Your browser doesn't support javascript.
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 59
Filtrar
Mais filtros










Base de dados
Intervalo de ano de publicação
1.
Curr Opin Plant Biol ; 54: 108-113, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32344327

RESUMO

Allopolyploids, which are formed from the hybridization of two or more diploid progenitor species, often experience subgenome dominance, where one of the parental genomes (subgenomes) has higher levels of gene expression and ultimately greater gene retention compared to the other subgenomes. Low transposable element (TE) abundance near genes has been associated with the dominant subgenome in several allopolyploids, but TEs are unlikely to be the only causal factor responsible for subgenome expression dominance. In this review, we will examine the role of TEs in subgenome dominance as well as discuss how genetic incompatibilities among subgenomes likely contributes to the rapid emergence of subgenome dominance. Lastly, we highlight several burning questions about subgenome dominance that remain largely unanswered.

2.
Nat Commun ; 11(1): 884, 2020 02 14.
Artigo em Inglês | MEDLINE | ID: mdl-32060277

RESUMO

Teff (Eragrostis tef) is a cornerstone of food security in the Horn of Africa, where it is prized for stress resilience, grain nutrition, and market value. Here, we report a chromosome-scale assembly of allotetraploid teff (variety Dabbi) and patterns of subgenome dynamics. The teff genome contains two complete sets of homoeologous chromosomes, with most genes maintaining as syntenic gene pairs. TE analysis allows us to estimate that the teff polyploidy event occurred ~1.1 million years ago (mya) and that the two subgenomes diverged ~5.0 mya. Despite this divergence, we detect no large-scale structural rearrangements, homoeologous exchanges, or biased gene loss, in contrast to many other allopolyploids. The two teff subgenomes have partitioned their ancestral functions based on divergent expression across a diverse expression atlas. Together, these genomic resources will be useful for accelerating breeding of this underutilized grain crop and for fundamental insights into polyploid genome evolution.


Assuntos
Eragrostis/genética , Evolução Molecular , Genoma de Planta , África , Eragrostis/classificação , Filogenia , Tetraploidia
3.
New Phytol ; 226(6): 1725-1737, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31999829

RESUMO

Plants produce a range of volatile organic compounds (VOCs), some of which are perceived by the human olfactory system, contributing to a myriad flavors. Despite the importance of flavor for consumer preference, most plant breeding programs have neglected it, mainly because of the costs of phenotyping and the complexity of disentangling the role of VOCs in human perception. To develop molecular breeding tools aimed at improving fruit flavor, we carried out target genotyping of and VOC extraction from a blueberry population. Metabolite genome-wide association analysis was used to elucidate the genetic architecture, while predictive models were tested to prove that VOCs can be accurately predicted using genomic information. A historical sensory panel was considered to assess how the volatiles influenced consumers. By gathering genomics, metabolomics, and the sensory panel, we demonstrated that VOCs are controlled by a few major genomic regions, some of which harbor biosynthetic enzyme-coding genes; can be accurately predicted using molecular markers; and can enhance or decrease consumers' overall liking. Here we emphasized how the understanding of the genetic basis and the role of VOCs in consumer preference can assist breeders in developing more flavorful cultivars at a more inexpensive and accelerated pace.

5.
Hortic Res ; 6: 96, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31645954

RESUMO

The molecular mechanism underlying dormancy release and the induction of flowering remains poorly understood in woody plants. Mu-legacy is a valuable blueberry mutant, in which a transgene insertion caused increased expression of a RESPONSE REGULATOR 2-like gene (VcRR2). Mu-legacy plants, compared with nontransgenic 'Legacy' plants, show dwarfing, promotion of flower bud formation, and can flower under nonchilling conditions. We conducted transcriptomic comparisons in leaves, chilled and nonchilled flowering buds, and late-pink buds, and analyzed a total of 41 metabolites of six groups of hormones in leaf tissues of both Mu-legacy and 'Legacy' plants. These analyses uncovered that increased VcRR2 expression promotes the expression of a homolog of Arabidopsis thaliana ENT-COPALYL DIPHOSPHATE SYNTHETASE 1 (VcGA1), which induces new homeostasis of hormones, including increased gibberellin 4 (GA4) levels in Mu-legacy leaves. Consequently, increased expression of VcRR2 and VcGA1, which function in cytokinin responses and gibberellin synthesis, respectively, initiated the reduction in plant height and the enhancement of flower bud formation of the Mu-legacy plants through interactions of multiple approaches. In nonchilled flower buds, 29 differentially expressed transcripts of 17 genes of five groups of hormones were identified in transcriptome comparisons between Mu-legacy and 'Legacy' plants, of which 22 were chilling responsive. Thus, these analyses suggest that increased expression of VcRR2 was collectively responsible for promoting flower bud formation in highbush blueberry under nonchilling conditions. We report here for the first time the importance of VcRR2 to induce a suite of downstream hormones that promote flowering in woody plants.

