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1.
Braz. j. biol ; 83: e245372, 2023. tab, graf
Artigo em Inglês | LILACS, VETINDEX | ID: biblio-1339409

RESUMO

Abstract Hybridization and Polyploidization are most common of the phenomenon observed in plants, especially in the genus Nicotiana leading to the duplication of genome. Although genomic changes associated with these events has been studied at various levels but the genome size and GC content variation is less understood because of absence of sufficient genomic data. In this study the flow cytometry technique was used to uncover the genome size and GC contents of 46 Nicotiana species and we compared the genomic changes associated with the hybridization events along evolutionary time scale. The genome size among Nicotiana species varied between 3.28 pg and 11.88 pg whereas GC contents varied between 37.22% and 51.25%. The tetraploid species in genus Nicotiana including section Polydiclae, Repandae, Nicotiana, Rustica and Sauveolentes revealed both up and downsizing in their genome sizes when compared to the sum of genomes of their ancestral species. The genome sizes of three homoploid hybrids were found near their ancestral species. Loss of large genome sequence was observed in the evolutionary more aged species (>10 Myr) as compared to the recently evolved one's (<0.2 Myr). The GC contents were found homogenous with a mean difference of 2.46% among the Nicotiana species. It is concluded that genome size change appeared in either direction whereas the GC contents were found more homogenous in genus Nicotiana.


Resumo A hibridização e a poliploidização são os fenômenos mais comuns observados em plantas, principalmente no gênero Nicotiana, levando à duplicação do genoma. Embora as mudanças genômicas associadas a esses eventos tenham sido estudadas em vários níveis, o tamanho do genoma e a variação do conteúdo de GC são menos compreendidos devido à ausência de dados genômicos suficientes. Neste estudo, a técnica de citometria de fluxo foi usada para descobrir o tamanho do genoma e o conteúdo de GC de 46 espécies de Nicotiana, e comparamos as mudanças genômicas associadas aos eventos de hibridização ao longo da escala de tempo evolutiva. O tamanho do genoma entre as espécies de Nicotiana variou entre 3,28 pg e 11,88 pg, enquanto os conteúdos de GC variaram entre 37,22% e 51,25%. As espécies tetraploides do gênero Nicotiana, incluindo as seções Polydiclae, Repandae, Nicotiana, Rustica e Sauveolentes, revelaram aumento e redução do tamanho do genoma quando comparados à soma dos genomas de suas espécies ancestrais. Os tamanhos do genoma de três híbridos homoploides foram encontrados perto de suas espécies ancestrais. A perda da grande sequência do genoma foi observada nas espécies evolutivas mais velhas (> 10 Myr) em comparação com as que evoluíram recentemente (< 0,2 Myr). Os teores de GC foram homogêneos com diferença média de 2,46% entre as espécies de Nicotiana. Conclui-se que a mudança no tamanho do genoma apareceu em ambas as direções, enquanto os conteúdos de GC foram encontrados mais homogêneos no gênero Nicotiana.


Assuntos
Tabaco/genética , Genoma de Planta/genética , Filogenia , Composição de Bases , Tamanho do Genoma
2.
Genome Biol ; 23(1): 188, 2022 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-36071507

RESUMO

BACKGROUND: Garlic is an entirely sterile crop with important value as a vegetable, condiment, and medicine. However, the evolutionary history of garlic remains largely unknown. RESULTS: Here we report a comprehensive map of garlic genomic variation, consisting of amazingly 129.4 million variations. Evolutionary analysis indicates that the garlic population diverged at least 100,000 years ago, and the two groups cultivated in China were domesticated from two independent routes. Consequently, 15.0 and 17.5% of genes underwent an expression change in two cultivated groups, causing a reshaping of their transcriptomic architecture. Furthermore, we find independent domestication leads to few overlaps of deleterious substitutions in these two groups due to separate accumulation and selection-based removal. By analysis of selective sweeps, genome-wide trait associations and associated transcriptomic analysis, we uncover differential selections for the bulb traits in these two garlic groups during their domestication. CONCLUSIONS: This study provides valuable resources for garlic genomics-based breeding, and comprehensive insights into the evolutionary history of this clonal-propagated crop.


