scholarly journals Genome-wide and comparative phylogenetic analysis of senescence-associated NAC transcription factors in sunflower (Helianthus annuus)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Sofia A. Bengoa Luoni ◽  
Alberto Cenci ◽  
Sebastian Moschen ◽  
Salvador Nicosia ◽  
Laura M. Radonic ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Leaf Senescence ◽  
Large Scale ◽  
Gene Families ◽  
Orthologous Group ◽  
Specific Gene ◽  
Significant Differential Expression ◽  
Nac Transcription Factors ◽  
Functional Relationships

Abstract Background Leaf senescence delay impacts positively in grain yield by maintaining the photosynthetic area during the reproductive stage and during grain filling. Therefore a comprehensive understanding of the gene families associated with leaf senescence is essential. NAC transcription factors (TF) form a large plant-specific gene family involved in regulating development, senescence, and responses to biotic and abiotic stresses. The main goal of this work was to identify sunflower NAC TF (HaNAC) and their association with senescence, studying their orthologous to understand possible functional relationships between genes of different species. Results To clarify the orthologous relationships, we used an in-depth comparative study of four divergent taxa, in dicots and monocots, with completely sequenced genomes (Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa). These orthologous groups provide a curated resource for large scale protein sequence annotation of NAC TF. From the 151 HaNAC genes detected in the latest version of the sunflower genome, 50 genes were associated with senescence traits. These genes showed significant differential expression in two contrasting lines according to an RNAseq assay. An assessment of overexpressing the Arabidopsis line for HaNAC001 (a gene of the same orthologous group of Arabidopsis thaliana ORE1) revealed that this line displayed a significantly higher number of senescent leaves and a pronounced change in development rate. Conclusions This finding suggests HaNAC001 as an interesting candidate to explore the molecular regulation of senescence in sunflower.

scholarly journals Genome-Wide Analysis of NAC Transcription Factors in Sunflower (Helianthus Annuus), Their Comparative Phylogenetic Analysis and Association With Leaf Senescence

2021 ◽  
Author(s):  
Sofia A. Bengoa Luoni ◽  
Alberto Cenci ◽  
Sebastian Moschen ◽  
Salvador Nicosia ◽  
Laura M. Radonic ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Leaf Senescence ◽  
Large Scale ◽  
Gene Families ◽  
Orthologous Group ◽  
Specific Gene ◽  
Significant Differential Expression ◽  
Nac Transcription Factors ◽  
Functional Relationships

Abstract Background Leaf senescence delay impacts positively in grain yield by maintaining the photosynthetic area during the reproductive stage and during grain filling. Therefore a comprehensive understanding of the gene families associated with leaf senescence is essential. NAC transcription factors (TF) form a large plant-specific gene family involved in regulating development, senescence, and responses to biotic and abiotic stresses. The main goal of this work was to identify sunflower NAC TF (HaNAC) and their association with senescence, studying their orthologous to understand possible functional relationships between genes of different species. ResultsTo clarify the orthologous relationships, we used an in-depth comparative study of four divergent taxa, in dicots and monocots, with completely sequenced genomes (Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa). These orthologous groups provide a curated resource for large scale protein sequence annotation of NAC TF. From the 151 HaNAC genes detected in the latest version of the sunflower genome, 50 genes were associated with senescence traits. These genes showed significant differential expression in two contrasting lines according to an RNAseq assay. An assessment of overexpressing the Arabidopsis line for HaNAC001 (a gene of the same orthologous group of Arabidopsis thaliana ORE1) revealed that this line displayed a significantly higher number of senescent leaves and a pronounced change in development rate.ConclutionsThis finding suggests HaNAC001 as an interesting candidate to explore the molecular regulation of senescence in sunflower.

scholarly journals Genome Assemblies of the Warthog and Kenyan Domestic Pig Provide Insights into Suidae Evolution and Candidate Genes for African Swine Fever Tolerance

2021 ◽  
Author(s):  
Wen Feng ◽  
Lei Zhou ◽  
Pengju Zhao ◽  
Heng Du ◽  
Chenguang Diao ◽  
...  
Keyword(s):  
Large Scale ◽  
Genetic Resistance ◽  
African Swine Fever ◽  
Gene Families ◽  
Specific Gene ◽  
Chromosome 2 ◽  
Sequencing Data ◽  
Domestic Pig ◽  
Phacochoerus Africanus ◽  
Contraction And Expansion

