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1.
Nat Commun ; 12(1): 97, 2021 01 04.
Artículo en Inglés | MEDLINE | ID: mdl-33397978

RESUMEN

Globally, soybean is a major protein and oil crop. Enhancing our understanding of the soybean domestication and improvement process helps boost genomics-assisted breeding efforts. Here we present a genome-wide variation map of 10.6 million single-nucleotide polymorphisms and 1.4 million indels for 781 soybean individuals which includes 418 domesticated (Glycine max), 345 wild (Glycine soja), and 18 natural hybrid (G. max/G. soja) accessions. We describe the enhanced detection of 183 domestication-selective sweeps and the patterns of putative deleterious mutations during domestication and improvement. This predominantly selfing species shows 7.1% reduction of overall deleterious mutations in domesticated soybean relative to wild soybean and a further 1.4% reduction from landrace to improved accessions. The detected domestication-selective sweeps also show reduced levels of deleterious alleles. Importantly, genotype imputation with this resource increases the mapping resolution of genome-wide association studies for seed protein and oil traits in a soybean diversity panel.


Asunto(s)
Domesticación , Mutación/genética , Soja/genética , Cromosomas de las Plantas/genética , Bases de Datos Genéticas , Variación Genética , Genética de Población , Genoma de Planta , Estudio de Asociación del Genoma Completo , Haplotipos/genética , Filogenia , Selección Genética
2.
Nat Commun ; 12(1): 405, 2021 01 15.
Artículo en Inglés | MEDLINE | ID: mdl-33452249

RESUMEN

Plant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes' evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.


Asunto(s)
Camptotecina/biosíntesis , Evolución Molecular , Genoma de Planta/genética , Proteínas de Plantas/genética , Rubiaceae/metabolismo , Vías Biosintéticas/genética , Cromosomas de las Plantas/genética , Mapeo Contig , Genómica , Proteínas de Plantas/metabolismo , Raíces de Plantas/metabolismo , Plantas Medicinales/genética , Plantas Medicinales/metabolismo , Rubiaceae/genética , Alcaloides de la Vinca/biosíntesis
3.
Gene ; 770: 145348, 2021 Feb 20.
Artículo en Inglés | MEDLINE | ID: mdl-33333230

RESUMEN

Heat shock factors (Hsfs) and heat shock proteins (Hsps) play a critical role in the molecular mechanisms such as plant development and defense against abiotic. As an important food crop, maize is vulnerable to adverse environment such as heat stress and water logging, which leads to a decline in yield and quality. To date, very little is known regarding the structure and function of Hsf and Hsp genes in maize. Although some Hsf and Hsp genes have been characterized in maize, analysis of the entire Hsf and Hsp70 gene families were not completed following Maize (B73) Genome Sequencing Project. Therefore, studying their molecular mechanism and revealing their biological function in plant stress resistance process will contribute to reveal important theoretical significance and application value for improving corn yield and quality. In this study, we have identified 25 ZmHsf and 22 ZmHsp70 genes in maize. The structural characteristics and phylogenetic relationships of the Hsf and Hsp70 gene families of Arabidopsis thaliana, rice and maize were compared. The final 25 ZmHsf proteins and 22 ZmHsp70 proteins were divided into three and four subfamilies, respectively. In addition, chromosomal localization indicated that the ZmHsf and ZmHsp70 genes were unevenly distributed on the chromosome, and the gene structure map revealed the characteristics of their structures. Finally, transcriptome analysis indicated that most of the ZmHsf and ZmHsp70 genes showed different expression patterns at different developmental stages of maize. Further, by semi-quantitative RT-PCR and quantitative real-time PCR analysis, all 25 ZmHsf and 22 ZmHsp70 genes were confirmed to respond to heat stress treatment, indicating that they have potential effects in heat stress response. The analyses performed by combining co-expression network with protein-protein interaction network among the members of the Hsf and Hsp70 gene families in maize further enabled us to recognize components involved in the regulatory network associated with hsfs and hsp70s complex. The predicted subcellular location revealed that maize Hsp70 proteins exhibited a various subcellular distribution, which may be associated with functional diversification in heat stress response. Taken together, our study provides comprehensive information on the members of Hsf and Hsp70 gene families and will help in elucidating their exact function in maize.