Assuntos
Alho , Alho/genética , Genoma de Planta , Genômica , Melhoramento Vegetal , Polimorfismo de Nucleotídeo Único
4.
Int J Mol Sci ; 23(17)2022 Aug 26.
Artigo em Inglês | MEDLINE | ID: mdl-36077110

RESUMO

East Asia has an abundant resource of fragrant japonica rice that is gaining increasing interest among both consumers and producers. However, genomic resources and in particular complete genome sequences currently available for the breeding of fragrant japonica rice are still scarce. Here, integrating Nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C methods, we presented a high-quality chromosome-level genome assembly (~378.78 Mb) for a new fragrant japonica cultivar 'Changxianggeng 1813', with 31,671 predicated protein-coding genes. Based on the annotated genome sequence, we demonstrated that it was the badh2-E2 type of deletion (a 7-bp deletion in the second exon) that caused fragrance in 'Changxianggeng 1813'. Comparative genomic analyses revealed that multiple gene families involved in the abiotic stress response were expanded in the 'Changxianggeng 1813' genome, which further supported the previous finding that no generalized loss of abiotic stress tolerance associated with the fragrance phenotype. Although the 'Changxianggeng 1813' genome showed high genomic synteny with the genome of the non-fragrant japonica rice cultivar Nipponbare, a total of 289,970 single nucleotide polymorphisms (SNPs), 96,093 small insertion-deletion polymorphisms (InDels), and 8690 large structure variants (SVs, >1000 bp) were identified between them. Together, these genomic resources will be valuable for elucidating the mechanisms underlying economically important traits and have wide-ranging implications for genomics-assisted breeding in fragrant japonica rice.


Assuntos
Oryza , Cromossomos , Genoma de Planta , Genômica , Odorantes , Oryza/genética , Melhoramento Vegetal , Polimorfismo de Nucleotídeo Único/genética
5.
Int J Mol Sci ; 23(17)2022 Aug 29.
Artigo em Inglês | MEDLINE | ID: mdl-36077206

RESUMO

Precise editing of the plant genome has long been desired for functional genomic research and crop breeding. Prime editing is a newly developed precise editing technology based on CRISPR-Cas9, which uses an engineered reverse transcriptase (RT), a catalytically impaired Cas9 endonuclease (nCas9), and a prime editing guide RNA (pegRNA). In addition, prime editing has a wider range of editing types than base editing and can produce nearly all types of edits. Although prime editing was first established in human cells, it has recently been applied to plants. As a relatively new technique, optimization will be needed to increase the editing efficiency in different crops. In this study, we successfully edited a mutant GFP in rice, peanut, chickpea, and cowpea protoplasts. In rice, up to 16 times higher editing efficiency was achieved with a dual pegRNA than the single pegRNA containing vectors. Edited-mutant GFP protoplasts have also been obtained in peanut, chickpea, and cowpea after transformation with the dual pegRNA vectors, albeit with much lower editing efficiency than in rice, ranging from 0.2% to 0.5%. These initial results promise to expedite the application of prime editing in legume breeding programs to accelerate crop improvement.


Assuntos
Cicer , Oryza , Vigna , Arachis/genética , Sistemas CRISPR-Cas/genética , Cicer/genética , Produtos Agrícolas/genética , Edição de Genes/métodos , Genoma de Planta , Humanos , Oryza/genética , Melhoramento Vegetal , Protoplastos , RNA Guia/genética , Vigna/genética
6.
Plant Genome ; 15(3): e20256, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-36069430

Assuntos
Genoma de Planta
7.
Int J Mol Sci ; 23(17)2022 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-36077571

RESUMO

CRISPR/Cas-based genome editing technology provides straightforward, proficient, and multifunctional ways for the site-directed modification of organism genomes and genes. The application of CRISPR-based technology in plants has a vast potential value in gene function research, germplasm innovation, and genetic improvement. The complexity of woody plants genome may pose significant challenges in the application and expansion of various new editing techniques, such as Cas9, 12, 13, and 14 effectors, base editing, particularly for timberland species with a long life span, huge genome, and ploidy. Therefore, many novel optimisms have been drawn to molecular breeding research based on woody plants. This review summarizes the recent development of CRISPR/Cas applications for essential traits, including wood properties, flowering, biological stress, abiotic stress, growth, and development in woody plants. We outlined the current problems and future development trends of this technology in germplasm and the improvement of products in woody plants.


