scholarly journals Phylotranscriptomic analyses reveal asymmetrical gene duplication dynamics and signatures of ancient polyploidy in mints

2019 ◽  
Author(s):  
Grant T Godden ◽  
Taliesin J Kinser ◽  
Pamela S Soltis ◽  
Douglas E Soltis
Keyword(s):  
Gene Duplication ◽  
Large Scale ◽  
Plant Traits ◽  
Divergence Time ◽  
Evolutionary Process ◽  
Driver Gene ◽  
Important Species ◽  
Plant Groups ◽  
Duplication Events ◽  
Gene Duplicates

Abstract Ancient duplication events and retained gene duplicates have contributed to the evolution of many novel plant traits and, consequently, to the diversity and complexity within and across plant lineages. While mounting evidence highlights the importance of whole-genome duplication (WGD; polyploidy) and its key role as an evolutionary driver, gene duplication dynamics and mechanisms, both of which are fundamental to our understanding of evolutionary process and patterns of plant diversity, remain poorly characterized in many clades. We use newly available transcriptomic data and a robust phylogeny to investigate the prevalence, occurrence, and timing of gene duplications in Lamiaceae (mints), a species-rich and chemically diverse clade with many ecologically, economically, and culturally important species. We also infer putative WGDs—an extreme mechanism of gene duplication—using large-scale data sets from synonymous divergence (KS), phylotranscriptomic, and divergence time analyses. We find evidence for widespread but asymmetrical levels of gene duplication and ancient polyploidy in Lamiaceae that correlate with species richness, including pronounced levels of gene duplication and putative ancient WGDs (7–18 events) within the large subclade Nepetoideae and up to 10 additional WGD events in other subclades. Our results help disentangle WGD-derived gene duplicates from those produced by other mechanisms and illustrate the non-uniformity of duplication dynamics in mints, setting the stage for future investigations that explore their impacts on trait diversity and species diversification. Our results also provide a practical context for evaluating the benefits and limitations of transcriptome-based approaches to inferring WGD, and we offer recommendations for researchers interested in investigating ancient WGDs in other plant groups.

Ancestral genome duplication in rice

Genome ◽  
2004 ◽  
Vol 47 (3) ◽  
pp. 610-614 ◽  
Author(s):  
Romain Guyot ◽  
Beat Keller
Keyword(s):  
Large Scale ◽  
Genome Duplication ◽  
Rice Genome ◽  
Block Size ◽  
Pairwise Comparisons ◽  
Comparative Genome Analysis ◽  
Important Species ◽  
Duplication Events ◽  
First Time ◽  
Grass Genomes

The recent availability of the pseudochromosome sequences of rice allows for the first time the investigation of the extent of intra-genomic duplications on a large scale in this agronomically important species. Using a dot-matrix plotter as a tool to display pairwise comparisons of ordered predicted coding sequences along rice pseudochromosomes, we found that the rice genome contains extensive chromosomal duplications accounting for 53% of the available sequences. The size of duplicated blocks is considerably larger than previously reported. In the rice genome, a duplicated block size of >1 Mb appears to be the rule and not the exception. Comparative mapping has shown high genetic colinearity among chromosomes of cereals, promoting rice as a model for studying grass genomes. Further comparative genome analysis should allow the study of the conservation and evolution of these duplication events in other important cereals such as rye, barley, and wheat.Key words: rice, genome duplication, genome evolution.

scholarly journals The evolution of developmental patterning under genetic duplication constraints

2007 ◽  
Vol 5 (19) ◽  
pp. 237-245 ◽  
Author(s):  
Miguel A Fuentes ◽  
David C Krakauer
Keyword(s):  
Gene Duplication ◽  
Phenotypic Variability ◽  
Three Dimensional ◽  
Evolutionary Process ◽  
Evolutionary Model ◽  
Dimensional System ◽  
Genetic Robustness ◽  
Complex Adaptive ◽  
Duplication Events ◽  
The Stability