Asunto(s)
Cromosomas de las Plantas , Regulación de la Expresión Génica de las Plantas/fisiología , Proteínas HSP70 de Choque Térmico , Familia de Multigenes/fisiología , Proteínas de Plantas , Zea mays , Cromosomas de las Plantas/genética , Cromosomas de las Plantas/metabolismo , Estudio de Asociación del Genoma Completo , Proteínas HSP70 de Choque Térmico/biosíntesis , Proteínas HSP70 de Choque Térmico/genética , Proteínas de Plantas/biosíntesis , Proteínas de Plantas/genética , Zea mays/genética , Zea mays/metabolismo
4.
Gene ; 764: 145078, 2021 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-32858175

RESUMEN

In maize, eat rot and stalk rot caused by Fusarium verticillioides and Fusarium graminearum lead to contamination of moldy grains to produce mycotoxins. Identification of resistance genes against these pathogens for maize breeding is an effective way for disease control. Several 2-oxoglutarate-dependent dioxygenase (2OGD) proteins have been found to confer resistance to different pathogens in diverse plant species. However, little is known about the 2OGD superfamily in maize. Here, we identified 103 putative 2OGD genes in maize from a genome-wide analysis, and divided them into three classes - DOXA, DOXB, and DOXC. We further comprehensively investigated their gene structure, chromosome distribution, phylogenetic tree, gene-function enrichment, and expression profiles among different tissues. The genes encoding three 2OGD proteins, ACO, F3H, and NCS involved in ethylene biosynthesis, flavonoids biosynthesis, and alkaloids biosynthesis pathways, respectively, were identified to be induced by F. verticillioides and F. graminearum. The promoters of the three genes contain the binding sites for the transcription factor ZmDOF and ZmHSF, which are also induced by the two pathogens. The results imply that the three 2OGDs and the two transcription factors might be involved in the resistance to the two pathogens. This study provided a comprehensive understanding of the 2OGD superfamily in maize and laid the foundation for the further functional analysis of their roles in maize resistance to eat rot and stalk rot.


Asunto(s)
Dioxigenasas/genética , Fusarium/inmunología , Proteínas de Plantas/genética , Zea mays/fisiología , Secuencia de Bases/genética , Sitios de Unión/genética , Cromosomas de las Plantas/genética , Coenzimas/metabolismo , Secuencia Conservada/genética , Dioxigenasas/inmunología , Dioxigenasas/metabolismo , Resistencia a la Enfermedad/genética , Evolución Molecular , Fusarium/patogenicidad , Regulación del Desarrollo de la Expresión Génica , Regulación de la Expresión Génica de las Plantas/fisiología , Estudio de Asociación del Genoma Completo , Ácidos Cetoglutáricos/metabolismo , Filogenia , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/microbiología , Proteínas de Plantas/inmunología , Proteínas de Plantas/metabolismo , Tallos de la Planta/enzimología , Tallos de la Planta/crecimiento & desarrollo , Tallos de la Planta/microbiología , Regiones Promotoras Genéticas/genética , RNA-Seq , Factores de Transcripción/metabolismo , Zea mays/microbiología
5.
Gene ; 766: 145156, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32949696

RESUMEN

Plant Glycogen Synthase Kinase 3 (GSK3)/SHAGGY-like kinase (GSK) proteins play important roles in modulating growth, development, and stress responses in several plant species. However, little is known about the members of the potato GSK (StGSK) family. Here, nine StGSK genes were identified and phylogenetically grouped into four clades. Gene duplication analysis revealed that segmental duplication contributed to the expansion of the StGSK family. Gene structure and motif pattern analyses indicated that similar exon/intron and motif organizations were found in StGSKs from the same clade. Conserved motif and kinase activity analyses indicated that the StGSKs encode active protein kinases, and they were shown to be distributed throughout whole cells. Cis-acting regulatory element analysis revealed the presence of many growth-, hormone-, and stress-responsive elements within the promoter regions of the StGSKs, which is consistent with their expression in different organs, and their altered expression in response to hormone and stress treatments. Association network analysis indicated that various proteins, including two confirmed BES1 family transcription factors, potentially interact with StGSKs. Overexpression of StSK21 provides enhanced sensitivity to salt stress in Arabidopsis thaliana plants. Overall, these results reveal that StGSK proteins are active protein kinases with purported functions in regulating growth, development, and stress responses.