Assuntos
Sistemas CRISPR-Cas/genética , Edição de Genes , Genoma de Planta/genética , Árvores/genética , Edição de Genes/métodos , Madeira/genética
8.
Pak J Biol Sci ; 25(6): 468-475, 2022 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-36098181

RESUMO

<b>Background and Objective:</b> In high plants, the 70 kDa heat stress proteins (Hsp70-s) have been regarded as one of the vital components of the cellular network of chaperones and folding catalysts that play important roles in numerous biological processes during growth and development. The Hsp70 families have been reported in many plant species, unfortunately, no information on this important protein family in papaya (<i>Carica papaya</i>). The objective of this study was to provide comprehensive information on the CpHsp70 family in papaya. <b>Materials and Methods:</b> The <i>CpHsp70</i> genes in the papaya genome were identified by a basic local alignment search tool against the papaya genome database by using well-known <i>Arabidopsis</i> Hsp70-s. Sequences were then analyzed by various bioinformatics tools to investigate the characteristics of the CpHsp70 family. <b>Results:</b> A total of 12 members of the CpHsp70 family has been identified and characterized in papaya. By using various computational tools, these results revealed that all general characteristics of the CpHsp70 family, like physic-chemical parameters, gene structure, phylogenetic tree and subcellular localization were provided. The transcriptome atlas was applied to re-analyze the expression patterns of genes encoding the CpHsp70 family in major tissues/organs during the growth and development of papaya plants. <b>Conclusion:</b> Results from this work exhibited the characteristics and expression analysis of the <i>CpHsp70</i> genes of this important tropical fruit crop. Taken together, this study could provide a solid foundation of the CpHsp70 family, which will be helpful in the construction of stress tolerance in papaya plants.


Assuntos
Arabidopsis , Carica , Arabidopsis/genética , Carica/genética , Genoma de Planta , Proteínas de Choque Térmico HSP70/genética , Proteínas de Choque Térmico HSP70/metabolismo , Filogenia , Verduras/genética
9.
Database (Oxford) ; 20222022 09 07.
Artigo em Inglês | MEDLINE | ID: mdl-36069936

RESUMO

CarrotOmics (https://carrotomics.org/) is a comprehensive database for carrot (Daucus carota L.) breeding and research. CarrotOmics was developed using resources available at the MainLab Bioinformatics core (https://www.bioinfo.wsu.edu/) and is implemented using Tripal with Drupal modules. The database delivers access to download or visualize the carrot reference genome with gene predictions, gene annotations and sequence assembly. Other genomic resources include information for 11 224 genetic markers from 73 linkage maps or genotyping-by-sequencing and descriptions of 371 mapped loci. There are records for 1601 Apiales species (or subspecies) and descriptions of 9408 accessions from 11 germplasm collections representing more than 600 of these species. Additionally, 204 Apiales species have phenotypic information, totaling 28 517 observations from 10 041 biological samples. Resources on CarrotOmics are freely available, search functions are provided to find data of interest and video tutorials are available to describe the search functions and genomic tools. CarrotOmics is a timely resource for the Apiaceae research community and for carrot geneticists developing improved cultivars with novel traits addressing challenges including an expanding acreage in tropical climates, an evolving consumer interested in sustainably grown vegetables and a dynamic environment due to climate change. Data from CarrotOmics can be applied in genomic-assisted selection and genetic research to improve basic research and carrot breeding efficiency. DATABASE URL: https://carrotomics.org/.


Assuntos
Daucus carota , Bases de Dados Genéticas , Daucus carota/genética , Genoma de Planta/genética , Genômica , Melhoramento Vegetal
10.
Commun Biol ; 5(1): 947, 2022 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-36088518

RESUMO

Whole genomes of plants should be ideal databases for their species identification, but unfortunately there was no such method before this exploration. Here we report a plant species identification method based on the whole Genome Analysis and Genome Editing (GAGE). GAGE searches for target sequences from the whole genome of the subject plant and specifically detects them by employing a CRISPR/Cas12a system. Similar to how Mendel chose Pisum sativum (pea), we selected Crocus sativus (saffron) to establish GAGE, in which we constructed a library containing all candidate target sequences. Taking a target sequence in the ITS2 region as an example, we confirmed the feasibility, specificity, and sensitivity of GAGE. Consequently, we succeeded in not only using GAGE to identify Cr. sativus and its adulterants, but also executing GAGE in the plants from different classes including angiosperms, gymnosperms, ferns, and lycophytes. This sensitive and rapid method is the first plant species identification method based on the whole genome and provides new insights into the application of the whole genome in species identification.


