scholarly journals Gene Duplication to Reveal Adaptation Clue of Plant to Environmental Stress: A Case Study of NBS-LRR Genes in Soybean

2018 ◽  
Vol 12 (2) ◽  
pp. 119
Author(s):  
Puji Lestari ◽  
Suk-Ha Lee ◽  
I Made Tasma ◽  
Asadi Asadi
Keyword(s):  
Gene Duplication ◽  
Environmental Stress ◽  
Biotic Stress ◽  
Genome Duplication ◽  
Environmental Changes ◽  
Plant Genome ◽  
Small Scale ◽  
Duplicated Genes ◽  
Duplication Events

<p><strong>Gene duplication to reveal adaptation </strong><strong>clue</strong><strong> of plant to environmental stress: A case study of NBS-LRR genes in soybean. <em>Puji Lestari, Suk-Ha Lee</em></strong><strong><em>, I Made Tasma</em></strong><strong><em>, </em></strong><strong><em>and </em></strong><strong><em>Asadi</em></strong><strong>. </strong>Adaptive strategies of plant to stress are fine-tuned by adjusting several activities including molecular mechanism which involve duplicated genes responsive to environmental changes. Genes responsive to the environmental stresses which are retained after small scale duplication are part of plant genome duplication. However, less information of duplicated genes could be adaptive to environmental changes in plant. This review presents an overview of duplication events in plant genomes which impact to gene duplication in relation to environmental changes, gene duplication as an adaptation mechanism, a case of duplicated nucleotide binding site-<em>leucine</em>-<em>rich</em> repeat (NBS-LRR) genes in soybean, and the gene duplication implementation for plant breeding in Indonesia. Notably, genome duplication events generate gene duplication and contribute to adaptive evolution against environmental changes. Generalization of plants to adapt the stressful conditions also probably improves our understanding of gene duplication as a mechanism of adaptation. Several recently duplicated NBS-LRR genes in soybean retain disease resistance QTL and the differential expression convince their contribution to biotic stress resistance in soybean. Proposed models of NBS-LRR genes duplication process may help to understand these genes response to the environmental changes. The duplication of genes resistant to pest/disease particularly NBS-LRR provides important information to select breeding parents and develop molecular markers related to desease resistance to genetically improve soybean in Indonesia. Overall, it may therefore be possible to enhance breeding which targets on genes tolerance/resistance to abiotic/biotic stress, and provide a molecular basis for crop-stress protection strategy and more improved soybean varieties specified for harsh environment.</p>

scholarly journals Enhanced functional divergence of duplicate genes several million years after gene duplication in the Arabidopsis lineage

2016 ◽  
Author(s):  
Kousuke Hanada ◽  
Ayumi Tezuka ◽  
Masafumi Nozawa ◽  
Yutaka Suzuki ◽  
Sumio Sugano ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Functional Divergence ◽  
Purifying Selection ◽  
Orthologous Gene ◽  
Synonymous Substitution ◽  
Duplicate Genes ◽  
Duplicated Genes ◽  
Highly Qualified ◽  
Duplication Events ◽  
Synonymous Substitution Rates

AbstractLineage-specifically duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selective pressures immediately after gene duplication is clear in the speciation process. Plants have substantially higher gene duplication rates than most other eukaryotes. Here, using Illumina short reads from Arabidopsis halleri, which has highly qualified plant genomes in close species (Brassica rapa, A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups among B. rapa, A. thaliana, A. lyrata and A. halleri. The frequency of duplication events in the Arabidopsis lineage was approximately 10 times higher than the frequency inferred by comparative genomics of Arabidopsis, poplar, rice and moss. Of the currently retained genes in A. halleri, 11–24% had undergone gene duplication in the Arabidopsis lineage. To examine the degree of selective pressure for duplicated genes, we calculated the ratios of nonsynonymous to synonymous substitution rates (KA/KS) in the A. halleri-lyrata and A. halleri lineages. Using a maximum-likelihood framework, we examined positive (KA/KS > 1) and purifying selection (KA/KS < 1) at a significant level (P < 0.01). Duplicate genes tended to have a higher proportion of positive selection compared with non-duplicated genes. More interestingly, we found that functional divergence of duplicated genes was accelerated several million years after gene duplication at a higher proportion than immediately after gene duplication.