As warthog (Phacochoerus africanus) has innate immunity against African swine fever (ASF), it is critical to understanding the evolutionary novelty of warthog to explain its specific ASF resistance. Here, we present two completed new genomes of one warthog and one Kenyan domestic pig, as the fundamental genomic references to decode the genetic mechanism on ASF tolerance. Our results indicated, multiple genomic variations, including gene losses, independent contraction and expansion of specific gene families, likely moulded warthog's genome to adapt the environment. Importantly, the analysis of presence and absence of genomic sequences revealed that, the warthog genome had a DNA sequence absence of the lactate dehydrogenase B (LDHB) gene on chromosome 2 compared to the reference genome. The overexpression and siRNA of LDHB indicated that its inhibition on the replication of ASFV. The Combining with large scale sequencing data of 123 pigs from all over world, contraction and expansion of TRIM genes families revealed that TRIM family genes in the warthog genome were potentially responsible for its tolerance to ASF. Our results will help further improve the understanding of genetic resistance ASF in pigs.

scholarly journals Role of the Arabidopsis thaliana NAC transcription factors ANAC019 and ANAC055 in regulating jasmonic acid-signaled defense responses

Cell Research ◽  
2008 ◽  
Vol 18 (7) ◽  
pp. 756-767 ◽  
Author(s):  
Qingyun Bu ◽  
Hongling Jiang ◽  
Chang-Bao Li ◽  
Qingzhe Zhai ◽  
Jie Zhang ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Jasmonic Acid ◽  
Defense Responses ◽  
Nac Transcription Factors

scholarly journals SNAC‐As, stress‐responsive NAC transcription factors, mediate ABA‐inducible leaf senescence

2015 ◽  
Vol 84 (6) ◽  
pp. 1114-1123 ◽  
Author(s):  
Hironori Takasaki ◽  
Kyonoshin Maruyama ◽  
Fuminori Takahashi ◽  
Miki Fujita ◽  
Takuya Yoshida ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Leaf Senescence ◽  
Nac Transcription Factors ◽  
As Stress

scholarly journals Comparative transcriptomic analysis reveals conserved transcriptional programs underpinning organogenesis and reproduction in land plants

2020 ◽  
Author(s):  
Irene Julca ◽  
Camilla Ferrari ◽  
María Flores-Tornero ◽  
Sebastian Proost ◽  
Ann-Cathrin Lindner ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Large Scale ◽  
Expression Profiles ◽  
Gene Families ◽  
Male Reproduction ◽  
Land Plants ◽  
Easy Access ◽  
Specific Gene ◽  
Male Gametes ◽  
Organ Specific

AbstractThe evolution of plant organs, including leaves, stems, roots, and flowers, mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. Furthermore, the fertilization products of angiosperms, seeds serve as the basis for most of our food. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes, and the development of novel regulatory programs. However, our knowledge of these events is limited, as no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we have generated gene expression atlases for various organs and gametes of 10 plant species comprising bryophytes, vascular plants, gymnosperms, and flowering plants. Comparative analysis of the atlases identified hundreds of organ- and gamete-specific gene families and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, the appearance of organ-specific gene families does not coincide with the corresponding organ’s appearance, suggesting that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, suggesting that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function. To provide easy access to the expression atlases and these comparative analyses, we provide an online database, www.evorepro.plant.tools, that allows the exploration of expression profiles, organ-specific genes, phylogenetic trees, co-expression networks, and others.

scholarly journals Genome-wide sequence and expression analysis of the NAC transcription factor family in polyploid wheat

2017 ◽  
Author(s):  
Philippa Borrill ◽  
Sophie A. Harrington ◽  
Cristobal Uauy
Keyword(s):  
Transcription Factors ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Rna Seq ◽  
Phylogenetic Groups ◽  
Future Studies ◽  
Nac Transcription Factors ◽  
Wide Range ◽  
Nac Family

ARTICLE SUMMARYTranscription factors are vital in plants to regulate gene expression in response to environmental stimuli and to control developmental processes. In this study, we annotated and classified transcription factors in polyploid bread wheat into gene families and explored the NAC family in detail. We combined phylogenetic analysis and transcriptome analysis, using publicly available RNA-seq data, to characterize the NAC gene family and provide hypotheses for putative functions of many NAC transcription factors. This study lays the groundwork for future studies on transcription factors in wheat which may be of great agronomic relevance.ABSTRACTMany important genes in agriculture correspond to transcription factors which regulate a wide range of pathways from flowering to responses to disease and abiotic stresses. In this study, we identified 5,776 transcription factors in hexaploid wheat (Triticum aestivum) and classified them into gene families. We further investigated the NAC family exploring the phylogeny, C-terminal domain conservation and expression profiles across 308 RNA-seq samples. Phylogenetic trees of NAC domains indicated that wheat NACs divided into eight groups similar to rice (Oryza sativa) and barley (Hordeum vulgare). C-terminal domain motifs were frequently conserved between wheat, rice and barley within phylogenetic groups, however this conservation was not maintained across phylogenetic groups. We explored gene expression patterns across a wide range of developmental stages, tissues, and abiotic stresses. We found that more phylogenetically related NACs shared more similar expression patterns compared to more distant NACs. However, within each phylogenetic group there were clades with diverse expression profiles. We carried out a co-expression analysis on all wheat genes and identified 37 modules of co-expressed genes of which 23 contained NACs. Using GO term enrichment we obtained putative functions for NACs within co-expressed modules including responses to heat and abiotic stress and responses to water: these NACs may represent targets for breeding or biotechnological applications. This study provides a framework and data for hypothesis generation for future studies on NAC transcription factors in wheat.

scholarly journals Conserved residues in the wheat (Triticum aestivum) NAM-A1 NAC domain are required for protein binding and when mutated lead to delayed peduncle and flag leaf senescence

2019 ◽  
Author(s):  
Sophie A. Harrington ◽  
Lauren E. Overend ◽  
Nicolas Cobo ◽  
Philippa Borrill ◽  
Cristobal Uauy
Keyword(s):  
Transcription Factors ◽  
Leaf Senescence ◽  
Protein Function ◽  
Flag Leaf ◽  
Missense Mutations ◽  
In Planta ◽  
Conserved Residues ◽  
Nac Domain ◽  
Nac Transcription Factors ◽  
The Impact

AbstractBackgroundNAC transcription factors contain five highly conserved subdomains which are required for protein dimerisation and DNA binding. Few residues within these subdomains have been identified as essential for protein function, and fewer still have been shown to be of biological relevancein planta. Here we use a positive regulator of senescence in wheat,NAM-A1, to test the impact of missense mutations at specific, highly conserved residues of the NAC domain on protein function.ResultsWe identified missense mutations in five highly conserved residues of the NAC domain ofNAM-A1in a tetraploid TILLING population. TILLING lines containing these mutations, alongside synonymous and non-conserved mutation controls, were grown under glasshouse conditions and scored for senescence. Four of the five mutations showed a significant and consistent delay in peduncle senescence but had no consistent effects on flag leaf senescence. All four mutant alleles with the delayed senescence phenotype also lost the ability to interact with the homoeolog NAM-B1 in a yeast two-hybrid assay. Two of these residues were previously shown to be involved in NAC domain function in Arabidopsis, suggesting conservation of residue function between species. Three of these four alleles led to an attenuated cell death response compared to wild-typeNAM-A1when transiently over-expressed inNicotiana benthamiana. One of these mutations was further tested under field conditions, in which there was a significant and consistent delay in both peduncle and leaf senescence.ConclusionsWe combined field and glasshouse studies of a series of mutant alleles with biochemical analyses to identify four residues of the NAC domain which are required forNAM-A1function and protein interaction. We show that mutations in these residues lead to a gradient of phenotypes, raising the possibility of developing allelic series of mutations for traits of agronomic importance. We also show that mutations inNAM-A1more severely impact peduncle senescence, compared to the more commonly studied flag leaf senescence, highlighting this as an area deserving of further study. The results from this integrated approach provide strong evidence that conserved residues within the functional domains of NAC transcription factors have biological significancein planta.

scholarly journals Mosaic evolution of molecular pathways for sex pheromone communication in a butterfly

2020 ◽  
Author(s):  
Caroline M. Nieberding ◽  
Patrícia Beldade ◽  
Véronique Baumlé ◽  
Gilles San Martin ◽  
Alok Arun ◽  
...  
Keyword(s):  
Sex Pheromone ◽  
Large Scale ◽  
Olfactory Receptors ◽  
Gene Families ◽  
Pheromone Biosynthesis ◽  
Specific Gene ◽  
Evolutionary Divergence ◽  
Molecular Pathways ◽  
Pheromone Communication ◽  
Bicyclus Anynana

AbstractUnraveling the origin of molecular pathways underlying the evolution of adaptive traits is essential for understanding how new lineages emerge, including the relative contribution of conserved, ancestral traits, and newly evolved, derived traits. Here, we investigated the evolutionary divergence of sex pheromone communication from moths (mostly nocturnal) to butterflies (mostly diurnal) that occurred ~98 million years ago. In moths, females typically emit pheromones to attract male mates, but in butterflies pheromones and used by females for mate choice. The molecular bases of sex pheromone communication are well understood in moths, but have remained virtually unexplored in butterflies. We used a combination of transcriptomics, real time qPCR, and phylogenetics, to identify genes involved in different steps of sex pheromone communication in the butterfly Bicyclus anynana. Our results show that the biosynthesis and reception of sex pheromones relies both on moth-specific gene families (reductases) and on more ancestral insect gene families (desaturases, olfactory receptors, odorant binding proteins). Interestingly, B. anynana further appears to use what was believed to be the moth-specific neuropeptide Pheromone Biosynthesis Activating Neuropeptide (PBAN) for regulation of sex pheromone production. Altogether, our results suggest that a mosaic pattern best explains how sex pheromone communication evolved in butterflies, with some molecular components derived from moths, and others conserved from more ancient insect ancestors. This is the first large-scale analysis of the genetic pathways underlying sex pheromone communication in a butterfly.

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