Assuntos
Gleiquênias , Edição de Genes , Gleiquênias/genética , Genoma de Planta , Plantas/genética
11.
Int J Mol Sci ; 23(17)2022 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-36077556

RESUMO

Long terminal repeat (LTR)-retrotransposons (LTR-RTs) comprise a major portion of many plant genomes and may exert a profound impact on genome structure, function, and evolution. Although many studies have focused on these elements in an individual species, their dynamics on a family level remains elusive. Here, we investigated the abundance, evolutionary dynamics, and impact on associated genes of LTR-RTs in 16 species in an economically important plant family, Cucurbitaceae. Results showed that full-length LTR-RT numbers and LTR-RT content varied greatly among different species, and they were highly correlated with genome size. Most of the full-length LTR-RTs were amplified after the speciation event, reflecting the ongoing rapid evolution of these genomes. LTR-RTs highly contributed to genome size variation via species-specific distinct proliferations. The Angela and Tekay lineages with a greater evolutionary age were amplified in Trichosanthes anguina, whereas a recent activity burst of Reina and another ancient round of Tekay activity burst were examined in Sechium edule. In addition, Tekay and Retand lineages belonging to the Gypsy superfamily underwent a recent burst in Gynostemma pentaphyllum. Detailed investigation of genes with intronic and promoter LTR-RT insertion showed diverse functions, but the term of metabolism was enriched in most species. Further gene expression analysis in G.pentaphyllum revealed that the LTR-RTs within introns suppress the corresponding gene expression, whereas the LTR-RTs within promoters exert a complex influence on the downstream gene expression, with the main function of promoting gene expression. This study provides novel insights into the organization, evolution, and function of LTR-RTs in Cucurbitaceae genomes.


Assuntos
Evolução Molecular , Retroelementos , Tamanho do Genoma , Genoma de Planta , Filogenia , Retroelementos/genética , Sequências Repetidas Terminais/genética
12.
Elife ; 112022 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-36083267

RESUMO

The development of multiple chromosome-scale reference genome sequences in many taxonomic groups has yielded a high-resolution view of the patterns and processes of molecular evolution. Nonetheless, leveraging information across multiple genomes remains a significant challenge in nearly all eukaryotic systems. These challenges range from studying the evolution of chromosome structure, to finding candidate genes for quantitative trait loci, to testing hypotheses about speciation and adaptation. Here, we present GENESPACE, which addresses these challenges by integrating conserved gene order and orthology to define the expected physical position of all genes across multiple genomes. We demonstrate this utility by dissecting presence-absence, copy-number, and structural variation at three levels of biological organization: spanning 300 million years of vertebrate sex chromosome evolution, across the diversity of the Poaceae (grass) plant family, and among 26 maize cultivars. The methods to build and visualize syntenic orthology in the GENESPACE R package offer a significant addition to existing gene family and synteny programs, especially in polyploid, outbred, and other complex genomes.


The genome is the complete DNA sequence of an individual. It is a crucial foundation for many studies in medicine, agriculture, and conservation biology. Advances in genetics have made it possible to rapidly sequence, or read out, the genome of many organisms. For closely related species, scientists can then do detailed comparisons, revealing similar genes with a shared past or a common role, but comparing more distantly related organisms remains difficult. One major challenge is that genes are often lost or duplicated over evolutionary time. One way to be more confident is to look at 'synteny', or how genes are organized or ordered within the genome. In some groups of species, synteny persists across millions of years of evolution. Combining sequence similarity with gene order could make comparisons between distantly related species more robust. To do this, Lovell et al. developed GENESPACE, a software that links similarities between DNA sequences to the order of genes in a genome. This allows researchers to visualize and explore related DNA sequences and determine whether genes have been lost or duplicated. To demonstrate the value of GENESPACE, Lovell et al. explored evolution in vertebrates and flowering plants. The software was able to highlight the shared sequences between unique sex chromosomes in birds and mammals, and it was able to track the positions of genes important in the evolution of grass crops including maize, wheat, and rice. Exploring the genetic code in this way could lead to a better understanding of the evolution of important sections of the genome. It might also allow scientists to find target genes for applications like crop improvement. Lovell et al. have designed the GENESPACE software to be easy for other scientists to use, allowing them to make graphics and perform analyses with few programming skills.