Of considerable interest are the evolutionary and developmental origins of complex, adaptive structures and the mechanisms that stabilize these structures. We consider the relationship between the evolutionary process of gene duplication and deletion and the stability of morphogenetic patterns produced by interacting activators and inhibitors. We compare the relative stability of patterns with a single activator and inhibitor (two-dimensional system) against a ‘redundant’ system with two activators or two inhibitors (three-dimensional system). We find that duplication events can both expand and contract the space of patterns. We study developmental robustness in terms of stochastic escape times from this space, also known as a ‘canalization potential’. We embed the output of pattern formation into an explicit evolutionary model of gene duplication, gene loss and variation in the steepness of the canalization potential. We find that under all constant conditions, the system evolves towards a preference for steep potentials associated with low phenotypic variability and longer lifespans. This preference leads to an overall decrease in the density of redundant genotypes as developmental robustness neutralizes the advantages of genetic robustness.

scholarly journals Duplication accelerates the evolution of structural complexity in protein quaternary structure

2020 ◽  
Author(s):  
Alexander S. Leonard ◽  
Sebastian E. Ahnert
Keyword(s):  
Gene Duplication ◽  
Lattice Model ◽  
Self Assembly ◽  
Large Scale ◽  
Quaternary Structure ◽  
Protein Complexes ◽  
Structural Complexity ◽  
Data Bank ◽  
Coarse Grained ◽  
Duplication Events

AbstractGene duplication, from single genes to whole genomes, has been observed in organisms across all taxa. Despite its prevalence, the evolutionary benefits of this mechanism are the subject of ongoing debate. Gene duplication can significantly alter the self-assembly of protein quaternary structures, impacting the dosage or interaction proclivity. Here we use a lattice model of self-assembly as a coarse-grained representation of protein complex assembly, and show that it can be used to examine potential evolutionary advantages of duplication. Duplication provides a unique mechanism for increasing the evolvability of protein complexes by enabling the transformation of symmetric homomeric interactions into heteromeric ones. This transformation is extensively observed in in silico evolutionary simulations of the lattice model, with duplication events significantly accelerating the rate at which structural complexity increases. These coarse-grained simulation results are corroborated with a large-scale analysis of complexes from the Protein Data Bank.

Microevolution of the VQ gene family in six species of Fragaria

Genome ◽  
2018 ◽  
Vol 61 (1) ◽  
pp. 49-57 ◽  
Author(s):  
Yan Zhong ◽  
Cong Guo ◽  
Jinjin Chu ◽  
Hui Liu ◽  
Zong-Ming Cheng
Keyword(s):  
Gene Duplication ◽  
Stress Responses ◽  
Plant Stress ◽  
Evolutionary Process ◽  
Purifying Selection ◽  
Plant Stress Responses ◽  
Duplication Events ◽  
Motif Composition ◽  
Important Basis ◽  
Evolutionary Fate

VQ motif-containing proteins play crucial roles in plant growth, development, and stress responses. However, no information of VQ motif-containing proteins has been studied at the microevolutionary level in species of Fragaria. In this study, a total of 19, 21, 23, 23, 23, and 25 genes containing the VQ motif were identified from the genomes of F. nipponica, F. iinumae, F. orientalis, F. vesca, F. nubicola, and F. x ananassa, respectively. We classified the VQ genes into 15 clades with grapevine VQ genes, which indicated that at least 15 ancient VQ genes existed before the divergence of the six studied species of Fragaria. Phylogenetic analysis indicated that 28 gene duplication events have occurred in the evolutionary process of the six species of Fragaria. Structural analysis showed that most of the VQ genes have no introns and that VQ proteins in each clade have a similar motif composition. The majority of gene pairs had Ka/Ks ratios less than 1, which illustrated that most of the VQ genes underwent purifying selection in the six species of Fragaria. Four types of cis-elements in promoters of VQ genes were detected, which is an important basis for further studies about plant stress responses. Furthermore, the expression analysis of FvVQ genes indicated that these genes are expressed differentially in the examined organs and tissues. The identification of VQ genes and the analysis of VQ gene duplication and polyploidization events in the six species of Fragaria provide important information on the evolutionary fate of VQ genes during the divergence of the six species of Fragaria.

scholarly journals Correlates of hybridization in plants

2019 ◽  
Author(s):  
Nora Mitchell ◽  
Lesley G. Campbell ◽  
Jeffrey R. Ahern ◽  
Kellen C. Paine ◽  
Aelton B. Giroldo ◽  
...  
Keyword(s):  
Life History ◽  
Path Analysis ◽  
Range Expansion ◽  
Plant Traits ◽  
Evolutionary Process ◽  
Generalized Least Squares ◽  
Global Scale ◽  
Least Squares Regression ◽  
Pollination Syndromes ◽  
Plant Groups

ABSTRACTHybridization is a biological phenomenon increasingly recognized as an important evolutionary process in both plants and animals, as it is linked to speciation, radiation, extinction, range expansion and invasion, and allows for increased trait diversity in agricultural and horticultural systems. Estimates of hybridization frequency vary across taxonomic groups, and previous work has demonstrated that some plant groups hybridize more frequently than others. Here, we ask on a global scale whether hybridization is linked to any of 11 traits related to plant life history, reproduction, genetic predisposition, and environment or opportunity. Given that hybridization is not evenly distributed across the plant tree of life, we use phylogenetic generalized least squares regression models and phylogenetic path analysis to detect statistical associations between hybridization and plant traits at both the family and genus levels. We find that perenniality and woodiness are each associated with an increased frequency of hybridization in univariate analyses, but path analysis suggests that the direct linkage is between perenniality and increased hybridization (with woodiness having only an indirect relationship with hybridization via perenniality). Associations between higher rates of hybridization and higher outcrossing rates, abiotic pollination syndromes, vegetative reproductive modes, larger genomes, and less variable genome sizes are detectable in some cases but not others. We argue that correlational evidence at the global scale, such as that presented here, provides a robust framework for forming hypotheses to examine and test drivers of hybridization at a more mechanistic level.IMPACT SUMMARYAlthough historically thought of as rare, inter-specific mating is increasingly recognized as an important evolutionary process. Hybridization can generate increased genetic and morphological variation and has been tied to increased diversification and other biological phenomena such as geographic range expansion and the success of invasive species. Here, we examine hybridization of plants on a global scale. Previous work has demonstrated that some plant groups hybridize more than others, but the reasons for this pattern remain unclear. We combine data from eight regional floras with trait data to test for associations between hybridization and different aspects of plant biology, such as life history, growth form, reproduction, and opportunity, all while accounting for the fact that plant lineages are related to each other.We find that plant groups that are dominated by perennial species and species with woody growth forms tend to hybridize more than those dominated by annual or herbaceous species. We also find some evidence that frequent hybridization is found in plant families that are predominantly pollinated abiotically (such as by wind or water) or have higher rates of outcrossing, plant genera that have less variable genome sizes, and plant groups (both genera and families) that can reproduce asexually and have larger genome sizes. This study provides the first analysis of the global correlates of hybridization in plants. Although this correlational evidence does not provide any mechanistic explanations for these patterns, the trends we find are novel in terms of both geographic and taxonomic sale. The correlations detected provide robust hypotheses for understanding the conditions for hybridization and its contributions to evolution.

scholarly journals High-Throughput Phenotyping Methods for Breeding Drought-Tolerant Crops

2021 ◽  
Vol 22 (15) ◽  
pp. 8266
Author(s):  
Minsu Kim ◽  
Chaewon Lee ◽  
Subin Hong ◽  
Song Lim Kim ◽  
Jeong-Ho Baek ◽  
...  
Keyword(s):  
Drought Stress ◽  
High Throughput ◽  
Large Scale ◽  
Crop Yields ◽  
Plant Traits ◽  
Rapid Development ◽  
Plant Responses ◽  
Phenotypic Data ◽  
Agricultural Technologies ◽  
High Throughput Phenotyping