6.
G3 (Bethesda) ; 9(10): 3315-3332, 2019 10 07.
Artigo em Inglês | MEDLINE | ID: mdl-31420323

RESUMO

Octoploid strawberry (Fragaria ×ananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to identify and introgress useful disease resistance genes (R-genes) in breeding programs are complicated by strawberry's complex octoploid genome. Recently-developed resources in strawberry, including a complete octoploid reference genome and high-resolution octoploid genotyping, enable new analyses in strawberry disease resistance genetics. This study characterizes the complete R-gene collection in the genomes of commercial octoploid strawberry and two diploid ancestral relatives, and introduces several new technological and data resources for strawberry disease resistance research. These include octoploid R-gene transcription profiling, dN/dS analysis, expression quantitative trait loci (eQTL) analysis and RenSeq analysis in cultivars. Octoploid fruit eQTL were identified for 76 putative R-genes. R-genes from the ancestral diploids Fragaria vesca and Fragaria iinumae were compared, revealing differential inheritance and retention of various octoploid R-gene subtypes. The mode and magnitude of natural selection of individual F. ×ananassa R-genes was also determined via dN/dS analysis. R-gene sequencing using enriched libraries (RenSeq) has been used recently for R-gene discovery in many crops, however this technique somewhat relies upon a priori knowledge of desired sequences. An octoploid strawberry capture-probe panel, derived from the results of this study, is validated in a RenSeq experiment and is presented for community use. These results give unprecedented insight into crop disease resistance genetics, and represent an advance toward exploiting variation for strawberry cultivar improvement.


Assuntos
Resistência à Doença/genética , Fragaria/classificação , Fragaria/genética , Genoma de Planta , Genômica , Doenças das Plantas/genética , Poliploidia , Evolução Molecular , Perfilação da Expressão Gênica , Genes de Plantas , Genômica/métodos , Locos de Características Quantitativas , Especificidade da Espécie , Transcriptoma
7.
Nat Genet ; 51(4): 765, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30842601

RESUMO

In the version of this article originally published, author Joshua R. Puzey was incorrectly listed as having affiliation 7 (School of Plant Sciences, University of Arizona, Tucson, AZ, USA); affiliation 6 (Department of Biology, College of William and Mary, Williamsburg, VA, USA) is the correct affiliation. The error has been corrected in the HTML and PDF versions of the article.

