LOH largely involved recombining existing variation between the parental genotypes, but also was observed after de novo, presumably beneficial, mutations occurred in the presence of canavanine, a toxic analog of arginine. One highly parallel LOH event involved the ENA salt efflux pump locus on chromosome IV, which showed repeated LOH to the allele from the European parent, an allele originally derived by introgression from S. paradoxus Using CRISPR-engineered LOH we showed that the fitness advantage provided by this single LOH event was 27%. Overall, we found extensive evidence that LOH could be adaptive and is likely to be a greater source of initial variation than de novo mutation for rapid evolution of diploid genotypes.


Assuntos
Cromossomos Fúngicos/genética , Evolução Clonal/genética , Perda de Heterozigosidade/genética , Saccharomyces cerevisiae/genética , Adaptação Fisiológica/genética , Alelos , Aneuploidia , Reparo do DNA/genética , Diploide , Conversão Gênica/genética , Heterozigoto , Recombinação Genética
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