Asunto(s)
Regulación de la Expresión Génica de las Plantas/genética , Genes de Plantas/genética , Familia de Multigenes/genética , Proteínas de Plantas/genética , Estrés Salino/genética , Solanum tuberosum/genética , Estrés Fisiológico/genética , Arabidopsis/genética , Cromosomas de las Plantas/genética , Duplicación de Gen/genética , Perfilación de la Expresión Génica/métodos , Estudio de Asociación del Genoma Completo/métodos , Filogenia , Reguladores del Crecimiento de las Plantas/genética , Factores de Transcripción/genética
6.
PLoS One ; 15(10): e0233254, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33052910

RESUMEN

Herbicide application is crucial for weed management in most crop production systems, but for sorghum herbicide options are limited. Sorghum is sensitive to residual protoporphyrinogen oxidase (PPO)-inhibiting herbicides, such as fomesafen, and a long re-entry period is required before sorghum can be planted after its application. Improving sorghum for tolerance to such residual herbicides would allow for increased sorghum production and the expansion of herbicide options for growers. In this study, we observed sorghum tolerance to residual fomesafen. To investigate the underlying tolerance mechanism a genome-wide association mapping study was conducted using field-collected sorghum biomass panel (SBP) data, and a greenhouse assay was developed to confirm the field phenotypes. A total of 26 significant SNPs (FDR<0.05), spanning a 215.3 kb region on chromosome 3, were detected. The ten most significant SNPs included two in genic regions (Sobic.003G136800, and Sobic.003G136900) and eight SNPs in the intergenic region encompassing the genes Sobic.003G136700, Sobic.003G136800, Sobic.003G137000, Sobic.003G136900, and Sobic.003G137100. The gene Sobic.003G137100 (PPXI), which encodes the PPO1 enzyme, one of the targets of PPO-inhibiting herbicides, was located 12kb downstream of the significant SNP S03_13152838. We found that PPXI is highly conserved in sorghum and expression does not significantly differ between tolerant and sensitive sorghum lines. Our results suggest that PPXI most likely does not underlie the observed herbicide tolerance. Instead, the mechanism underlying herbicide tolerance in the SBP is likely metabolism-based resistance, possibly regulated by the action of multiple genes. Further research is necessary to confirm candidate genes and their functions.


Asunto(s)
Benzamidas/farmacología , Resistencia a los Herbicidas , Polimorfismo de Nucleótido Simple , Protoporfirinógeno-Oxidasa/genética , Sorghum/crecimiento & desarrollo , Biomasa , Mapeo Cromosómico , Cromosomas de las Plantas/genética , Estudio de Asociación del Genoma Completo , Técnicas de Genotipaje , Proteínas de Plantas/antagonistas & inhibidores , Proteínas de Plantas/genética , Protoporfirinógeno-Oxidasa/antagonistas & inhibidores , Sorghum/efectos de los fármacos , Sorghum/genética
7.
Nat Commun ; 11(1): 5442, 2020 10 28.
Artículo en Inglés | MEDLINE | ID: mdl-33116128

RESUMEN

Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.


Asunto(s)
Poaceae/genética , Biomasa , Cromosomas de las Plantas/genética , Elementos Transponibles de ADN , Diploidia , Evolución Molecular , Regulación de la Expresión Génica de las Plantas , Variación Genética , Genoma de Planta , Genómica , Modelos Genéticos , Filogenia , Poaceae/clasificación , Poaceae/crecimiento & desarrollo , Poliploidía , Saccharum/genética , Estaciones del Año , Sorghum/genética
8.
Nat Commun ; 11(1): 5269, 2020 10 19.
Artículo en Inglés | MEDLINE | ID: mdl-33077749

RESUMEN

Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii, the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing to the genomic architecture of flowering time. Small-scale gene duplications contribute to the expansion of gene families involved in azalea pigment biosynthesis. We reconstruct entire metabolic pathways for anthocyanins and carotenoids and their potential regulatory networks by detailed analysis of time-ordered gene co-expression networks. MYB, bHLH, and WD40 transcription factors may collectively regulate anthocyanin accumulation in R. simsii, particularly at the initial stages of flower coloration, and with WRKY transcription factors controlling progressive flower coloring at later stages. This work provides a cornerstone for understanding the underlying genetics governing flower timing and coloration and could accelerate selective breeding in azalea.


Asunto(s)
Cromosomas de las Plantas/genética , Genoma de Planta , Proteínas de Plantas/genética , Rhododendron/genética , Antocianinas/biosíntesis , Vías Biosintéticas , Carotenoides/metabolismo , Cromosomas de las Plantas/metabolismo , Flores/genética , Flores/crecimiento & desarrollo , Flores/metabolismo , Regulación de la Expresión Génica de las Plantas , Familia de Multigenes , Proteínas de Plantas/metabolismo , Rhododendron/crecimiento & desarrollo , Rhododendron/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
9.
Plant Dis ; 104(11): 2940-2948, 2020 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-32897842