scholarly journals An ancient whole-genome duplication event and its contribution to flavor compounds in the tea plant (Camellia sinensis)

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Ya Wang ◽  
Fei Chen ◽  
Yuanchun Ma ◽  
Taikui Zhang ◽  
Pengchuan Sun ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Tea Plant ◽  
Plant Evolution ◽  
Plant Genome ◽  
Whole Genome ◽  
Biosynthesis Pathway ◽  
Duplicated Genes ◽  
Tandem Gene Duplication ◽  
Tea Plants

AbstractTea, coffee, and cocoa are the three most popular nonalcoholic beverages in the world and have extremely high economic and cultural value. The genomes of four tea plant varieties have recently been sequenced, but there is some debate regarding the characterization of a whole-genome duplication (WGD) event in tea plants. Whether the WGD in the tea plant is shared with other plants in order Ericales and how it contributed to tea plant evolution remained unanswered. Here we re-analyzed the tea plant genome and provided evidence that tea experienced only WGD event after the core-eudicot whole-genome triplication (WGT) event. This WGD was shared by the Polemonioids-Primuloids-Core Ericales (PPC) sections, encompassing at least 17 families in the order Ericales. In addition, our study identified eight pairs of duplicated genes in the catechins biosynthesis pathway, four pairs of duplicated genes in the theanine biosynthesis pathway, and one pair of genes in the caffeine biosynthesis pathway, which were expanded and retained following this WGD. Nearly all these gene pairs were expressed in tea plants, implying the contribution of the WGD. This study shows that in addition to the role of the recent tandem gene duplication in the accumulation of tea flavor-related genes, the WGD may have been another main factor driving the evolution of tea flavor.

scholarly journals Phenological tracking og agricultural feilds investigated by using dual polarimetry tanDEM-X images

2015 ◽  
Vol XL-7/W3 ◽  
pp. 73-76
Author(s):  
S. Mirzaee ◽  
M. Motagh ◽  
H. Arefi ◽  
A. Nooryazdan
Keyword(s):  
High Resolution ◽  
Environmental Changes ◽  
Weather Conditions ◽  
Synthetic Aperture ◽  
Small Scale ◽  
Imaging Characteristics ◽  
X Band ◽  
Phenological Changes ◽  
Extract Information

Remote sensing plays a key role in monitoring and assessing environmental changes. Because of its special imaging characteristics such as high-resolution, capabilities to obtain data in all weather conditions and sensitivity to geometrical and dielectric properties of the features, Synthetic Aperture Radar (SAR) technology has become a powerful technique to detect small scale changes related to earth surface.SAR images contain the information of both phase and intensity in different modes like single, dual and full polarimetric states which are important in order to extract information about various targets. In this study we investigate phenological changes in an agricultural region using high-resolution X-band SAR data. The case study is located in Doroud region of Lorestan province, west of Iran. The purpose is to investigate the ability of copolar and interferometric coherence extracted from TanDEM-X dual polarimetry (HH/VV) in bistatic StripMap mode for tracking the phenological changes of crops during growing season. The data include 11 images acquired between 12.06.2012 and 02.11.2012 and 6 images acquired between 30.05.2013 and 04.08.2013 in the CoSSC format. Results show that copolar coherence is almost able to follow phenological changes but interferometric coherence has a near constant behaviour with fluctuations mainly related to baseline variations.

scholarly journals Stout camphor tree genome fills gaps in understanding of flowering plant genome and gene family evolution