8.
BMC Genomics ; 20(1): 95, 2019 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-30700268

RESUMO

BACKGROUND: RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy - producing both a less dormant mucilaginous (M+) seed morph and a more dormant non-mucilaginous (NM) seed morph. Here, we compared de novo and reference-genome based transcriptome assemblies to investigate Ae. arabicum seed dimorphism and to evaluate the reference-free versus -dependent approach for identifying differentially expressed genes (DEGs). RESULTS: A de novo transcriptome assembly was generated using sequences from M+ and NM Ae. arabicum dry seed morphs. The transcripts of the de novo assembly contained 63.1% complete Benchmarking Universal Single-Copy Orthologs (BUSCO) compared to 90.9% for the transcripts of the reference genome. DEG detection used the strict consensus of three methods (DESeq2, edgeR and NOISeq). Only 37% of 1533 differentially expressed de novo assembled transcripts paired with 1876 genome-derived DEGs. Gene Ontology (GO) terms distinguished the seed morphs: the terms translation and nucleosome assembly were overrepresented in DEGs higher in abundance in M+ dry seeds, whereas terms related to mRNA processing and transcription were overrepresented in DEGs higher in abundance in NM dry seeds. DEGs amongst these GO terms included ribosomal proteins and histones (higher in M+), RNA polymerase II subunits and related transcription and elongation factors (higher in NM). Expression of the inferred DEGs and other genes associated with seed maturation (e.g. those encoding late embryogenesis abundant proteins and transcription factors regulating seed development and maturation such as ABI3, FUS3, LEC1 and WRI1 homologs) were put in context with Arabidopsis thaliana seed maturation and indicated that M+ seeds may desiccate and mature faster than NM. The 1901 transcriptomic DEG set GO-terms had almost 90% overlap with the 2191 genome-derived DEG GO-terms. CONCLUSIONS: Whilst there was only modest overlap of DEGs identified in reference-free versus -dependent approaches, the resulting GO analysis was concordant in both approaches. The identified differences in dry seed transcriptomes suggest mechanisms underpinning previously identified contrasts between morphology and germination behaviour of M+ and NM seeds.


Assuntos
Brassicaceae/crescimento & desenvolvimento , Brassicaceae/genética , Regulação da Expressão Gênica de Plantas , Sementes/crescimento & desenvolvimento , Sementes/genética , Transcriptoma , Perfilação da Expressão Gênica , Ontologia Genética , Genoma de Planta , Germinação , Sequenciamento de Nucleotídeos em Larga Escala , Anotação de Sequência Molecular , Proteínas de Plantas/genética
9.
Gigascience ; 8(3)2019 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-30715294

RESUMO

BACKGROUND: Highbush blueberry (Vaccinium corymbosum) has long been consumed for its unique flavor and composition of health-promoting phytonutrients. However, breeding efforts to improve fruit quality in blueberry have been greatly hampered by the lack of adequate genomic resources and a limited understanding of the underlying genetics encoding key traits. The genome of highbush blueberry has been particularly challenging to assemble due, in large part, to its polyploid nature and genome size. FINDINGS: Here, we present a chromosome-scale and haplotype-phased genome assembly of the cultivar "Draper," which has the highest antioxidant levels among a diversity panel of 71 cultivars and 13 wild Vaccinium species. We leveraged this genome, combined with gene expression and metabolite data measured across fruit development, to identify candidate genes involved in the biosynthesis of important phytonutrients among other metabolites associated with superior fruit quality. Genome-wide analyses revealed that both polyploidy and tandem gene duplications modified various pathways involved in the biosynthesis of key phytonutrients. Furthermore, gene expression analyses hint at the presence of a spatial-temporal specific dominantly expressed subgenome including during fruit development. CONCLUSIONS: These findings and the reference genome will serve as a valuable resource to guide future genome-enabled breeding of important agronomic traits in highbush blueberry.


Assuntos
Mirtilos Azuis (Planta)/genética , Evolução Molecular , Genoma de Planta , Haplótipos/genética , Compostos Fitoquímicos/genética , Tetraploidia , Antioxidantes/metabolismo , Vias Biossintéticas/genética , Cromossomos de Plantas/genética , Frutas/genética , Frutas/crescimento & desenvolvimento , Duplicação Gênica , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Anotação de Sequência Molecular , Família Multigênica , Compostos Fitoquímicos/química , RNA Mensageiro/genética , RNA Mensageiro/metabolismo
10.
Nat Genet ; 51(3): 541-547, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30804557

RESUMO

Cultivated strawberry emerged from the hybridization of two wild octoploid species, both descendants from the merger of four diploid progenitor species into a single nucleus more than 1 million years ago. Here we report a near-complete chromosome-scale assembly for cultivated octoploid strawberry (Fragaria × ananassa) and uncovered the origin and evolutionary processes that shaped this complex allopolyploid. We identified the extant relatives of each diploid progenitor species and provide support for the North American origin of octoploid strawberry. We examined the dynamics among the four subgenomes in octoploid strawberry and uncovered the presence of a single dominant subgenome with significantly greater gene content, gene expression abundance, and biased exchanges between homoeologous chromosomes, as compared with the other subgenomes. Pathway analysis showed that certain metabolomic and disease-resistance traits are largely controlled by the dominant subgenome. These findings and the reference genome should serve as a powerful platform for future evolutionary studies and enable molecular breeding in strawberry.


