scholarly journals Site-Specific Insertion Polymorphism of the MITE Alex-1 in the Genus Coffea Suggests Interspecific Gene Flow

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Christine Dubreuil-Tranchant ◽  
Romain Guyot ◽  
Amira Guellim ◽  
Caroline Duret ◽  
Marion de la Mare ◽  
...  
Keyword(s):  
Gene Flow ◽  
Transposable Elements ◽  
Phylogenetic Relationships ◽  
Insertion Site ◽  
Coffea Canephora ◽  
Insertion Polymorphism ◽  
Interspecific Gene Flow ◽  
Species Analysis ◽  
Eukaryotic Genomes ◽  
Mite Family

Miniature Inverted-repeat Transposable Elements (MITEs) are small nonautonomous class-II transposable elements distributed throughout eukaryotic genomes. We identified a novel family of MITEs (named Alex) in the Coffea canephora genome often associated with expressed sequences. The Alex-1 element is inserted in an intron of a gene at the CcEIN4 locus. Its mobility was demonstrated by sequencing the insertion site in C. canephora accessions and Coffea species. Analysis of the insertion polymorphism of Alex-1 at this locus in Coffea species and in C. canephora showed that there was no relationship between the geographical distribution of the species, their phylogenetic relationships, and insertion polymorphism. The intraspecific distribution of C. canephora revealed an original situation within the E diversity group. These results suggest possibly greater gene flow between species than previously thought. This MITE family will enable the study of the C. canephora genome evolution, phylogenetic relationships, and possible gene flows within the Coffea genus.

scholarly journals TEsorter: lineage-level classification of transposable elements using conserved protein domains

2019 ◽  
Author(s):  
Ren-Gang Zhang ◽  
Zhao-Xuan Wang ◽  
Shujun Ou ◽  
Guang-Yuan Li
Keyword(s):  
Transposable Elements ◽  
Phylogenetic Relationships ◽  
Protein Domains ◽  
Ltr Retrotransposons ◽  
Link Type ◽  
Eukaryotic Genomes

AbstractSummaryTransposable elements (TEs) constitute an import part in eukaryotic genomes, but their classification, especially in the lineage or clade level, is still challenging. For this purpose, we propose TEsorter, which is based on conserved protein domains of TEs. It is easy-to-use, fast with multiprocessing, sensitive and precise to classify TEs especially LTR retrotransposons (LTR-RTs). Its results can also directly reflect phylogenetic relationships and diversities of the classified LTR-RTs.AvailabilityThe code in Python is freely available at https://github.com/zhangrengang/TEsorter.

scholarly journals Extensive Interspecific Gene Flow Shaped Complex Evolutionary History and Underestimated Species Diversity in Rapidly Radiated Dolphins

2021 ◽  
Author(s):  
Weijian Guo ◽  
Di Sun ◽  
Yang Cao ◽  
Linlin Xiao ◽  
Xin Huang ◽  
...  
Keyword(s):  
Gene Flow ◽  
Bayesian Methods ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Phylogenetic Reconstruction ◽  
Genomic Data ◽  
Sliding Window ◽  
Interspecific Gene Flow ◽  
History Of ◽  
Relationship Of

AbstractRecently diverged taxa are often characterized by high rates of hybridization, which can complicate phylogenetic reconstruction. For this reason, the phylogenetic relationships and evolutionary history of dolphins are still not very well resolved; the question of whether the genera Tursiops and Stenella are monophyletic is especially controversial. Here, we performed re-sequencing of six dolphin genomes and combined them with eight previously published dolphin SRA datasets and six whole-genome datasets to investigate the phylogenetic relationships of dolphins and test the monophyly hypothesis of Tursiops and Stenella. Phylogenetic reconstruction with the maximum likelihood and Bayesian methods of concatenated loci, as well as with coalescence analyses of sliding window trees, produced a concordant and well-supported tree. Our studies support the non-monophyletic status of Tursiops and Stenella because the species referred these genera do not form exclusive monophyletic clades. This suggests that the current taxonomy of both genera might not reflect their evolutionary history and may underestimate their diversity. A four-taxon D-statistic (ABBA-BABA) test, five-taxon DFOIL test, and tree-based PhyloNet analyses all showed extensive gene flow across dolphin species, which could explain the instability in resolving phylogenetic relationship of oceanic dolphins with different and limited markers. This study could be a good case to demonstrate how genomic data can reveal complex speciation and phylogeny in rapidly radiating animal groups.

scholarly journals Phylogenetic relationships among accessions in Citrus and related genera based on the insertion polymorphism of the CIRE1 retrotransposon

2020 ◽  
Vol 5 (1) ◽  
pp. 243-251
Author(s):  
Akira Horibata ◽  
Tsuneo Kato
Keyword(s):  
Phylogenetic Relationships ◽  
Sweet Orange ◽  
Point Of View ◽  
Insertion Polymorphism ◽  
Navel Orange ◽  
Citrus Germplasm ◽  
Outgroup Species ◽  
Blood Orange

AbstractA total of 145 accessions of the genus Citrus and related genera, maintained in the Conservation Garden for Citrus Germplasm at the Experimental Farm of Kindai University, Yuasa, Wakayama, Japan, were examined for their phylogenetic relationships. The present classification was conducted using an inter-retrotransposon amplified polymorphism (IRAP) method based on the insertion polymorphism of a retrotransposon, CIRE1, identified in C. sinensis. The objective of this study was to evaluate the applicability of the IRAP method for citrus classification. The constructed dendrogram showed that the 145 accessions and two outgroup species were successfully classified into five major clades. A large number of C. sinensis accessions were divided into three traditional groups, navel orange, sweet orange, and blood orange, almost corresponding to the sub-clades in the dendrogram. Several other accessions belonging to the same species, and also many hybrid cultivars from crossbreeding, were localized into the respective sub-clades or near positions in the dendrogram. Several unclassified accessions could also be located in the dendrogram, suggesting novel relationships with other accessions. It was concluded that the IRAP method based on CIRE1 insertion polymorphism was suitable for the classification of citrus from a molecular point of view.

scholarly journals Transposable Elements and Teleost Migratory Behaviour

2021 ◽  
Vol 22 (2) ◽  
pp. 602
Author(s):  
Elisa Carotti ◽  
Federica Carducci ◽  
Adriana Canapa ◽  
Marco Barucca ◽  
Samuele Greco ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Environmental Changes ◽  
Chromosomal Rearrangements ◽  
Quantitative Difference ◽  
Regulatory Elements ◽  
Phylogenetic Position ◽  
Migratory Behaviour ◽  
Relative Contribution ◽  
Migratory Routes ◽  
Eukaryotic Genomes

Transposable elements (TEs) represent a considerable fraction of eukaryotic genomes, thereby contributing to genome size, chromosomal rearrangements, and to the generation of new coding genes or regulatory elements. An increasing number of works have reported a link between the genomic abundance of TEs and the adaptation to specific environmental conditions. Diadromy represents a fascinating feature of fish, protagonists of migratory routes between marine and freshwater for reproduction. In this work, we investigated the genomes of 24 fish species, including 15 teleosts with a migratory behaviour. The expected higher relative abundance of DNA transposons in ray-finned fish compared with the other fish groups was not confirmed by the analysis of the dataset considered. The relative contribution of different TE types in migratory ray-finned species did not show clear differences between oceanodromous and potamodromous fish. On the contrary, a remarkable relationship between migratory behaviour and the quantitative difference reported for short interspersed nuclear (retro)elements (SINEs) emerged from the comparison between anadromous and catadromous species, independently from their phylogenetic position. This aspect is likely due to the substantial environmental changes faced by diadromous species during their migratory routes.

scholarly journals Chromosomal Distribution of Transposable Elements in Drosophila melanogaster Test of the Ectopic Recombination Model for Maintenance of Insertion Site Number

Genetics ◽  
1996 ◽  
Vol 144 (1) ◽  
pp. 197-204
Author(s):  
Christine Hoogland ◽  
Christian Biémont
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Dna Content ◽  
Recombination Rate ◽  
Alternative Hypothesis ◽  
Insertion Site ◽  
Polytene Chromosomes ◽  
Negative Relationship ◽  
Site Occupancy ◽  
Site Number

Abstract Data of insertion site localization and site occupancy frequency of P, hobo, I, copia, mdg1, mdg3, 412, 297, and roo transposable elements (TEs) on the polytene chromosomes of Drosophila melanogaster were extracted from the literature. We show that TE insertion site number per chromosomal division was significantly correlated with the amount of DNA. The insertion site number weighted by DNA content was not correlated with recombination rate for all TEs except hobo, for which a positive correlation was detected. No global tendency emerged in the relationship between TE site occupancy frequency, weighted by DNA content, and recombination rate; a strong negative correlation was, however, found for the 3L arm. A possible dominant deleterious effect of chromosomal rearrangements due to recombination between TE insertions is thus not the main factor explaining the dynamics of TEs, since this hypothesis implies a negative relationship between recombination rate and both TE insertion site number and site occupancy frequency. The alternative hypothesis of selection against deleterious effects of insertional mutations is discussed.

scholarly journals Molecular Signatures of Reticulate Evolution within the Complex of European Pine Taxa

Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 489
Author(s):  
Bartosz Łabiszak ◽  
Witold Wachowiak
Keyword(s):  
Gene Flow ◽  
Reticulate Evolution ◽  
Modeling Framework ◽  
Closely Related Species ◽  
Interspecific Gene Flow ◽  
Nucleotide Sequence Variation ◽  
History Of ◽  
Best Fitting ◽  
Species Integrity