2018 ◽  
Author(s):  
Shu-Miaw Chaw ◽  
Yu-Ching Liu ◽  
Han-Yu Wang ◽  
Yu-Wei Wu ◽  
Chan-Yi Ivy Lin ◽  
...  
Keyword(s):  
Gene Family Evolution ◽  
Plant Genome ◽  
Flowering Plant ◽  
Small Scale ◽  
Phylogenomic Analysis ◽  
Segmental Duplications ◽  
Duplication Events ◽  
Reference Quality ◽  
Terpenoid Synthase ◽  
Camphor Tree

AbstractWe present reference-quality genome assembly and annotation for the stout camphor tree (SCT; Cinnamomum kanehirae [Laurales, Lauraceae]), the first sequenced member of the Magnoliidae comprising four orders (Laurales, Magnoliales, Canellales, and Piperales) and over 9,000 species. Phylogenomic analysis of 13 representative seed plant genomes indicates that magnoliid and eudicot lineages share more recent common ancestry relative to monocots. Two whole genome duplication events were inferred within the magnoliid lineage, one before divergence of Laurales and Magnoliales and the other within the Lauraceae. Small scale segmental duplications and tandem duplications also contributed to innovation in the evolutionary history of Cinnamomum. For example, expansion of terpenoid synthase subfamilies within the Laurales spawned the diversity of Cinnamomum monoterpenes and sesquiterpenes.

scholarly journals Evolutionary contribution of duplicated genes to genome evolution in the ginseng species complex

2021 ◽  
Author(s):  
Ming-Rui Li ◽  
Ning Ding ◽  
Tianyuan Lu ◽  
Jing Zhao ◽  
Zhen-Hui Wang ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Species Complex ◽  
Cytosine Methylation ◽  
Functional Enrichment ◽  
Small Scale ◽  
Nucleotide Variation ◽  
Duplicated Genes ◽  
Evolutionary Patterns ◽  
Genome Wide ◽  
Duplication Events

Abstract Genes duplicated by whole genome duplication (WGD) and small-scale duplication (SSD) have played important roles in adaptive evolution of all flowering plants. However, it still remains under-investigated how the distinct models of duplication events and their contending evolutionary patterns have shaped the genome and epigenomes of extant plant species. In this study, we investigated the contribution of the WGD- and SSD-derived duplicate genes to the genome evolution of one diploid and three closely related allotetraploid Panax species based on genome, methylome and proteome datasets. Our genome-wide comparative analyses revealed that while the ginseng species complex were recently diverged, they have evolved distinct overall patterns of nucleotide variation, cytosine methylation and protein-level expression. In particular, genetic and epigenetic asymmetries observed in the recent WGD-derived genes are largely consistent across the ginseng species complex. In addition, our results revealed that gene duplicates generated by ancient WGD and SSD mechanisms exhibited distinct evolutionary patterns. We found the ancient WGD-derived genes (i.e., ancient collinear gene) are genetically more conserved and hypo-methylated at the cytosine sites. In contrast, some of the SSD-derived genes (i.e., dispersal duplicated gene) showed hyper-methylation and high variance in nucleotide variation pattern. Functional enrichment analyses of the duplicated genes indicated that adaptation-related traits (i.e., photosynthesis) created during the distant ancient WGDs are further strengthened by both the more recent WGD and SSD. Together, our findings suggest that different types of duplicated genes may have played distinct but relaying evolutionary roles in the polyploidization and speciation processes in the ginseng species complex.

scholarly journals Impact of small-scale environmental perturbations on local marine food resources: a case study of a predator, the little penguin

2009 ◽  
Vol 276 (1676) ◽  
pp. 4105-4109 ◽  
Author(s):  
Yan Ropert-Coudert ◽  
Akiko Kato ◽  
André Chiaradia
Keyword(s):  
Breeding Success ◽  
Environmental Changes ◽  
Foraging Efficiency ◽  
Small Scale ◽  
Breeding Period ◽  
Environmental Perturbations ◽  
Top Predators ◽  
The Impact ◽  
Mixed Water