Assuntos
Fragaria/genética , Genoma de Planta/genética , Cromossomos de Plantas/genética , Diploide , Evolução Molecular , Expressão Gênica/genética , Hibridização Genética/genética , Melhoramento Vegetal/métodos , Poliploidia
11.
Sci Rep ; 9(1): 1833, 2019 02 12.
Artigo em Inglês | MEDLINE | ID: mdl-30755671

RESUMO

Many insect species have acquired the ability to redirect plant development to form unique organs called galls, which provide these insects with unique, enhanced food and protection from enemies and the elements. Many galls resemble flowers or fruits, suggesting that elements of reproductive development may be involved. We tested this hypothesis using RNA sequencing to quantify the transcriptional responses of wild grapevine (Vitis riparia) leaves to a galling parasite, phylloxera (Daktulosphaira vitifoliae). If development of reproductive structures is part of gall formation, we expected to find significantly elevated expression of genes involved in flower and/or fruit development in developing galls as opposed to ungalled leaves. We found that reproductive gene ontology categories were significantly enriched in developing galls, and that expression of many candidate genes involved in floral development were significantly increased, particularly in later gall stages. The patterns of gene expression found in galls suggest that phylloxera exploits vascular cambium to provide meristematic tissue and redirects leaf development towards formation of carpels. The phylloxera leaf gall appears to be phenotypically and transcriptionally similar to the carpel, due to the parasite hijacking underlying genetic machinery in the host plant.

12.
Plant Genome ; 11(3)2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30512037

RESUMO

Garden strawberry ( × Duchesne ex Rozier) arose from spontaneous hybridization of distinct octoploid species 300 yr ago. Since its discovery in the 1700s, migration and selection restructured the genetic diversity of early hybrids to produce elite fruit-bearing groups. Breeders' understanding of the genetic architecture of domesticated populations is incomplete. To resolve the impacts of domestication on strawberry genetic diversity, we analyzed genome-wide DNA profiles of 1300 octoploid individuals (1814-present), including wild species, historic varieties, and the University of California germplasm collection. Commercially important California genotypes, adapted to mild coastal climates and accounting for a large fraction of global production, have diverged from temperate cultivars originating in eastern North America and Europe. Whereas temperate cultivars were shown to have selected North American Miller ssp. ancestral diversity at higher frequencies, coastal breeding increased selection of (L.) Miller (beach strawberry) alleles in . × , in addition to photoperiod-insensitive flowering alleles from nonancestral (S.Watson) Staudt ssp. , underscoring the role of continued adaptive introgressions in the domestication of artificial hybrids. Selection for mass production traits in coastal climates over the last 20 to 30 yr has restructured domesticated strawberry diversity on a scale similar to the first 200 yr of breeding; coastal × has diverged further from temperate × than the latter from their wild progenitors. Selection signatures indicate that strawberry domestication targeted genes regulating hormone-mediated fruit expansion, providing a blueprint for genetic factors underlying elite phenotypes.


Assuntos
Domesticação , Fragaria/genética , Genes de Plantas , Hibridização Genética , Evolução Molecular , Fragaria/crescimento & desenvolvimento , Melhoramento Vegetal , Seleção Genética , Transcriptoma
13.
Gigascience ; 7(8)2018 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-30107523