Assuntos
Variações do Número de Cópias de DNA , Evolução Molecular , Dosagem de Genes , Genoma de Planta , Locos de Características Quantitativas , Sintenia
13.
BMC Genomics ; 23(1): 650, 2022 Sep 13.
Artigo em Inglês | MEDLINE | ID: mdl-36100898

RESUMO

BACKGROUND: As one of the largest transcription factor families in plants, AP2/ERF gene superfamily plays important roles in plant growth, development, fruit ripening and biotic and abiotic stress responses. Despite the great progress has been made in kiwifruit genomic studies, little research has been conducted on the AP2/ERF genes of kiwifruit. The increasing kiwifruit genome resources allowed us to reveal the tissue expression profiles of AP2/ERF genes in kiwifruit on a genome-wide basis. RESULTS: In present study, a total of 158 AP2/ERF genes in A. eriantha were identified. All genes can be mapped on the 29 chromosomes. Phylogenetic analysis divided them into four main subfamilies based on the complete protein sequences. Additionally, our results revealed that the same subfamilies contained similar gene structures and conserved motifs. Ka/Ks calculation indicated that AP2/ERF gene family was undergoing a strong purifying selection and the evolutionary rates were slow. RNA-seq showed that the AP2/ERF genes were expressed differently in different flower development stages and 56 genes were considered as DEGs among three contrasts. Moreover, qRT-PCR suggested partial genes showed significant expressions as well, suggesting they could be key regulators in flower development in A. eriantha. In addition, two genes (AeAP2/ERF061, AeAP2/ERF067) had abundant transcription level based on transcriptomes, implying that they may play a crucial role in plant flower development regulation and flower tissue forming. CONCLUSIONS: We identified AP2/ERF genes and demonstrated their gene structures, conserved motifs, and phylogeny relationships of AP2/ERF genes in two related species of kiwifruit, A. eriantha and A. chinensis, and their potential roles in flower development in A. eriantha. Such information would lay the foundation for further functional identification of AP2/ERF genes involved in kiwifruit flower development.


Assuntos
Actinidia , Actinidia/genética , Flores/genética , Flores/metabolismo , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Filogenia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo
14.
GM Crops Food ; 13(1): 218-241, 2022 Dec 31.
Artigo em Inglês | MEDLINE | ID: mdl-35996854

RESUMO

Achieving global food security is becoming increasingly challenging and many stakeholders around the world are searching for new ways to reach this demanding goal. Here we demonstrate examples of genetically modified and genome edited plants introduced to the market in different world regions. Transgenic crops are regulated based on the characteristics of the product in many countries including the United States and Canada, while the European Union, India, China and others regulate process-based i.e. on how the product was made. We also present the public perception of state-of-the-art plant gene technologies in different regions of the world in the past 20 years. The results of literature analysis show that the public in Europe and North America is more familiar with the notion of genome editing and genetically modified organisms than the public in other world regions.


Assuntos
Genes de Plantas , Opinião Pública , Biotecnologia , Segurança Alimentar , Edição de Genes/métodos , Genoma de Planta , Melhoramento Vegetal/métodos , Plantas Geneticamente Modificadas/genética , Estados Unidos
15.
DNA Res ; 29(5)2022 Aug 23.
Artigo em Inglês | MEDLINE | ID: mdl-36007888

RESUMO

Onions are one of the most widely cultivated vegetables worldwide; however, the development and utilization of molecular markers have been limited because of the large genome of this plant. We present a genome-wide marker design workflow for onions and its application in a high-throughput genotyping method based on target amplicon sequencing. The efficiency of the method was evaluated by genotyping of F2 populations. In the marker design workflow, unigene and genomic sequence data sets were constructed, and polymorphisms between parental lines were detected through transcriptome sequence analysis. The positions of polymorphisms detected in the unigenes were mapped onto the genome sequence, and primer sets were designed. In total, 480 markers covering the whole genome were selected. By genotyping an F2 population, 329 polymorphic sites were obtained from the estimated positions or the flanking sequences. However, missing or sparse marker regions were observed in the resulting genetic linkage map. We modified the markers to cover these regions by genotyping the other F2 populations. The grouping and order of markers on the linkages were similar across the genetic maps. Our marker design workflow and target amplicon sequencing are useful for genome-wide genotyping of onions owing to their reliability, cost effectiveness, and flexibility.