RESUMEN

Wheat-rye T1RS·1BL translocations have been widely used worldwide in wheat production for multiple disease resistance and superior yield traits. However, many T1RS·1BL translocations have successively lost their resistance to pathogens due to the coevolution of pathogen virulence with host resistance. Because of the extensive variation in rye (Secale cereale L.) as a naturally cross-pollinating relative of wheat, it still has promise to widen the variation of 1RS and to fully realize its application value in wheat improvement. In the present study, the wheat-rye breeding line R2207 was characterized by comprehensive analyses using genomic in situ hybridization (GISH), multicolor fluorescence in situ hybridization with multiple probes, multicolor GISH, and molecular marker analysis, and then was proven to be a cytogenetically stable wheat-rye T1RS·1BL translocation line. Based on the disease responses to different isolates of powdery mildew and genetic analysis, R2207 appears to possess a novel variation for resistance, which was confirmed to be located on the rye chromosome arm 1RS. Line R2207 also exhibited high levels of resistance to stripe rust at both seedling and adult stages, as well as enhanced agronomic performance, so it has been transferred into a large number of commercial cultivars using an efficient 1RS-specific kompetitive allele specific PCR marker for marker-assisted selection.


Asunto(s)
Secale , Triticum , Cromosomas de las Plantas/genética , Hibridación Fluorescente in Situ , Enfermedades de las Plantas/genética , Secale/genética , Triticum/genética
10.
PLoS One ; 15(9): e0239377, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32986735

RESUMEN

Double pollen fertility neutral genes, San and Sbn, can control pollen sterility in intersubspecific (indica × japonica) rice hybrids, which has excellent potential to increase rice yield. Previous studies showed that polyploidy could increase the interaction of three pollen sterility loci, i.e. Sa, Sb and Sc, which cause pollen sterility in autotetraploid rice hybrids, and hybrid fertility could be improved by double neutral genes, San and Sbn, in autotetraploid rice hybrids. We compared cytological and transcriptome data between autotetraploid and diploid rice hybrid during meiosis and single microspore stages to understand the molecular mechanism of neutral genes for overcoming pollen sterility in autotetraploid rice hybrids, which harbored double neutral genes. Cytological results revealed that the double neutral genes resulted in higher pollen fertility (76.74%) and lower chromosomal abnormalities in autotetraploid hybrid than in parents during metaphase I, metaphase II, anaphase I and anaphase II. Moreover, autotetraploid rice hybrid displayed stronger heterosis than a diploid hybrid. Compared with diploid rice hybrid, a total of 904 and 68 differently expressed genes (DEGs) were identified explicitly in autotetraploid hybrid at meiosis and single microspore stages, respectively. Of these, 133 and 41 genes were detected in higher-parent dominance and transgressive up-regulation dominance, respectively, which were considered autotetraploid potential heterosis genes, including a meiosis-related gene (Os01g0917500, MSP1) and two meiosis specific-genes (Os07g0624900 and Os04g0208600). Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genomes pathway (KEGG) analysis revealed that DEGs significantly enriched in amino acid metabolism and photosynthesis metabolism. These results indicated that meiosis-specific and meiosis-related genes, and amino acids and photosynthesis metabolism-related genes contribute to higher yield and pollen fertility in autotetraploid rice hybrid. This study provides a theoretical basis for molecular mechanisms of heterosis in autotetraploid rice harboring double neutral genes for pollen fertility.


Asunto(s)
Análisis Citogenético , Diploidia , Perfilación de la Expresión Génica , Genes de Plantas/genética , Oryza/genética , Tetraploidía , Cromosomas de las Plantas/genética , Fenotipo , Infertilidad Vegetal/genética , Polen/genética , Polen/fisiología
11.
PLoS One ; 15(8): e0237774, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32797075

RESUMEN

The source-sink relationship determines the ultimate grain yield of rice. In this study, we used a set of reciprocal introgression lines (ILs) derived from Xuishui09 × IR2061 to map quantitative trait loci (QTLs) that were associated with sink-, source-, and grain yield-related traits. A total of 95 QTLs influencing eight measured traits were identified using 6181 high-quality single nucleotide polymorphism markers. Nine background-independent QTLs were consistently detected in seven chromosomal regions in different genetic backgrounds. Seven QTLs clusters simultaneously affected sink-, source-, and grain yield-related traits, probably due to the genetic basis of significant correlations of grain yield with source and sink traits. We selected 15 candidate genes in the four QTLs consistently identified in the two populations by performing gene-based association and haplotype analyses using 2288 accessions from the 3K project. Among these, LOC_Os03g48970 for qTSN3b, LOC_Os06g04710 for qFLL6a, and LOC_Os07g32510 for qTGW7 were considered as the most likely candidate genes based on functional annotations. These results provide a basis for further study of candidate genes and for the development of high-yield rice varieties by balancing source-sink relationships using marker-assisted selection.


