Horizontal transfers of LTR retrotransposons in seven species of Rosales

Genome ◽  
2018 ◽  
Vol 61 (8) ◽  
pp. 587-594 ◽  
Author(s):  
Fei Hou ◽  
Bi Ma ◽  
Youchao Xin ◽  
Lulu Kuang ◽  
Ningjia He
Keyword(s):  
Phylogenetic Relationships ◽  
Genetic Material ◽  
Genomic Variation ◽  
Ltr Retrotransposons ◽  
Conserved Genes ◽  
Ziziphus Jujuba ◽  
Element Transfer ◽  
Horizontal Transfers ◽  
Evolution Of Genomes ◽  
Eukaryotic Genomes

Horizontal transposable element transfer (HTT) events have occurred among a large number of species and play important roles in the composition and evolution of eukaryotic genomes. HTTs are also regarded as effective forces in promoting genomic variation and biological innovation. In the present study, HTT events were identified and analyzed in seven sequenced species of Rosales using bioinformatics methods by comparing sequence conservation and Ka/Ks value of reverse transcriptase (RT) with 20 conserved genes, estimating the dating of HTTs, and analyzing the phylogenetic relationships. Seven HTT events involving long terminal repeat (LTR) retrotransposons, two HTTs between Morus notabilis and Ziziphus jujuba, and five between Malus domestica and Pyrus bretschneideri were identified. Further analysis revealed that these LTR retrotransposons had functional structures, and the copy insertion times were lower than the dating of HTTs, particularly in Mn.Zj.1 and Md.Pb.3. Altogether, the results demonstrate that LTR retrotransposons still have potential transposition activity in host genomes. These results indicate that HTT events are another strategy for exchanging genetic material among species and are important for the evolution of genomes.

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 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 Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon

2021 ◽  
Author(s):  
Nusrat Sultana ◽  
Gerhard Menzel ◽  
Kathrin M. Seibt ◽  
Sonia Garcia ◽  
Beatrice Weber ◽  
...  
Keyword(s):  
Long Terminal Repeat ◽  
Genome Assembly ◽  
In Silico ◽  
Transcriptional Activity ◽  
Long Terminal Repeat Retrotransposons ◽  
Genomic Variation ◽  
Terminal Repeat ◽  
Vaccinium Macrocarpon ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons

BACKGROUND: Long terminal repeat (LTR) retrotransposons are widespread in plant genomes and play a large role in the generation of genomic variation. Despite this, their identification and characterization remains challenging, especially for non-model genomes. Hence, LTR retrotransposons remain undercharacterized in Vaccinium genomes, although they may be beneficial for current berry breeding efforts. OBJECTIVE: Exemplarily focusing on the genome of American cranberry (Vaccinium macrocarpon Aiton), we aim to generate an overview of the LTR retrotransposon landscape, highlighting the abundance, transcriptional activity, sequence, and structure of the major retrotransposon lineages. METHODS: Graph-based clustering of whole genome shotgun Illumina reads was performed to identify the most abundant LTR retrotransposons and to reconstruct representative in silico full-length elements. To generate insights into the LTR retrotransposon diversity in V. macrocarpon, we also queried the genome assembly for presence of reverse transcriptases (RTs), the key domain of LTR retrotransposons. Using transcriptomic data, transcriptional activity of retrotransposons corresponding to the consensuses was analyzed. RESULTS: We provide an in-depth characterization of the LTR retrotransposon landscape in the V. macrocarpon genome. Based on 475 RTs harvested from the genome assembly, we detect a high retrotransposon variety, with all major lineages present. To better understand their structural hallmarks, we reconstructed 26 Ty1-copia and 28 Ty3-gypsyin silico consensuses that capture the detected diversity. Accordingly, we frequently identify association with tandemly repeated motifs, extra open reading frames, and specialized, lineage-typical domains. Based on the overall high genomic abundance and transcriptional activity, we suggest that retrotransposons of the Ale and Athila lineages are most promising to monitor retrotransposon-derived polymorphisms across accessions. CONCLUSIONS: We conclude that LTR retrotransposons are major components of the V. macrocarpon genome. The representative consensuses provide an entry point for further Vaccinium genome analyses and may be applied to derive molecular markers for enhancing cranberry selection and breeding.