Assuntos
Genoma de Planta , Cebolas , Mapeamento Cromossômico/métodos , Ligação Genética , Genótipo , Técnicas de Genotipagem/métodos , Cebolas/genética , Polimorfismo de Nucleotídeo Único , Reprodutibilidade dos Testes , Análise de Sequência , Fluxo de Trabalho
16.
Proc Natl Acad Sci U S A ; 119(34): e2206973119, 2022 Aug 23.
Artigo em Inglês | MEDLINE | ID: mdl-35969753

RESUMO

The fate of new mitochondrial and plastid mutations depends on their ability to persist and spread among the numerous organellar genome copies within a cell (heteroplasmy). The extent to which heteroplasmies are transmitted across generations or eliminated through genetic bottlenecks is not well understood in plants, in part because their low mutation rates make these variants so infrequent. Disruption of MutS Homolog 1 (MSH1), a gene involved in plant organellar DNA repair, results in numerous de novo point mutations, which we used to quantitatively track the inheritance of single nucleotide variants in mitochondrial and plastid genomes in Arabidopsis. We found that heteroplasmic sorting (the fixation or loss of a variant) was rapid for both organelles, greatly exceeding rates observed in animals. In msh1 mutants, plastid variants sorted faster than those in mitochondria and were typically fixed or lost within a single generation. Effective transmission bottleneck sizes (N) for plastids and mitochondria were N ∼ 1 and 4, respectively. Restoring MSH1 function further increased the rate of heteroplasmic sorting in mitochondria (N ∼ 1.3), potentially because of its hypothesized role in promoting gene conversion as a mechanism of DNA repair, which is expected to homogenize genome copies within a cell. Heteroplasmic sorting also favored GC base pairs. Therefore, recombinational repair and gene conversion in plant organellar genomes can potentially accelerate the elimination of heteroplasmies and bias the outcome of this sorting process.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis , Heteroplasmia , Proteína MutS de Ligação de DNA com Erro de Pareamento , Arabidopsis/genética , DNA Mitocondrial/genética , DNA de Plantas/genética , Genoma de Planta , Mitocôndrias/genética , Proteína MutS de Ligação de DNA com Erro de Pareamento/metabolismo , Plastídeos/genética , Plastídeos/metabolismo
17.
Genome Biol ; 23(1): 178, 2022 Aug 23.
Artigo em Inglês | MEDLINE | ID: mdl-35999561

RESUMO

BACKGROUND: Maize (Zea mays L.) is at the vanguard facing the upcoming breeding challenges. However, both a super pan-genome for the Zea genus and a comprehensive genetic variation map for maize breeding are still lacking. RESULTS: Here, we construct an approximately 6.71-Gb pan-Zea genome that contains around 4.57-Gb non-B73 reference sequences from fragmented de novo assemblies of 721 pan-Zea individuals. We annotate a total of 58,944 pan-Zea genes and find around 44.34% of them are dispensable in the pan-Zea population. Moreover, 255,821 common structural variations are identified and genotyped in a maize association mapping panel. Further analyses reveal gene presence/absence variants and their potential roles during domestication of maize. Combining genetic analyses with multi-omics data, we demonstrate how structural variants are associated with complex agronomic traits. CONCLUSIONS: Our results highlight the underexplored role of the pan-Zea genome and structural variations to further understand domestication of maize and explore their potential utilization in crop improvement.


Assuntos
Genoma de Planta , Zea mays , Mapeamento Cromossômico/métodos , Domesticação , Humanos , Melhoramento Vegetal/métodos , Zea mays/genética
18.
Int J Mol Sci ; 23(16)2022 Aug 11.
Artigo em Inglês | MEDLINE | ID: mdl-36012213

RESUMO

Growing evidence indicates that transposons or transposable elements (TEs)-derived accessible chromatin regions (ACRs) play essential roles in multiple biological processes by interacting with trans-acting factors. However, the function of TE-derived ACRs in the regulation of gene expression in the rice genome has not been well characterized. In this study, we examined the chromatin dynamics in six types of rice tissues and found that ~8% of ACRs were derived from TEs and exhibited distinct levels of accessibility and conservation as compared to those without TEs. TEs exhibited a TE subtype-dependent impact on ACR formation, which can be mediated by changes in the underlying DNA methylation levels. Moreover, we found that tissue-specific TE-derived ACRs might function in the tissue development through the modulation of nearby gene expression. Interestingly, many genes in domestication sweeps were found to overlap with TE-derived ACRs, suggesting their potential functions in the rice domestication. In addition, we found that the expression divergence of 1070 duplicate gene pairs were associated with TE-derived ACRs and had distinct distributions of TEs and ACRs around the transcription start sites (TSSs), which may experience different selection pressures. Thus, our study provides some insights into the biological implications of TE-derived ACRs in the rice genome. Our results imply that these ACRs are likely involved in the regulation of tissue development, rice domestication and functional divergence of duplicated genes.