Asunto(s)
Grano Comestible/genética , Oryza/genética , Sitios de Carácter Cuantitativo , Cromosomas de las Plantas/genética , Grano Comestible/crecimiento & desarrollo , Genes de Plantas , Oryza/crecimiento & desarrollo , Polimorfismo de Nucleótido Simple
12.
DNA Cell Biol ; 39(10): 1850-1861, 2020 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-32790504

RESUMEN

Strigolactones (SLs) are the major plant hormones that play important roles in regulating organ development and environmental stress tolerance in plants. Even though the SL-related genes have been identified and well characterized in some plants, the information of SL-related genes in soybean is not fully established yet, especially in response to salt and alkaline stresses. In this study, we identified nine SL biosynthetic genes that include two D27, two CCD7, two CCD8, and three MAX1, as well as seven SL signaling genes that comprised two D14, two MAX2, and three D53 in the soybean genome. We found that SL biosynthetic and signaling genes are evolutionary conserved among different species. Syntenic analysis of these genes revealed their location on nine chromosomes as well as the presence of 10 pairs of duplication genes. Moreover, plant hormone and stress-responsive elements were identified in the promoter regions of SL biosynthetic and signaling genes. By using reverse transcription quantitative real-time PCR, we confirmed that SL genes have different tissue expressions in roots, stems, and leaves. The expression profile of SL biosynthetic and signaling genes under salt and alkaline stresses further confirmed the regulatory roles of SL biosynthetic and signaling genes under stress. In conclusion, we identified and provided valuable information on the soybean SL biosynthetic and signaling genes, and established a foundation for further functional analysis of soybean SL-related genes in response to salt and alkaline stresses.


Asunto(s)
Compuestos Heterocíclicos con 3 Anillos/metabolismo , Lactonas/metabolismo , Proteínas de Plantas/genética , Estrés Salino , Soja/genética , Cromosomas de las Plantas/genética , Duplicación de Gen , Proteínas de Plantas/metabolismo , Transducción de Señal , Soja/metabolismo , Sintenía
13.
Nat Commun ; 11(1): 3670, 2020 07 29.
Artículo en Inglés | MEDLINE | ID: mdl-32728126

RESUMEN

Our understanding of polyploid genome evolution is constrained because we cannot know the exact founders of a particular polyploid. To differentiate between founder effects and post polyploidization evolution, we use a pan-genomic approach to study the allotetraploid Brachypodium hybridum and its diploid progenitors. Comparative analysis suggests that most B. hybridum whole gene presence/absence variation is part of the standing variation in its diploid progenitors. Analysis of nuclear single nucleotide variants, plastomes and k-mers associated with retrotransposons reveals two independent origins for B. hybridum, ~1.4 and ~0.14 million years ago. Examination of gene expression in the younger B. hybridum lineage reveals no bias in overall subgenome expression. Our results are consistent with a gradual accumulation of genomic changes after polyploidization and a lack of subgenome expression dominance. Significantly, if we did not use a pan-genomic approach, we would grossly overestimate the number of genomic changes attributable to post polyploidization evolution.


Asunto(s)
Brachypodium/genética , Diploidia , Evolución Molecular , Genoma de Planta , Poliploidía , Cromosomas de las Plantas/genética , Genoma del Cloroplasto , Genómica , Hibridación Genética , Filogenia , Polimorfismo de Nucleótido Simple , Retroelementos/genética , Especificidad de la Especie
14.
Plant Mol Biol ; 104(1-2): 81-95, 2020 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-32621166

RESUMEN

KEY MESSAGE: Genome-wide identification of WD40-like genes reveals a duplication of COP1-like genes, one of the key players involved in regulation of flowering time and photomorphogenesis, with strong functional diversification in Rosaceae. WD40 proteins play crucial roles in a broad spectrum of developmental and physiological processes. Here, we conducted a systematic characterization of this family of genes in Rosa chinensis 'Old Blush' (OB), a founder genotype for modern rose domestication. We identified 187 rose WD40 genes and classified them into 5 clusters and 15 subfamilies with 11 of RcWD40s presumably generated via tandem duplication. We found RcWD40 genes were expressed differentially following stages of vegetative and reproductive development. We detected a duplication of CONSTITUTIVE PHOTOMORPHOGENIC1-like genes in rose (RcCOP1 and RcCOP1L) and other Rosaceae plants. Featuring a distinct expression pattern and a different profile of cis-regulatory-elements in the transcriptional regulatory regions, RcCOP1 seemed being evolutionarily conserved while RcCOP1L did not dimerize with RcHY5 and RcSPA4. Our data thus reveals a functional diversification of COP1-like genes in Rosacaeae plants, and provides a valuable resource to explore the potential function and evolution of WD40-like genes in Rosaceae plants.


Asunto(s)
Genes de Plantas , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Rosaceae/genética , Rosaceae/metabolismo , Ubiquitina-Proteína Ligasas/genética , Secuencia de Aminoácidos , Arabidopsis/genética , Arabidopsis/metabolismo , Cromosomas de las Plantas/genética , Domesticación , Duplicación de Gen , Regulación de la Expresión Génica de las Plantas , Genoma de Planta , Filogenia , Plantas Modificadas Genéticamente , Rosa/genética , Rosa/metabolismo , Ubiquitina-Proteína Ligasas/metabolismo
15.
BMC Evol Biol ; 20(1): 91, 2020 07 29.
Artículo en Inglés | MEDLINE | ID: mdl-32727363

RESUMEN

BACKGROUND: The SIAMESE (SIM) locus is a cell-cycle kinase inhibitor (CKI) gene that has to date been identified only in plants; it encodes a protein that promotes transformation from mitosis to endoreplication. Members of the SIAMESE-RELATED (SMR) family have similar functions, and some are related to cell-cycle responses and abiotic stresses. However, the functions of SMRs are poorly understood in maize (Zea mays L.). RESULTS: In the present study, 12 putative SMRs were identified throughout the entire genome of maize, and these were clustered into six groups together with the SMRs from seven other plant species. Members of the ZmSMR family were divided into four groups according to their protein sequences. Various cis-acting elements in the upstream sequences of ZmSMRs responded to abiotic stresses. Expression analyses revealed that all ZmSMRs were upregulated at 5, 20, 25, and 35 days after pollination. In addition, we found that ZmSMR9/11/12 may have regulated the initiation of endoreplication in endosperm central cells. Additionally, ZmSMR2/10 may have been primarily responsible for the endoreplication regulation of outer endosperm or aleurone cells. The relatively high expression levels of almost all ZmSMRs in the ears and tassels also implied that these genes may function in seed development. The effects of treatments with ABA, heat, cold, salt, and drought on maize seedlings and expression of ZmSMR genes suggested that ZmSMRs were strongly associated with response to abiotic stresses. CONCLUSION: The present study is the first to conduct a genome-wide analysis of members of the ZmSMR family by investigating their locations in chromosomes, identifying regulatory elements in their promoter regions, and examining motifs in their protein sequences. Expression analysis of different endosperm developmental periods, tissues, abiotic stresses, and hormonal treatments suggests that ZmSMR genes may function in endoreplication and regulate the development of reproductive organs. These results may provide valuable information for future studies of the functions of the SMR family in maize.


Asunto(s)
Evolución Molecular , Regulación de la Expresión Génica de las Plantas , Genoma de Planta , Familia de Multigenes , Zea mays/genética , Secuencia de Aminoácidos , Secuencia de Bases , Cromosomas de las Plantas/genética , Secuencia Conservada/genética , Endospermo/genética , Duplicación de Gen , Genes de Plantas , Filogenia , Proteínas de Plantas/química , Proteínas de Plantas/genética , Regiones Promotoras Genéticas/genética , Análisis de Regresión , Especificidad de la Especie , Estrés Fisiológico/efectos de los fármacos , Sintenía/genética
16.
PLoS Genet ; 16(7): e1008900, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32667955

RESUMEN

In this study we performed a genotype-phenotype association analysis of meiotic stability in 10 autotetraploid Arabidopsis lyrata and A. lyrata/A. arenosa hybrid populations collected from the Wachau region and East Austrian Forealps. The aim was to determine the effect of eight meiosis genes under extreme selection upon adaptation to whole genome duplication. Individual plants were genotyped by high-throughput sequencing of the eight meiosis genes (ASY1, ASY3, PDS5b, PRD3, REC8, SMC3, ZYP1a/b) implicated in synaptonemal complex formation and phenotyped by assessing meiotic metaphase I chromosome configurations. Our results reveal that meiotic stability varied greatly (20-100%) between individual tetraploid plants and associated with segregation of a novel ASYNAPSIS3 (ASY3) allele derived from A. lyrata. The ASY3 allele that associates with meiotic stability possesses a putative in-frame tandem duplication (TD) of a serine-rich region upstream of the coiled-coil domain that appears to have arisen at sites of DNA microhomology. The frequency of multivalents observed in plants homozygous for the ASY3 TD haplotype was significantly lower than in plants heterozygous for ASY3 TD/ND (non-duplicated) haplotypes. The chiasma distribution was significantly altered in the stable plants compared to the unstable plants with a shift from proximal and interstitial to predominantly distal locations. The number of HEI10 foci at pachytene that mark class I crossovers was significantly reduced in a plant homozygous for ASY3 TD compared to a plant heterozygous for ASY3 ND/TD. Fifty-eight alleles of the 8 meiosis genes were identified from the 10 populations analysed, demonstrating dynamic population variability at these loci. Widespread chimerism between alleles originating from A. lyrata/A. arenosa and diploid/tetraploids indicates that this group of rapidly evolving genes may provide precise adaptive control over meiotic recombination in the tetraploids, the very process that gave rise to them.


Asunto(s)
Proteínas de Arabidopsis/genética , Arabidopsis/genética , Proteínas Cromosómicas no Histona/genética , Meiosis/genética , Alelos , Arabidopsis/crecimiento & desarrollo , Emparejamiento Cromosómico/genética , Segregación Cromosómica , Cromosomas de las Plantas/genética , Proteínas de Unión al ADN/genética , Diploidia , Tetraploidía
17.
Mol Phylogenet Evol ; 150: 106881, 2020 09.
Artículo en Inglés | MEDLINE | ID: mdl-32512193

RESUMEN

Dennstaedtiaceae has 270 species, a worldwide distribution, and an edge-colonizing habit that is unusual among ferns. Aneuploidy, polyploidy, and hybrids are common in the family. Combining morphology, anatomy, chromosome number, and geographical distributions with our newly generated molecular phylogeny, we provide new insights into the evolution of the family. We paid special attention to Hypolepis. Our molecular dataset of five cpDNA markers is the most comprehensive to date, comprising 72 species (and a total of 98 taxa), of which 33 are Hypolepis (45 taxa). We also generated divergence-time estimates through BEAST with four fossil calibrations. We recovered three sub-families in Dennstaedtiaceae: Monachosoroideae (monogeneric), Dennstaedtioideae, and Hypolepidoideae. Monachosoroideae has a chromosome base number of x = 28; Hypolepidoideae of x = 26; while in Dennstaedtioideae this is still obscure, with different numbers ranging from 30 to 47. Dennstaedtioideae genera require re-circumscriptions because Dennstaedtia is polyphyletic. In Hypolepidoideae, the six genera are monophyletic. Within Hypolepis, seven geographically distinct clades were recovered; but we found no strong morphological characters to define them. Within the family, the long-creeping rhizome evolved with a change in habit: from shade-tolerant to edge-colonizers, to thicket-formers. Short or extremely large leaves are derived conditions. Sorus shape and position, glandular hairs, and prickles are homoplastic. Hybridization/allotetraploidy in Hypolepis can be suggested by the combined data. In our phylogenetic hypothesis, Dennstaedtiaceae originated around 135 Ma, with the split of Monachosoroideae around 94 Ma, and the split between Dennstaedtioideae/Hypolepidoideae around 78 Ma. All extant genera are inferred to be relatively young. Hypolepis started to diversify around 10 Ma, and it probably originated in east Asia and/or Oceania. Hypolepis reached the Neotropics twice: through elements of the Hypolepis rugosula clade (which originated at 7 Ma), and through the ancestor of the Neotropical clade, which originated at 3.1 Ma and was prickly.


Asunto(s)
Dennstaedtiaceae/clasificación , Cromosomas de las Plantas/genética , Dennstaedtiaceae/genética , Evolución Molecular , Fósiles , Hibridación Genética , Filogenia , Hojas de la Planta/genética , Poliploidía
18.
Cytogenet Genome Res ; 160(5): 272-282, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32516773

RESUMEN

Saccharum spontaneum is a wild germplasm resource of the genus Saccharum that has many valuable traits. Ty1-copia retrotransposons constitute a large proportion of plant genomes and affect genome sequence organization and evolution. This study aims to analyze the sequence heterogeneity, phylogenetic diversity, copy number, and chromosomal dispersion patterns of Ty1-copia retrotransposons in S. spontaneum. A total of 44 Ty1-copia reverse transcriptase subclones isolated from S. spontaneum showed a range of heterogeneity, and all sequences were A-T rich, averaging approximately 54.59%. Phylogenetic analysis divided the 44 reverse transcriptase sequences into 5 distinct lineages (Retrofit/Ale, Sire/Maximus, Bianca, Tork/TAR, and Ty1-copia like). Dot-blot hybridization revealed that Ty1-copia retrotransposons consisted of a significant component of approximately 38,900 copies and 16,300 copies per genome in the accessions YN82-114 (2n = 10x = 80) and AP85-441 (2n = 4x = 32), respectively. The results of a local blast analysis showed that there are 15,069 Ty1-copia retrotransposon copies in the genome of AP85-441, of which the Retrofit/Ale lineage had the highest copy number, followed by the Tork/TAR, Sire/Maximus, and Bianca lineages. Furthermore, both FISH and the local blast analysis with AP85-441 genomic data demonstrated that the Ty1-copia retrotransposons were unevenly distributed throughout the chromosomes. Taken together, this study provides insights into the role of Ty1-copia retrotransposons in the evolution and organization of the S. spontaneum genome.


