scholarly journals Comparative Genomics of Copia and Gypsy Retroelements in Three Banana Genomes: A, B, and S Genomes

2021 ◽  
Vol 44 (4) ◽  
Author(s):  
Sigit Nur Pratama ◽  
Fenny Martha Dwivany ◽  
Husna Nugrahapraja
Keyword(s):  
Phylogenetic Analysis ◽  
Transposable Elements ◽  
Evolutionary Relationship ◽  
Repetitive Elements ◽  
B Genome ◽  
Copy Numbers ◽  
Multiple Alignments ◽  
A Genome ◽  
Genome Assemblies ◽  
Relationship Of

In plants, the proportion of transposable elements (TEs) is generally dominated by long terminal repeat (LTR) retroelements. Therefore, it significantly impacts on genome expansion and genetic and phenotypic variation, namely Copia and Gypsy. Despite such contribution, TEs characterisation in an important crop such as banana [Musa balbisiana (B genome), Musa acuminata (A genome), and Musa schizocarpa (S genome)] remains poorly understood. This study aimed to compare B, A, and S genomes based on repetitive element proportions and copy numbers and determine the evolutionary relationship of LTR using phylogenetic analysis of the reverse transcriptase (RT) domain. Genome assemblies were acquired from the Banana Genome Hub (banana-genome-hub.southgreen.fr). Repetitive elements were masked by RepeatMasker 4.0.9 before Perl parsing. Phylograms were constructed according to domain analysis using DANTE (Domain-based ANnotation of Transposable Elements), alignments were made using MAFFT 7 (multiple alignments using fast Fourier transform), and trees were inferred using FastTree 2. The trees were inspected using SeaView 4 and visualised with FigTree 1.4.4. We reported that B, A, and S genomes are composed of repetitive elements with 19.38%, 20.78%, and 25.96%, respectively. The elements were identified with dominant proportions in the genome are LTR, in which Copia is more abundant than Gypsy. Based on RT phylogenetic analysis, LTR elements are clustered into 13 ancient lineages in which Sire (Copia) and Reina (Gypsy) are shown to be the most abundant LTR lineages in bananas.

scholarly journals De novo identification of satellite DNAs in the sequenced genomes of Drosophila virilis and D. americana using the RepeatExplorer and TAREAN pipelines

2019 ◽  
Author(s):  
Bráulio S.M.L. Silva ◽  
Pedro Heringer ◽  
Guilherme B. Dias ◽  
Marta Svartman ◽  
Gustavo C.S. Kuhn
Keyword(s):  
Transposable Elements ◽  
Tandem Repeat ◽  
Tandem Repeats ◽  
De Novo ◽  
Chromosome Mapping ◽  
Drosophila Virilis ◽  
Satellite Dnas ◽  
Bioinformatic Tools ◽  
A Genome ◽  
Genome Assemblies

AbstractSatellite DNAs are among the most abundant repetitive DNAs found in eukaryote genomes, where they participate in a variety of biological roles, from being components of important chromosome structures to gene regulation. Experimental methodologies used before the genomic era were not sufficient despite being too laborious and time-consuming to recover the collection of all satDNAs from a genome. Today, the availability of whole sequenced genomes combined with the development of specific bioinformatic tools are expected to foster the identification of virtually all of the “satellitome” from a particular species. While whole genome assemblies are important to obtain a global view of genome organization, most assemblies are incomplete and lack repetitive regions. Here, we applied short-read sequencing and similarity clustering in order to perform a de novo identification of the most abundant satellite families in two Drosophila species from the virilis group: Drosophila virilis and D. americana. These species were chosen because they have been used as a model to understand satDNA biology since early 70’s. We combined computational tandem repeat detection via similarity-based read clustering (implemented in Tandem Repeat Analyzer pipeline – “TAREAN”) with data from the literature and chromosome mapping to obtain an overview of satDNAs in D. virilis and D. americana. The fact that all of the abundant tandem repeats we detected were previously identified in the literature allowed us to evaluate the efficiency of TAREAN in correctly identifying true satDNAs. Our results indicate that raw sequencing reads can be efficiently used to detect satDNAs, but that abundant tandem repeats present in dispersed arrays or associated with transposable elements are frequent false positives. We demonstrate that TAREAN with its parent method RepeatExplorer, may be used as resources to detect tandem repeats associated with transposable elements and also to reveal families of dispersed tandem repeats.