RESUMO

Background: The fragmented nature of most draft plant genomes has hindered downstream gene discovery, trait mapping for breeding, and other functional genomics applications. There is a pressing need to improve or finish draft plant genome assemblies. Findings: Here, we present a chromosome-scale assembly of the black raspberry genome using single-molecule real-time Pacific Biosciences sequencing and high-throughput chromatin conformation capture (Hi-C) genome scaffolding. The updated V3 assembly has a contig N50 of 5.1 Mb, representing an ∼200-fold improvement over the previous Illumina-based version. Each of the 235 contigs was anchored and oriented into seven chromosomes, correcting several major misassemblies. Black raspberry V3 contains 47 Mb of new sequences including large pericentromeric regions and thousands of previously unannotated protein-coding genes. Among the new genes are hundreds of expanded tandem gene arrays that were collapsed in the Illumina-based assembly. Detailed comparative genomics with the high-quality V4 woodland strawberry genome (Fragaria vesca) revealed near-perfect 1:1 synteny with dramatic divergence in tandem gene array composition. Lineage-specific tandem gene arrays in black raspberry are related to agronomic traits such as disease resistance and secondary metabolite biosynthesis. Conclusions: The improved resolution of tandem gene arrays highlights the need to reassemble these highly complex and biologically important regions in draft plant genomes. The updated, high-quality black raspberry reference genome will be useful for comparative genomics across the horticulturally important Rosaceae family and enable the development of marker assisted breeding in Rubus.


Assuntos
Genoma de Planta , Rubus/genética , Análise de Sequência de DNA , Cromossomos de Plantas , Genômica
14.
New Phytol ; 220(1): 87-93, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-29882360

RESUMO

Contents Summary 87 I. Introduction 87 II. Evolution in action: subgenome dominance within newly formed hybrids and polyploids 88 III. Summary and future directions 90 Acknowledgements 92 References 92 SUMMARY: The merger of divergent genomes, via hybridization or allopolyploidization, frequently results in a 'genomic shock' that induces a series of rapid genetic and epigenetic modifications as a result of conflicts between parental genomes. This conflict among the subgenomes routinely leads one subgenome to become dominant over the other subgenome(s), resulting in subgenome biases in gene content and expression. Recent advances in methods to analyze hybrid and polyploid genomes with comparisons to extant parental progenitors have allowed for major strides in understanding the mechanistic basis for subgenome dominance. In particular, our understanding of the role that homoeologous exchange might play in subgenome dominance and genome evolution is quickly growing. Here we describe recent discoveries uncovering the underlying mechanisms and provide a framework to predict subgenome dominance in hybrids and allopolyploids with far-reaching implications for agricultural, ecological, and evolutionary research.


Assuntos
Genoma de Planta , Hibridização Genética , Poliploidia , Epigênese Genética , Evolução Molecular , Regulação da Expressão Gênica de Plantas
15.
G3 (Bethesda) ; 8(5): 1817-1828, 2018 05 04.
Artigo em Inglês | MEDLINE | ID: mdl-29602808

RESUMO

Fusarium wilt, a soil-borne disease caused by the fungal pathogen Fusarium oxysporum f. sp. fragariae, threatens strawberry (Fragaria × ananassa) production worldwide. The spread of the pathogen, coupled with disruptive changes in soil fumigation practices, have greatly increased disease pressure and the importance of developing resistant cultivars. While resistant and susceptible cultivars have been reported, a limited number of germplasm accessions have been analyzed, and contradictory conclusions have been reached in earlier studies to elucidate the underlying genetic basis of resistance. Here, we report the discovery of Fw1, a dominant gene conferring resistance to Fusarium wilt in strawberry. The Fw1 locus was uncovered in a genome-wide association study of 565 historically and commercially important strawberry accessions genotyped with 14,408 SNP markers. Fourteen SNPs in linkage disequilibrium with Fw1 physically mapped to a 2.3 Mb segment on chromosome 2 in a diploid F. vesca reference genome. Fw1 and 11 tightly linked GWAS-significant SNPs mapped to linkage group 2C in octoploid segregating populations. The most significant SNP explained 85% of the phenotypic variability and predicted resistance in 97% of the accessions tested-broad-sense heritability was 0.96. Several disease resistance and defense-related gene homologs, including a small cluster of genes encoding nucleotide-binding leucine-rich-repeat proteins, were identified in the 0.7 Mb genomic segment predicted to harbor Fw1 DNA variants and candidate genes identified in the present study should facilitate the development of high-throughput genotyping assays for accurately predicting Fusarium wilt phenotypes and applying marker-assisted selection.