Assuntos
Oryza , Cromatina/genética , Cromatina/metabolismo , Metilação de DNA , Elementos de DNA Transponíveis/genética , Domesticação , Genoma de Planta , Oryza/metabolismo
19.
BMC Genomics ; 23(1): 598, 2022 Aug 17.
Artigo em Inglês | MEDLINE | ID: mdl-35978316

RESUMO

Dehydration responsive element binding protein (DREB) is a significant transcription factor class known to be implicated in abiotic stresses. In this study, we systematically conducted a genome-wide identification and expression analysis of the DREB gene family, including gene structures, evolutionary relationships, chromosome distribution, conserved domains, and expression patterns. A total of 65 DREB family gene members were identified in Chinese cabbage (Brassica rapa L.) and were classified into five subgroups based on phylogenetic analysis. Through analysis of the conserved domains of BrDREB family genes, only one exon existed in the gene structure. Through the analysis of cis-acting elements, these genes were mainly involved in hormone regulation and adversity stress. In order to identify the function of BrDREB2B, overexpressed transgenic Arabidopsis was constructed. After different stress treatments, the germination rate, root growth, survival rate, and various plant physiological indicators were measured. The results showed that transgenic Arabidopsis thaliana plants overexpressing BrDREB2B exhibited enhanced tolerance to salt, heat and drought stresses. Taken together, our results are the first to report the BrDREB2B gene response to drought and heat stresses in Chinese cabbage and provide a basis for further studies to determine the function of BrDREBs in response to abiotic stresses.


Assuntos
Arabidopsis , Brassica , Arabidopsis/metabolismo , Brassica/genética , Brassica/metabolismo , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Filogenia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Estresse Fisiológico/genética
20.
Sci Rep ; 12(1): 13829, 2022 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-35970910

RESUMO

Sulfur is an essential element required for plant growth and development, physiological processes and stress responses. Sulfur-encoding biosynthetic genes are involved in the primary sulfur assimilation pathway, regulating various mechanisms at the gene, cellular and system levels, and in the biosynthesis of sulfur-containing compounds (SCCs). In this study, the SCC-encoding biosynthetic genes in rice were identified using a sulfur-dependent model plant, the Arabidopsis. A total of 139 AtSCC from Arabidopsis were used as reference sequences in search of putative rice SCCs. At similarity index > 30%, the similarity search against Arabidopsis SCC query sequences identified 665 putative OsSCC genes in rice. The gene synteny analysis showed a total of 477 syntenic gene pairs comprised of 89 AtSCC and 265 OsSCC biosynthetic genes in Arabidopsis and rice, respectively. Phylogenetic tree of the collated (AtSCCs and OsSCCs) SCC-encoding biosynthetic genes were divided into 11 different clades of various sizes comprised of branches of subclades. In clade 1, nearing equal representation of OsSCC and AtSCC biosynthetic genes imply the most ancestral lineage. A total of 25 candidate Arabidopsis SCC homologs were identified in rice. The gene ontology enrichment analysis showed that the rice-Arabidopsis SCC homologs were significantly enriched in the following terms at false discovery rate (FDR) < 0.05: (i) biological process; sulfur compound metabolic process and organic acid metabolic processes, (ii) molecular function; oxidoreductase activity, acting on paired donors with incorporation or reduction of molecular oxygen and (iii) KEGG pathway; metabolic pathways and biosynthesis of secondary metabolites. At less than five duplicated blocks of separation, no tandem duplications were observed among the SCC biosynthetic genes distributed in rice chromosomes. The comprehensive rice SCC gene description entailing syntenic events with Arabidopsis, motif distribution and chromosomal mapping of the present findings offer a foundation for rice SCC gene functional studies and advanced strategic rice breeding.


Assuntos
Arabidopsis , Oryza , Arabidopsis/genética , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Genoma de Planta/genética , Família Multigênica , Oryza/genética , Filogenia , Melhoramento Vegetal , Proteínas de Plantas/genética , Plantas/genética , Enxofre
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