Drought is a main factor limiting crop yields. Modern agricultural technologies such as irrigation systems, ground mulching, and rainwater storage can prevent drought, but these are only temporary solutions. Understanding the physiological, biochemical, and molecular reactions of plants to drought stress is therefore urgent. The recent rapid development of genomics tools has led to an increasing interest in phenomics, i.e., the study of phenotypic plant traits. Among phenomic strategies, high-throughput phenotyping (HTP) is attracting increasing attention as a way to address the bottlenecks of genomic and phenomic studies. HTP provides researchers a non-destructive and non-invasive method yet accurate in analyzing large-scale phenotypic data. This review describes plant responses to drought stress and introduces HTP methods that can detect changes in plant phenotypes in response to drought.

scholarly journals Induced sterility in fish and its potential and challenges for aquaculture and germ cell transplantation technology: a review

Biologia ◽  
2016 ◽  
Vol 71 (8) ◽  
Author(s):  
Amin Golpour ◽  
Mohammad Abdul Momin Siddique ◽  
Diógenes Henrique Siqueira-Silva ◽  
Martin Pšenička
Keyword(s):  
Germ Cell ◽  
Cell Transplantation ◽  
Large Scale ◽  
Hormonal Treatment ◽  
Important Species ◽  
Genetic Ablation ◽  
Germ Cell Transplantation ◽  
Commercially Important ◽  
Alternative Approaches ◽  
Hormone Signalling

AbstractInterest in reproductively sterile fish in aquaculture has prompted research into their production. Several methods are available for inducing sterility and optimizing its application in the global fishery industry. Sterilization can potentially be accomplished through irradiation, surgery, or chemical and hormonal treatment. Alternative approaches include triploidization, hybridization, and generation of new lines via advanced biotechnological techniques. Triploids of many commercially important species have been studied extensively and have been produced on a large scale for many years. Novel approaches, including disruption of gonadotropin releasing hormone signalling and genetic ablation of germ cells, have been developed that are effective in producing infertile fish but have the disadvantage of not being 100% reliable or are impractical for large-scale aquaculture. We review currently used technologies and recent advances in induction of sterility in fish, especially those intended for use in germ cell transplantation. Knowledge of the implications of these approaches remains incomplete, imposing considerable limitations.

scholarly journals Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Pengshuo Yang ◽  
Chongyang Tan ◽  
Maozhen Han ◽  
Lin Cheng ◽  
Xuefeng Cui ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Large Scale ◽  
Network Connectivity ◽  
Small Range ◽  
Environmental Disturbance ◽  
Target Species ◽  
Important Species ◽  
Metagenome Analysis ◽  
Occurrence Patterns ◽  
Edge Networks

Abstract Mainstream studies of microbial community focused on critical organisms and their physiology. Recent advances in large-scale metagenome analysis projects initiated new researches in the complex correlations between large microbial communities. Specifically, previous studies focused on the nodes (i.e. species) of the Species-Centric Networks (SCNs). However, little was understood about the change of correlation between network members (i.e. edges of the SCNs) when the network was disturbed. Here, we introduced a Correlation-Centric Network (CCN) to the microbial research based on the concept of edge networks. In CCN, each node represented a species–species correlation, and edge represented the species shared by two correlations. In this research, we investigated the CCNs and their corresponding SCNs on two large cohorts of microbiome. The results showed that CCNs not only retained the characteristics of SCNs, but also contained information that cannot be detected by SCNs. In addition, when the members of microbial communities were decreased (i.e. environmental disturbance), the CCNs fluctuated within a small range in terms of network connectivity. Therefore, by highlighting the important species correlations, CCNs could unveil new insights when studying not only the functions of target species, but also the stabilities of their residing microbial communities.

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