Assuntos
Mapeamento Cromossômico , Resistência à Doença/genética , Fragaria/genética , Fragaria/microbiologia , Fusarium/fisiologia , Genes Dominantes , Estudo de Associação Genômica Ampla , Doenças das Plantas/genética , Segregação de Cromossomos/genética , Cromossomos de Plantas/genética , Genes de Plantas , Desequilíbrio de Ligação/genética , Fenótipo , Doenças das Plantas/imunologia , Doenças das Plantas/microbiologia , Polimorfismo de Nucleotídeo Único/genética
16.
Genome Biol Evol ; 10(3): 999-1011, 2018 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-29617811

RESUMO

Genes that are inherently subject to strong selective constraints tend to be overretained in duplicate after polyploidy. They also continue to experience similar, but somewhat relaxed, constraints after that polyploidy event. We sought to assess for how long the influence of polyploidy is felt on these genes' selective pressures. We analyzed two nested polyploidy events in Brassicaceae: the At-α genome duplication that is the most recent polyploidy in the model plant Arabidopsis thaliana and a more recent hexaploidy shared by the genus Brassica and its relatives. By comparing the strength and direction of the natural selection acting at the population and at the species level, we find evidence for continued intensified purifying selection acting on retained duplicates from both polyploidies even down to the present. The constraint observed in preferentially retained genes is not a result of the polyploidy event: the orthologs of such genes experience even stronger constraint in nonpolyploid outgroup genomes. In both the Arabidopsis and Brassica lineages, we further find evidence for segregating mildly deleterious variants, confirming that the population-level data uncover patterns not visible with between-species comparisons. Using the A. thaliana metabolic network, we also explored whether network position was correlated with the measured selective constraint. At both the population and species level, nodes/genes tended to show similar constraints to their neighbors. Our results paint a picture of the long-lived effects of polyploidy on plant genomes, suggesting that even yesterday's polyploids still have distinct evolutionary trajectories.


Assuntos
Evolução Molecular , Genoma de Planta/genética , Seleção Genética/genética , Arabidopsis/genética , Brassica/genética , Dosagem de Genes/genética , Duplicação Gênica , Genes de Plantas/genética , Filogenia , Poliploidia
17.
Curr Opin Plant Biol ; 42: 76-80, 2018 04.
Artigo em Inglês | MEDLINE | ID: mdl-29649616

RESUMO

Whole genome duplications (WGDs), also known as polyploid events, have played a crucial role in the evolutionary success of angiosperms across recent and ancient timescales. A recurrent observation from the analysis of allopolyploids is that one of the parental subgenomes is generally more dominant, referred to as 'subgenome dominance', based on higher gene content and expression patterns. Subgenome dominance has far reaching implications to research areas ranging from crop improvement efforts to evolutionary and ecological studies. However, the analysis of subgenome dominance in more ancient polyploids is complicated by a long history of homoeologous exchanges among subgenomes. Here, we will discuss how resulting homoeolog rearrangements and replacements have been ignored in previous studies and urge future studies to integrate phylogenetic approaches to assign homoeologs to parental subgenomes.


Assuntos
Evolução Molecular , Genoma de Planta/genética , Poliploidia , Regulação da Expressão Gênica de Plantas/genética , Regulação da Expressão Gênica de Plantas/fisiologia , Filogenia
18.
Am J Bot ; 105(3): 463-469, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29574686

RESUMO

PREMISE OF THE STUDY: Previous phylogenetic studies employing molecular markers have yielded various insights into the evolutionary history across Brassicales, but many relationships between families remain poorly supported or unresolved. A recent phylotranscriptomic approach utilizing 1155 nuclear markers obtained robust estimates for relationships among 14 of 17 families. Here we report a complete family-level phylogeny estimated using the plastid genome. METHODS: We conducted phylogenetic analyses on a concatenated data set comprising 44,926 bp from 72 plastid genes for species distributed across all 17 families. Our analysis includes three additional families, Tovariaceae, Salvadoraceae, and Setchellanthaceae, that were omitted in the previous phylotranscriptomic study. KEY RESULTS: Our phylogenetic analyses obtained fully resolved and strongly supported estimates for all nodes across Brassicales. Importantly, these findings are congruent with the topology reported in the phylotranscriptomic study. This consistency suggests that future studies could utilize plastid genomes as markers for resolving relationships within some notoriously difficult clades across Brassicales. We used this new phylogenetic framework to verify the placement of the At-α event near the origin of Brassicaceae, with median date estimates of 31.8 to 42.8 million years ago and restrict the At-ß event to one of two nodes with median date estimates between 85 to 92.2 million years ago. These events ultimately gave rise to novel chemical defenses and are associated with subsequent shifts in net diversification rates. CONCLUSIONS: We anticipate that these findings will aid future comparative evolutionary studies across Brassicales, including selecting candidates for whole-genome sequencing projects.