Asunto(s)
Cromosomas de las Plantas/genética , Evolución Molecular , Genoma de Planta/genética , Retroelementos/genética , Saccharum/genética , Filogenia
19.
Proc Natl Acad Sci U S A ; 117(25): 14561-14571, 2020 06 23.
Artículo en Inglés | MEDLINE | ID: mdl-32518116

RESUMEN

Recombination between homeologous chromosomes, also known as homeologous exchange (HE), plays a significant role in shaping genome structure and gene expression in interspecific hybrids and allopolyploids of several plant species. However, the molecular mechanisms that govern HEs are not well understood. Here, we studied HE events in the progeny of a nascent allotetraploid (genome AADD) derived from two diploid progenitors of hexaploid bread wheat using cytological and whole-genome sequence analyses. In total, 37 HEs were identified and HE junctions were mapped precisely. HEs exhibit typical patterns of homologous recombination hotspots, being biased toward low-copy, subtelomeric regions of chromosome arms and showing association with known recombination hotspot motifs. But, strikingly, while homologous recombination preferentially takes place upstream and downstream of coding regions, HEs are highly enriched within gene bodies, giving rise to novel recombinant transcripts, which in turn are predicted to generate new protein fusion variants. To test whether this is a widespread phenomenon, a dataset of high-resolution HE junctions was analyzed for allopolyploid Brassica, rice, Arabidopsis suecica, banana, and peanut. Intragenic recombination and formation of chimeric genes was detected in HEs of all species and was prominent in most of them. HE thus provides a mechanism for evolutionary novelty in transcript and protein sequences in nascent allopolyploids.


Asunto(s)
Cromosomas de las Plantas/genética , Genes de Plantas/genética , Proteínas de Plantas/genética , Poliploidía , Recombinación Genética , Arabidopsis/genética , Arachis/genética , Brassica/genética , Biología Computacional , Evolución Molecular , Fusión Génica , Cariotipificación , Musa/genética , Oryza/genética , Transcripción Genética , Triticum/genética
20.
PLoS One ; 15(6): e0233800, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32497070

RESUMEN

Several studies suggest the relation of DNA methylation to diseases in humans and important phenotypes in plants drawing attention to this epigenetic mark as an important source of variability. In the last decades, several methodologies were developed to assess the methylation state of a genome. However, there is still a lack of affordable and precise methods for genome wide analysis in large sample size studies. Methyl sensitive double digestion MS-DArT sequencing method emerges as a promising alternative for methylation profiling. We developed a computational pipeline for the identification of DNA methylation using MS-DArT-seq data and carried out a pilot study using the Eucalyptus grandis tree sequenced for the species reference genome. Using a statistic framework as in differential expression analysis, 72,515 genomic sites were investigated and 5,846 methylated sites identified, several tissue specific, distributed along the species 11 chromosomes. We highlight a bias towards identification of DNA methylation in genic regions and the identification of 2,783 genes and 842 transposons containing methylated sites. Comparison with WGBS, DNA sequencing after treatment with bisulfite, data demonstrated a precision rate higher than 95% for our approach. The availability of a reference genome is useful for determining the genomic context of methylated sites but not imperative, making this approach suitable for any species. Our approach provides a cost effective, broad and reliable examination of DNA methylation profile on MspI/HpaII restriction sites, is fully reproducible and the source code is available on GitHub (https://github.com/wendelljpereira/ms-dart-seq).


Asunto(s)
Análisis Costo-Beneficio , Metilación de ADN/genética , Eucalyptus/genética , Técnicas de Genotipaje/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Hojas de la Planta/genética , Análisis de Secuencia de ADN/métodos , Árboles/genética , Cromosomas de las Plantas/genética , Enzimas de Restricción del ADN/genética , Elementos Transponibles de ADN/genética , Genes de Plantas/genética , Técnicas de Genotipaje/economía , Secuenciación de Nucleótidos de Alto Rendimiento/economía , Proyectos Piloto , Reproducibilidad de los Resultados , Mapeo Restrictivo , Análisis de Secuencia de ADN/economía , Sulfitos/farmacología
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