Speciation mechanisms, including the role of interspecific gene flow and introgression in the emergence of new species, are the major focus of evolutionary studies. Inference of taxonomic relationship between closely related species may be challenged by past hybridization events, but at the same time, it may provide new knowledge about mechanisms responsible for the maintenance of species integrity despite interspecific gene flow. Here, using nucleotide sequence variation and utilizing a coalescent modeling framework, we tested the role of hybridization and introgression in the evolutionary history of closely related pine taxa from the Pinus mugo complex and P. sylvestris. We compared the patterns of polymorphism and divergence between taxa and found a great overlap of neutral variation within the P. mugo complex. Our phylogeny reconstruction indicated multiple instances of reticulation events in the past, suggesting an important role of interspecific gene flow in the species divergence. The best-fitting model revealed P. mugo and P. uncinata as sister species with basal P. uliginosa and asymmetric migration between all investigated species after their divergence. The magnitude of interspecies gene flow differed greatly, and it was consistently stronger from representatives of P. mugo complex to P. sylvestris than in the opposite direction. The results indicate the prominent role of reticulation evolution in those forest trees and provide a genetic framework to study species integrity maintained by selection and local adaptation.

scholarly journals Interspecific Gene Flow Shaped the Evolution of the Genus Canis

2019 ◽  
Vol 29 (23) ◽  
pp. 4152 ◽  
Author(s):  
Shyam Gopalakrishnan ◽  
Mikkel-Holger S. Sinding ◽  
Jazmín Ramos-Madrigal ◽  
Jonas Niemann ◽  
Jose A. Samaniego Castruita ◽  
...  
Keyword(s):  
Gene Flow ◽  
Interspecific Gene Flow

Pleistocene survival, regional genetic structure and interspecific gene flow among three northern peat-mosses: Sphagnum inexspectatum , S. orientale and S. miyabeanum

2014 ◽  
Vol 42 (2) ◽  
pp. 364-376 ◽  
Author(s):  
A. Jonathan Shaw ◽  
Blanka Shaw ◽  
Hans K. Stenøien ◽  
G. Karen Golinski ◽  
Kristian Hassel ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Interspecific Gene Flow

scholarly journals Gene Flow in Phaseolus Beans and Its Role as a Plausible Driver of Ecological Fitness and Expansion of Cultigens

2021 ◽  
Vol 9 ◽  
Author(s):  
María Isabel Chacón-Sánchez ◽  
Jaime Martínez-Castillo ◽  
Jorge Duitama ◽  
Daniel G. Debouck
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Time Perspective ◽  
Lima Bean ◽  
Breeding Systems ◽  
Large Contribution ◽  
Interspecific Gene Flow ◽  
Ecological Fitness ◽  
Technological Advances ◽  
Evolutionary Force

The genus Phaseolus, native to the Americas, is composed of more than eighty wild species, five of which were domesticated in pre-Columbian times. Since the beginning of domestication events in this genus, ample opportunities for gene flow with wild relatives have existed. The present work reviews the extent of gene flow in the genus Phaseolus in primary and secondary areas of domestication with the aim of illustrating how this evolutionary force may have conditioned ecological fitness and the widespread adoption of cultigens. We focus on the biological bases of gene flow in the genus Phaseolus from a spatial and time perspective, the dynamics of wild-weedy-crop complexes in the common bean and the Lima bean, the two most important domesticated species of the genus, and the usefulness of genomic tools to detect inter and intraspecific introgression events. In this review we discuss the reproductive strategies of several Phaseolus species, the factors that may favor outcrossing rates and evidence suggesting that interspecific gene flow may increase ecological fitness of wild populations. We also show that wild-weedy-crop complexes generate genetic diversity over which farmers are able to select and expand their cultigens outside primary areas of domestication. Ultimately, we argue that more studies are needed on the reproductive biology of the genus Phaseolus since for most species breeding systems are largely unknown. We also argue that there is an urgent need to preserve wild-weedy-crop complexes and characterize the genetic diversity generated by them, in particular the genome-wide effects of introgressions and their value for breeding programs. Recent technological advances in genomics, coupled with agronomic characterizations, may make a large contribution.

scholarly journals Software Evaluation for de novo Detection of Transposons

2021 ◽  
Author(s):  
Matias Rodriguez ◽  
Wojciech Makałowski
Keyword(s):  
Transposable Elements ◽  
Genome Evolution ◽  
De Novo ◽  
Simulated Data ◽  
Genomic Sequences ◽  
Software Evaluation ◽  
Easy Task ◽  
Eukaryotic Genomes

AbstractTransposable elements (TEs) are major genomic components in most eukaryotic genomes and play an important role in genome evolution. However, despite their relevance the identification of TEs is not an easy task and a number of tools were developed to tackle this problem. To better understand how they perform, we tested several widely used tools for de novo TE detection and compared their performance on both simulated data and well curated genomic sequences. The results will be helpful for identifying common issues associated with TE-annotation and for evaluating how comparable are the results obtained with different tools.

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