Assuntos
Evolução Biológica , Resistência à Doença/genética , Genes de Plantas , Genomas de Plastídeos , Magnoliopsida/genética , Filogenia , Poliploidia , Brassicaceae/química , Brassicaceae/genética , Núcleo Celular , Evolução Molecular , Magnoliopsida/química , Plastídeos , Especificidade da Espécie
19.
PLoS Genet ; 14(3): e1007267, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29590103

RESUMO

Polyploidy is increasingly seen as a driver of both evolutionary innovation and ecological success. One source of polyploid organisms' successes may be their origins in the merging and mixing of genomes from two different species (e.g., allopolyploidy). Using POInT (the Polyploid Orthology Inference Tool), we model the resolution of three allopolyploidy events, one from the bakers' yeast (Saccharomyces cerevisiae), one from the thale cress (Arabidopsis thaliana) and one from grasses including Sorghum bicolor. Analyzing a total of 21 genomes, we assign to every gene a probability for having come from each parental subgenome (i.e., derived from the diploid progenitor species), yielding orthologous segments across all genomes. Our model detects statistically robust evidence for the existence of biased fractionation in all three lineages, whereby genes from one of the two subgenomes were more likely to be lost than those from the other subgenome. We further find that a driver of this pattern of biased losses is the co-retention of genes from the same parental genome that share functional interactions. The pattern of biased fractionation after the Arabidopsis and grass allopolyploid events was surprisingly constant in time, with the same parental genome favored throughout the lineages' history. In strong contrast, the yeast allopolyploid event shows evidence of biased fractionation only immediately after the event, with balanced gene losses more recently. The rapid loss of functionally associated genes from a single subgenome is difficult to reconcile with the action of genetic drift and suggests that selection may favor the removal of specific duplicates. Coupled to the evidence for continuing, functionally-associated biased fractionation after the A. thaliana At-α event, we suggest that, after allopolyploidy, there are functional conflicts between interacting genes encoded in different subgenomes that are ultimately resolved through preferential duplicate loss.


Assuntos
Brassicaceae/genética , Genes de Plantas , Impressão Genômica , Hibridização Genética , Poliploidia , Evolução Molecular , Modelos Genéticos
20.
Hortic Res ; 5: 8, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29423238

RESUMO

Black raspberry (Rubus occidentalis L.) is a niche fruit crop valued for its flavor and potential health benefits. The improvement of fruit and cane characteristics via molecular breeding technologies has been hindered by the lack of a high-quality reference genome. The recently released draft genome for black raspberry (ORUS 4115-3) lacks assembly of scaffolds to chromosome scale. We used high-throughput chromatin conformation capture (Hi-C) and Proximity-Guided Assembly (PGA) to cluster and order 9650 out of 11,936 contigs of this draft genome assembly into seven pseudo-chromosomes. The seven pseudo-chromosomes cover ~97.2% of the total contig length (~223.8 Mb). Locating existing genetic markers on the physical map resolved multiple discrepancies in marker order on the genetic map. Centromeric regions were inferred from recombination frequencies of genetic markers, alignment of 303 bp centromeric sequence with the PGA, and heat map showing the physical contact matrix over the entire genome. We demonstrate a high degree of synteny between each of the seven chromosomes of black raspberry and a high-quality reference genome for strawberry (Fragaria vesca L.) assembled using only PacBio long-read sequences. We conclude that PGA is a cost-effective and rapid method of generating chromosome-scale assemblies from Illumina short-read sequencing data.

SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA