Widespread Sequence Expression And Regulatory Divergence Occurred Following Gene Or Genome Duplication
Different modes of duplicated genes showed distinct evolutionary patterns in protein-coding region. Transposed genes and DSDs that are preserved in pear genome present more extensive divergence in non-synonymous substitutions per site than other modes of duplicated genes, suggesting their prominent roles in contribution to evolutionary novelty. PDs and TDs had relatively high Ka/Ks ratios but relatively small Ks values , implying that they have experienced more rapid functional divergence than other gene classes and also suggesting the important roles of positive selection in the early stage of duplicate gene retention . In contrast, WGD-derived pairs have relatively small Ka values and low Ka/Ks ratios, suggesting that they evolved under strong purifying selection over a long time.
Duplications Between Long Repeats
As outlined above, extended native direct sequence repeats can serve as the a and b elements in Figure 1 and initiate tandem duplications or deletions. Duplications between such repeats have often been detected by selection for cells with an increased copy number of an included gene. When measured in these assays, duplication shows a greater than 10-fold dependence on homologous recombination . However, as described below, some long repeats have been observed to produce duplications without participation of homologous recombination, suggesting formation by single-strand annealing . The RecA dependence seen in direct selection assays may reflect improved detection because of later recombination-dependent amplification events rather than the initial duplication exchange. To determine the role of recombination and avoid problems of higher amplification, several alternative assays were used to measure duplications formed between long repeats.
Assessing Reciprocal Recombination in a Duplication/Deletion System
Contribution Of Duplicate Genes To Evolutionary Novelty
A common theme among models of duplicate retention is that, for both copies of a gene to be maintained, differences in function, expression, or interaction occur in one if not both paralogs. In some cases, duplicates will acquire novel functions and contribute to evolutionary novelties. For certain duplicates, evidence for a novel function can be seen in the morphological phenotypes caused when they are knocked out, and the presence of such a phenotype is correlated with the extent of sequence and expression divergence . The impact of duplication on evolution has been discussed in depth . Here, we focus on plant examples and classify evolutionary novelties into three types: novel molecular function novel plant structure/function that results from a new molecular function and novel adaptive traits that result from a novel structure/function . This distinction is important because the novel functions/structures in types 1 and 2 need not be adaptive and, thus, may be novel without being selected for. What is the evidence that gene duplication has contributed to these three types of novelties in plants?
Also Check: All Geometry Dash Vault Codes
Mechanisms Of Gene Duplication And Translocation And Progress Towards Understanding Their Relative Contributions To Animal Genome Evolution
David E. K. Ferrier
1The Scottish Oceans Institute, School of Biology, University of St Andrews, East Sands, Fife KY16 8LB, UK
Duplication of genetic material is clearly a major route to genetic change, with consequences for both evolution and disease. A variety of forms and mechanisms of duplication are recognised, operating across the scales of a few base pairs upto entire genomes. With the ever-increasing amounts of gene and genome sequence data that are becoming available, our understanding of the extent of duplication is greatly improving, both in terms of the scales of duplication events as well as their rates of occurrence. An accurate understanding of these processes is vital if we are to properly understand important events in evolution as well as mechanisms operating at the level of genome organisation. Here we will focus on duplication in animal genomes and how the duplicated sequences are distributed, with the aim of maintaining a focus on principles of evolution and organisation that are most directly applicable to the shaping of our own genome.
Branchiostoma floridaeMus musculusMus musculusBranchiostoma floridaeBranchiostoma floridaeDrosophila melanogaster,Homo sapiensMus musculus
2. Terminology: Beware Overlap, Synonyms, and Ambiguity
3. Whole Genome Duplications : Origin of Vertebrates and 2R
4. Subchromosomal Duplications: Variable Sizes, Rates, and Mechanisms
Genome Duplication May Play A Role In Escaping Extinction
A potential explanation for the lack of a tight correlation between genome duplication and increased diversification is that the former is an event and the latter is a process. While it is likely that genome duplication contributes to opportunities for adaptation, adaptation requires ecological necessity. Novel gene functions must evolve in response to changing environmental or ecological pressures, but the origination of beneficial mutations may not occur on the same timescale as changes in external factors. Therefore, in the face of changing environmental and ecological conditions, lineages must first, or simultaneously, escape extinction. Remarkably, estimates of several genome duplication events in vertebrate history are preceded by multiple extinct lineages, resulting in preduplication gaps in extant taxa . argue that preduplication extinct lineages were relatively diverse and hence there is no postduplication increase in diversity, however, the authors did not consider a correlation between genome duplication and reduced extinction risk.
Don’t Miss: Beth Child Of Rage Brother
How Is Genome Duplication Related To Extinction
Three by-products of gene duplication could contribute to decreased probabilities of extinction: mutational robustness, increased genetic variation, and increased tolerance to environmental conditions. In yeast, mutations to one copy of a duplicated gene had a reduced probability of lethal effect compared to single-copy genes, and gene silencing had an increased probability of weak or no effect in yeast and Caenorhabditis elegans .
Factors that contribute to increased genetic variation will reduce the probability of extinction and mediate the effects of changing environmental and ecological factors. Because genome duplication is much more common in plants than in animals, there are more data that bear on factors directly related to genetic variation and reduced probability of extinction. We know that genome duplication is often followed by rapid genomic rearrangements, variable patterns of gene loss, and decay of synteny . These factors contribute to increased genetic variation which may allow stronger responses to various selection pressures, thereby providing more opportunities for survival in changing environments .
Gene Duplication As An Evolutionary Event
Gene duplications are an essential source of genetic novelty that can lead to evolutionary innovation. Duplication creates genetic redundancy and if one copy of a gene experiences a mutation that affects its original function, the second copy can serve as a âspare partâ and continue to function correctly. Thus, duplicate genes accumulate mutations faster than a functional single-copy gene, over generations of organisms, and it is possible for one of the two copies to develop a new and different function. This is an examples of neofunctionalization.
Gene duplication is believed to play a major role in evolution this stance has been held by members of the scientific community for over 100 years. It has been argued that gene duplication is the most important evolutionary force since the emergence of the universal common ancestor.
Don’t Miss: Where Is Beth Thomas Now
Selection On Existing Functions
Duplicates can be retained without acquiring new functions via one of the following four mechanisms: gene dosage increase , , gene balance , and paralog interference . recognized that, in situations where increased gene dosage confers an advantage by meeting metabolic demands, the presence of duplicate copies is beneficial . Unlike redundancy, the robustness of duplicates is clearly selectable although the molecular function of the duplicates may be unchanged, the effect of increased dosage is new. Models of budding yeast gene networks suggest that likely contributed to increased flux in the glycolytic pathways, which confers a fitness benefit in high-Glc environments . Similarly, in Arabidopsis, duplicate retention after is associated with reactions with high metabolic flux , suggesting that increased gene dosage results in increased metabolic activity, which may be beneficial. The impact of duplicate gene dosage is emphasized in a recent review .
Ecological Impacts Of Duplicate Genes
The evolutionary innovations ascribed to duplicate genes can have important ecological implications. Gene duplication has contributed to developmental novelties that facilitate interactions between plants and other species. For example, the evolution of floral characteristics is strongly associated with functional groups of pollinators . The concept of a pollinator syndrome suggests that selective pressure exerted by pollinators results in the convergent evolution of a common set of floral traits. In orchids, the majority of species have only a single pollinator , but the evolution of specialized morphology for certain pollinators has occurred multiple times . According to the orchid code hypothesis, the proximal cause of the diversity of orchid floral structures can be attributed to two DEFICIENS-like transcription factor duplication events followed by gain and/or loss of function in different orchid lineages . Similarly, the duplication and subsequent diversification of CYCLOIDEA2-like transcription factors in Malpighiaceae is thought to have been important for the evolution of bilateral symmetry in flowers from radial symmetry .
Don’t Miss: Segment Addition Postulate Kuta
How Does Gene Duplication Occur How Might It Play A Role In Evolution
How does gene duplication occur? Gene duplications that do not have severe effects can persist over generations, allowing mutations to accumulate. The result is an expanded genome with new genes that may take on new functions. Such beneficial increases in gene number appear to have played a major role in evolution.
Contribution Of Selection On New Functions To Duplicate Retention
Duplicates, although originally sharing the same functions, may acquire new functions. If these functions are beneficial, selection will act to retain both duplicates. Two models that explain duplicate retention due to the acquisition of novel adaptive functions are neofunctionalization and . Under the neofunctionalization model, one duplicate retains the ancestral function while its paralog gains a novel function . If the novel function contributes to better fitness, selection should maintain both duplicates. Note that determining whether neofunctionalization has taken place requires knowledge of gene functions prior to duplication. Some examples where neofunctionalization after duplication has likely contributed to duplicate retention include MADS box transcription factors involved in the evolution of novel floral structures , 4,5-dioxygenase and cytochrome P450 genes that contribute to pigment variation in Caryophyllales , and the recruitment of duplicated primary metabolite genes into specialized metabolite pathways . At the gene expression level, it is estimated that approximately 10% of Arabidopsis duplicate genes have gained a novel response to stress conditions , although it remains to be determined whether these novel responses are adaptive or not.
Don’t Miss: Beth Thomas Therapy
Analysis Of Duplicated Genes
Classification of duplicates using MCScanX
The data used to perform these analyses were, for P. tepidariorum, the aug3 version, and for C. sculpturatus, the 0.5.53 version of the MAKER annotation available at Centruroides sculpturatus MAKER annotation . The same analysis was also performed on the Limulus polyphemus genome as a comparison.
Out of the 32,949 gene models in the aug3 annotation of the P. tepidariorum genome , only the main transcript of each gene was retained, yielding a set of 28,746 gene models. This list was further shortened by removing all instances of 755 gene models that had become artifactually duplicated during the annotation transfer process from aug2 to aug3, resulting in a final set of 27,203 gene models. All of the 30,465 gene models in the C. sculpturatus annotation were retained for the synteny analyses. Finally, out of the 23,287 annotated proteins of L. polyphemus, 21,170 were retained for the synteny analyses after filtering out annotated isoforms of the same genes .
Hits within and between gene sets were catalogued using BLASTP using an E value threshold of 1010 and keeping only the five best hits as recommended in the instruction manual of MCScanX . Then, MCScanX was used with default parameters to classify genes into five categories, namely singletons , dispersed , proximal , tandem , and segmental .
Orthology assessment of arthropod genomes
Analysis of gene tree topologies from six-genome dataset
Genetic Drift And Genetic Redundancy
Over the course of plant evolution, hundreds of thousands of new genes were created by duplication, and most of these duplicates were lost over time. Nonetheless, considering that more than half of the gene content in most plant species consists of duplicates, some duplicates have clearly escaped this fate. Why do some duplicates persist while others are lost? Models for duplicate gene retention in general have been reviewed elsewhere here, we will focus on examples of duplicate retention in plants . It is important to note that these models are not mutually exclusive. For example, selection on both duplicates to maintain dosage balance contributes to increased duplicate longevity, which may allow time for the evolution of novel functions . Here, we discuss each model independently to emphasize the distinct mechanisms that contribute to duplicate retention. First, we discuss the idea that both duplicates are retained without a significant change in function, either because insufficient time has passed for deleterious mutations to accumulate or because there is selection pressure to retain redundant functions.
Medical Definition Of Chromosome Duplication
- Medical Editor: Charles Patrick Davis, MD, PhD
Reviewed on 3/29/2021
Chromosome duplication: Part of a chromosome in duplicate. A particular kind of mutation involving the production of one or more copies of any piece of DNA, including sometimes a gene or even an entire chromosome.
A duplication is the opposite of a deletion.
Duplications have been important in the evolution of the human genome . Duplications typically arise from an event termed unequal crossing-over that occurs between misaligned homologous chromosomes during meiosis . The chance of this event happening is a function of the degree of sharing of repetitive elements between two chromosomes. The recombination products of such an event are a duplication at the site of the exchange and a reciprocal deletion. A remarkable class of duplications in which the duplicated region has popped up far away from home base has also been discovered.
Availability Of Data And Material
The raw sequences for P. tepidariorum have been deposited in the NCBI SRA: BioSample ID SAMN01932302. For C. sculpturatus, the raw sequences have been deposited in the NCBI SRA: BioSample SAMN02617800. For P. tepidariorum the assembly has been deposited in the NCBI: BioProject PRJNA167405 . For C. sculpturatus the final assembly has been deposited in the NCBI: BioProject PRJNA168116.
The annotated P. tepidariorum genome is available at .
The C. sculpturatus RNA-Seq reads from a juvenile, adult female and adult males, respectively, are available at .
The annotated C. sculpturatus genome is available at .
Read Also: Who Is Paris Jacksons Father
Medical Definition Of Duplication
- Medical Editor: Charles Patrick Davis, MD, PhD
Reviewed on 3/29/2021
Duplication: Part of a chromosome in duplicate, a particular kind of mutation involving the production of one or more copies of any piece of DNA, including a gene or even an entire chromosome.
Duplications typically arise from an event termed unequal crossing-over that occurs between misaligned homologous chromosomes during meiosis . The chance of this event happening is a function of the degree of sharing of repetitive elements between two chromosomes. The recombination products of such an event are a duplication at the site of the exchange and a reciprocal deletion. A remarkable class of duplications in which the duplicated region has popped up far away from home base has also been discovered.
Duplications have been important in the evolution of the human genome .
A duplication is the opposite of a deletion.
Signatures Of An Ancient Wgd In The Last Common Ancestor Of Spiders And Scorpions
Our study of the assembly and annotation of the P. tepidariorum genome revealed a high number of duplicated genes in accordance with previous observations . This finding is further supported by our detection of a colinearity signal across many of the largest P. tepidariorum scaffolds. The fact that we find many smaller synteny blocks across scaffolds suggests that the WGD event occurred early during spider evolution and was followed by extensive disruption of previously larger blocks, for instance, by recombination or the activity of transposable elements. Intriguingly, the comparison of the gene content of the P. tepidariorum genome with other chelicerates and other arthropods suggests that a WGD likely occurred in the lineage leading to spiders and scorpions. Our dating efforts indeed confirmed that this WGD most likely occurred after the divergence of the common ancestor of spiders and scorpions from other arachnid lineages prior to 430 MYA . Furthermore, our results suggest that this event was independent of the apparent WGDs shared by all extant horseshoe crabs .
You May Like: My.hrw.com Answer
Identification Of Different Modes Of Duplicated Genes
The MCScanX software package was used to identify the WGDs/segmental, tandem and proximal duplications in the pear genome. Genes within the pear genome were classified as singletons, dispersed, proximal, tandem and segmental/WGD duplicates using the MCScanX package. First, an all-vs.-all local BLASTP algorithm-based search was performed for all protein sequences from the pear genome . Second, duplicate gene classifier, the core program of MCScanX, was executed using the BLASTP output and annotation file as the input files. The modes of gene duplication were determined using the algorithm within MCScanX according to the following procedure: all genes were initially ranked according to their order along chromosomes and were labeled as singletons. Gene pairs within BLASTP hits were then evaluated. If the genes had BLASTP hits to other genes, then they were re-labeled as dispersed duplicates. If the two genes in a BLASTP hit had a difference of gene rank < 20 , then they were re-labeled as proximal duplicates. If the two genes had a difference of gene rank = 1, then they were re-labeled as tandem duplicates. Finally, the anchor genes in collinear blocks were re-labeled as WGD/segmental duplicates . Duplicated genes were assigned to a unique pattern according to the order of priority: WGD/segmental > tandem > proximal .