scholarly journals De novo identification of LTR retrotransposons in eukaryotic genomes

BMC Genomics ◽  
2007 ◽  
Vol 8 (1) ◽  
pp. 90 ◽  
Author(s):  
Mina Rho ◽  
Jeong-Hyeon Choi ◽  
Sun Kim ◽  
Michael Lynch ◽  
Haixu Tang
Keyword(s):  
De Novo ◽  
Ltr Retrotransposons ◽  
Eukaryotic Genomes

scholarly journals IsoPlotter+: A Tool for Studying the Compositional Architecture of Genomes

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Eran Elhaik ◽  
Dan Graur
Keyword(s):  
Gc Content ◽  
Data Repository ◽  
Computational Tools ◽  
Domain Composition ◽  
Automated Pipeline ◽  
Indispensable Tool ◽  
Genomic Regions ◽  
Evolution Of Genomes ◽  
Eukaryotic Genomes ◽  
Animal Genomes

Eukaryotic genomes, particularly animal genomes, have a complex, nonuniform, and nonrandom internal compositional organization. The compositional organization of animal genomes can be described as a mosaic of discrete genomic regions, called “compositional domains,” each with a distinct GC content that significantly differs from those of its upstream and downstream neighboring domains. A typical animal genome consists of a mixture of compositionally homogeneous and nonhomogeneous domains of varying lengths and nucleotide compositions that are interspersed with one another. We have devised IsoPlotter, an unbiased segmentation algorithm for inferring the compositional organization of genomes. IsoPlotter has become an indispensable tool for describing genomic composition and has been used in the analysis of more than a dozen genomes. Applications include describing new genomes, correlating domain composition with gene composition and their density, studying the evolution of genomes, testing phylogenomic hypotheses, and detect regions of potential interbreeding between human and extinct hominines. To extend the use of IsoPlotter, we designed a completely automated pipeline, called IsoPlotter+ to carry out all segmentation analyses, including graphical display, and built a repository for compositional domain maps of all fully sequenced vertebrate and invertebrate genomes. The IsoPlotter+ pipeline and repository offer a comprehensive solution to the study of genome compositional architecture. Here, we demonstrate IsoPlotter+ by applying it to human and insect genomes. The computational tools and data repository are available online.

scholarly journals HSDFinder: A BLAST-Based Strategy for Identifying Highly Similar Duplicated Genes in Eukaryotic Genomes

2021 ◽  
Vol 1 ◽  
Author(s):  
Xi Zhang ◽  
Yining Hu ◽  
David Roy Smith
Keyword(s):  
Gene Duplication ◽  
Genetic Material ◽  
Duplicate Genes ◽  
Functional Categories ◽  
Web Tool ◽  
Eukaryotic Species ◽  
External Software ◽  
Multiple Species ◽  
User Friendly ◽  
Eukaryotic Genomes

Gene duplication is an important evolutionary mechanism capable of providing new genetic material for adaptive and nonadaptive evolution. However, bioinformatics tools for identifying duplicate genes are often limited to the detection of paralogs in multiple species or to specific types of gene duplicates, such as retrocopies. Here, we present a user-friendly, BLAST-based web tool, called HSDFinder, which can identify, annotate, categorize, and visualize highly similar duplicate genes (HSDs) in eukaryotic nuclear genomes. HSDFinder includes an online heatmap plotting option, allowing users to compare HSDs among different species and visualize the results in different Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway functional categories. The external software requirements are BLAST, InterProScan, and KEGG. The utility of HSDFinder was tested on various model eukaryotic species, including Chlamydomonas reinhardtii, Arabidopsis thaliana, Oryza sativa, and Zea mays as well as the psychrophilic green alga Chlamydomonas sp. UWO241, and was proven to be a practical and accurate tool for gene duplication analyses. The web tool is free to use at http://hsdfinder.com. Documentation and tutorials can be found via the GitHub: https://github.com/zx0223winner/HSDFinder.

scholarly journals BK Polyomavirus—Biology, Genomic Variation and Diagnosis

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1502
Author(s):  
Jacek Furmaga ◽  
Marek Kowalczyk ◽  
Tomasz Zapolski ◽  
Olga Furmaga ◽  
Leszek Krakowski ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Clinical Symptoms ◽  
Quantitative Polymerase Chain Reaction ◽  
Genetic Material ◽  
Genomic Variation ◽  
Chain Reaction ◽  
Haemorrhagic Cystitis ◽  
Genotype I ◽  
Bk Polyomavirus ◽  
Polymerase Chain

The BK polyomavirus (BKPyV), a representative of the family Polyomaviridae, is widespread in the human population. While the virus does not cause significant clinical symptoms in immunocompetent individuals, it is activated in cases of immune deficiency, both pharmacological and pathological. Infection with the BKPyV is of particular importance in recipients of kidney transplants or HSC transplantation, in which it can lead to the loss of the transplanted kidney or to haemorrhagic cystitis, respectively. Four main genotypes of the virus are distinguished on the basis of molecular differentiation. The most common genotype worldwide is genotype I, with a frequency of about 80%, followed by genotype IV (about 15%), while genotypes II and III are isolated only sporadically. The distribution of the molecular variants of the virus is associated with the region of origin. BKPyV subtype Ia is most common in Africa, Ib-1 in Southeast Asia, and Ib-2 in Europe, while Ic is the most common variant in Northeast Asia. The development of molecular methods has enabled significant improvement not only in BKPyV diagnostics, but in monitoring the effectiveness of treatment as well. Amplification of viral DNA from urine by PCR (Polymerase Chain Reaction) and qPCR Quantitative Polymerase Chain Reaction) is a non-invasive method that can be used to confirm the presence of the genetic material of the virus and to determine the viral load. Sequencing techniques together with bioinformatics tools and databases can be used to determine variants of the virus, analyse their circulation in populations, identify relationships between them, and investigate the directions of evolution of the virus.

scholarly journals A molecular marker set combining a retrotransposon insertion and SSR polymorphisms is useful for assessing diversity in Vitis

OENO One ◽  
2021 ◽  
Vol 55 (2) ◽  
pp. 403-414
Author(s):  
Frederique Pelsy ◽  
Lucie Bevilacqua ◽  
Sophie Blanc ◽  
Didier Merdinoglu
Keyword(s):  
Molecular Markers ◽  
Molecular Marker ◽  
Phylogenetic Relationships ◽  
Genetic Material ◽  
Dna Polymorphisms ◽  
Heterozygous State ◽  
Empty Site ◽  
Microsatellite Sequence ◽  
Vitis Species ◽  
Ssr Polymorphism

Molecular markers, based on DNA polymorphisms, are useful tools for identifying individuals, establishing phylogenetic relationships, managing collections of genetic material or assisting breeding. In the present study, we developed a marker set to differentiate Vitis species, grapevine varieties or clones belonging to the same variety. This novel marker set combines, in four PCR amplifications, the presence/absence of a remarkable retrotransposon, Tvv1-Δ3460, inserted at its single locus and the SSR polymorphism present within its two LTRs. By studying a collection of Vitaceaeaccessions, we showed the prevalence of two allelic forms of Tvv1-Δ3460 - one of which was partially truncated - in Vitis species. Out of the twenty-five studied Vitis species, the insertion of a Tvv1-Δ3460 element was detected in twenty, including Vitis vinifera. The homozygous vs heterozygous state of the element insertion was determined by amplifying the empty site. Additionally, each Tvv1-Δ3460 LTRs included a microsatellite sequence useful for designing markers based on LTR length. The LTR-SSR markers distinguished most of the fifty-two cultivars and revealed polymorphism within five of the seven varieties studied.

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