Although the impact of environmental changes on the demographic parameters of top predators is well established, the mechanisms by which populations are affected remain poorly understood. Here, we show that a reduction in the thermal stratification of coastal water masses between 2005 and 2006 was associated with reduced foraging and breeding success of little penguins Eudyptula minor , major bio-indicators of the Bass Strait ecosystem in southern Australia. The foraging patterns of the penguins suggest that their prey disperse widely in poorly stratified waters, leading to reduced foraging efficiency and poor breeding success. Mixed water regimes resulting from storms are currently unusual during the breeding period of these birds, but are expected to become more frequent due to climate change.

scholarly journals Two ancient genome duplication events shape diversity in Hibiscus L. (Malvaceae)

2020 ◽  
Author(s):  
Jonna Sofia Eriksson ◽  
Christine D. Bacon ◽  
Dominic J. Bennett ◽  
Bernard E. Pfeil ◽  
Bengt Oxelman ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Genome Size ◽  
Genome Duplication ◽  
Single Copy ◽  
Genomic Diversity ◽  
Plant Genome ◽  
Genome Doubling ◽  
Gene Copies ◽  
Plant Groups ◽  
Duplication Events

Abstract Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e., genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and an allegedly complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, as more are still likely to be found, considering its diverse background. To reappraise the group’s genomic history, we tested a series of scenarios describing different polyploidization events using previously identified duplications in Hibiscus syriacus.Results: The data showed that >54% of the single-copy genes where in fact paralogues. When testing for different genome duplication scenarios using gene count data; species of Hibiscus was shown to have shared one genome duplication with H. syriacus, -- while one whole genome duplication was contained within H. syriacus, -- to be the preferred model given the observed distribution of paralogous gene copies in Hibiscus.Conclusions: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.

scholarly journals Transcriptional Rewiring, Adaptation, and the Role of Gene Duplication in the Metabolism of Ethanol of Saccharomyces cerevisiae

mSystems ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Beatriz Sabater-Muñoz ◽  
Florian Mattenberger ◽  
Mario A. Fares ◽  
Christina Toft
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Carbon Source ◽  
Gene Duplication ◽  
Growth Parameters ◽  
Small Scale ◽  
Whole Genome ◽  
Duplicated Genes ◽  
Content Type ◽  
Transcriptional Rewiring

ABSTRACT Ethanol is the main by-product of yeast sugar fermentation that affects microbial growth parameters, being considered a dual molecule, a nutrient and a stressor. Previous works demonstrated that the budding yeast arose after an ancient hybridization process resulted in a tier of duplicated genes within its genome, many of them with implications in this ethanol “produce-accumulate-consume” strategy. The evolutionary link between ethanol production, consumption, and tolerance versus ploidy and stability of the hybrids is an ongoing debatable issue. The implication of ancestral duplicates in this metabolic rewiring, and how these duplicates differ transcriptionally, remains unsolved. Here, we study the transcriptomic adaptive signatures to ethanol as a nonfermentative carbon source to sustain clonal yeast growth by experimental evolution, emphasizing the role of duplicated genes in the adaptive process. As expected, ethanol was able to sustain growth but at a lower rate than glucose. Our results demonstrate that in asexual populations a complete transcriptomic rewiring was produced, strikingly by downregulation of duplicated genes, mainly whole-genome duplicates, whereas small-scale duplicates exhibited significant transcriptional divergence between copies. Overall, this study contributes to the understanding of evolution after gene duplication, linking transcriptional divergence with duplicates’ fate in a multigene trait as ethanol tolerance. IMPORTANCE Gene duplication events have been related with increasing biological complexity through the tree of life, but also with illnesses, including cancer. Early evolutionary theories indicated that duplicated genes could explore alternative functions due to relaxation of selective constraints in one of the copies, as the other remains as ancestral-function backup. In unicellular eukaryotes like yeasts, it has been demonstrated that the fate and persistence of duplicates depend on duplication mechanism (whole-genome or small-scale events), shaping their actual genomes. Although it has been shown that small-scale duplicates tend to innovate and whole-genome duplicates specialize in ancestral functions, the implication of duplicates’ transcriptional plasticity and transcriptional divergence on environmental and metabolic responses remains largely obscure. Here, by experimental adaptive evolution, we show that Saccharomyces cerevisiae is able to respond to metabolic stress (ethanol as nonfermentative carbon source) due to the persistence of duplicated genes. These duplicates respond by transcriptional rewiring, depending on their transcriptional background. Our results shed light on the mechanisms that determine the role of duplicates, and on their evolvability.

scholarly journals Reduced Translational Efficiency of Eukaryotic Genes after Duplication Events

2020 ◽  
Vol 37 (5) ◽  
pp. 1452-1461
Author(s):  
Andrew Ying-Fei Chang ◽  
Ben-Yang Liao
Keyword(s):  
Gene Duplication ◽  
Transcriptional Control ◽  
Gene Dosage ◽  
Protein Translation ◽  
Mrna Abundance ◽  
The Other ◽  
Translational Efficiency ◽  
Duplicated Genes ◽  
Control Of Gene Expression ◽  
Duplication Events

Abstract Control of gene expression has been found to be predominantly determined at the level of protein translation. However, to date, reduced expression from duplicated genes in eukaryotes for dosage maintenance has only been linked to transcriptional control involving epigenetic mechanisms. Here, we hypothesize that dosage maintenance following gene duplication also involves regulation at the protein level. To test this hypothesis, we compared transcriptome and proteome data of yeast models, Saccharomyces cerevisiae and Schizosaccharomyces pombe, and worm models, Caenorhabditis elegans and Caenorhabditis briggsae, to investigate lineage-specifically duplicated genes. Duplicated genes in both eukaryotic models exhibited a reduced protein-to-mRNA abundance ratio. Moreover, dosage sensitive genes, represented by genes encoding protein complex subunits, reduced their protein-to-mRNA abundance ratios more significantly than the other genes after duplication events. An analysis of ribosome profiling (Ribo-Seq) data further showed that reduced translational efficiency was more prominent for dosage sensitive genes than for the other genes. Meanwhile, no difference in protein degradation rate was associated with duplication events. Translationally repressed duplicated genes were also more likely to be inhibited at the level of transcription. Taken together, these results suggest that translation-mediated dosage control is partially contributed by natural selection and it enhances transcriptional control in maintaining gene dosage after gene duplication events during eukaryotic genome evolution.

scholarly journals Gene and Genome Duplication in Acanthamoeba polyphaga Mimivirus

2005 ◽  
Vol 79 (22) ◽  
pp. 14095-14101 ◽  
Author(s):  
Karsten Suhre
Keyword(s):  
Gene Duplication ◽  
Model Comparison ◽  
Genome Duplication ◽  
Gene Families ◽  
Detection Methods ◽  
Acanthamoeba Polyphaga ◽  
Homology Detection ◽  
Dna Viruses ◽  
Duplication Events ◽  
Acanthamoeba Polyphaga Mimivirus

ABSTRACT Gene duplication is key to molecular evolution in all three domains of life and may be the first step in the emergence of new gene function. It is a well-recognized feature in large DNA viruses but has not been studied extensively in the largest known virus to date, the recently discovered Acanthamoeba polyphaga Mimivirus. Here, I present a systematic analysis of gene and genome duplication events in the mimivirus genome. I found that one-third of the mimivirus genes are related to at least one other gene in the mimivirus genome, either through a large segmental genome duplication event that occurred in the more remote past or through more recent gene duplication events, which often occur in tandem. This shows that gene and genome duplication played a major role in shaping the mimivirus genome. Using multiple alignments, together with remote-homology detection methods based on Hidden Markov Model comparison, I assign putative functions to some of the paralogous gene families. I suggest that a large part of the duplicated mimivirus gene families are likely to interfere with important host cell processes, such as transcription control, protein degradation, and cell regulatory processes. My findings support the view that large DNA viruses are complex evolving organisms, possibly deeply rooted within the tree of life, and oppose the paradigm that viral evolution is dominated by lateral gene acquisition, at least in regard to large DNA viruses.

Sign in / Sign up

Export Citation Format

Share Document