Green-Spinach, Red-Spinach, and Tree-Spinach (‘Three-Fold Spinach’ in Sri Lanka): An Insight into Phylogenetics and Consumer Preference

2020 ◽  
pp. 82
Author(s):  
T. H. I. Gayathree ◽  
S. I. Karunarathne ◽  
L. T. Ranaweera ◽  
H. S. M. Jayarathne ◽  
S. K. Kannangara ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sri Lanka ◽  
Genomic Dna ◽  
Evolutionary Relationship ◽  
Consumer Preference ◽  
Basella Alba ◽  
The Poor ◽  
Definition Of ◽  
Relationship Of ◽  
Insight Into

Three types of spinach, green spinach (GS), red spinach (RS), and tree spinach (TS) are consumed in Sri Lanka. GS, RS, and TS are referred to as Basella alba, Basella rubra, and Talinum fruticosum respectively. However, some taxonomists categorize GS and RS under B. alba causing an ambiguity. Due to the poor sanitation, consumers prefer to purchase greenhouse-grown spinach over field grown material. However, the taste parameters of field grown and greenhouse-grown spinach have not been assessed. The objectives of the present study were to resolve the taxonomic ambiguity between GS and RS, identify the evolutionary relationship of TS to other two species and to assess the organoleptic preference on the dishes prepared using greenhouse and field-grown shoot-tops of three spinach. The genomic DNA extracted from GS, RS, and TS, PCR amplified and sequenced for the barcoding markers rbcL, ITS, matK-trnT and atpB-rbcL. The sequences obtained along with other reported related sequences were subjected to phylogenetic analysis.  A sensory test was carried out using the shoot-tops of three species grown under greenhouse and field conditions. The taste panelists were asked to rank the dishes for preferred levels of color, aroma, texture, bitterness, and overall taste and the data were subjected to the association analysis. The rbcL and ITS markers separate GS and RS into two well -supported clades, B. alba and B. rubra respectively. The polymorphisms of atpB-rbcL and matK-trnT markers support the definition of two species. The monophyly of B. alba and B. rubra with T. fruticosum must be the reason for the same palate in dishes and designation of all three species under “spinach” in Sri Lanka. The taste panel data demonstrated that there is no specific fondness for greenhouse or field grown materials enabling the popularization of greenhouse-grown spinach to answer the safety concerns.

scholarly journals Genome-wide protein phylogenies for four African cichlid species

2017 ◽  
Author(s):  
Ajay Ramakrishnan Varadarajan ◽  
Rohini Mopuri ◽  
J. Todd Streelman ◽  
Patrick T. McGrath
Keyword(s):  
Protein Function ◽  
Evolutionary Relationship ◽  
Trait Variation ◽  
Cichlid Species ◽  
Genome Wide ◽  
A Genome ◽  
History Of ◽  
Astatotilapia Burtoni ◽  
African Cichlids ◽  
Relationship Of

ABSTRACTBackgroundThe thousands of species of closely related cichlid fishes in the great lakes of East Africa are a powerful model for understanding speciation and the genetic basis of trait variation. Recently, the genomes of five species of African cichlids representing five distinct lineages were sequenced and used to predict protein products at a genome-wide level. Here we characterize the evolutionary relationship of each cichlid protein to previously sequenced animal species.ResultsWe used the Treefam database, a set of preexisting protein phylogenies built using 109 previously sequenced genomes, to identify Treefam families for each protein annotated from four cichlid species: Metriaclima zebra, Astatotilapia burtoni, Pundamilia nyererei and Neolamporologus brichardi. For each of these Treefam families, we built new protein phylogenies containing each of the cichlid protein hits. Using these new phylogenies we identified the evolutionary relationship of each cichlid protein to its nearest human and zebrafish protein. This data is available either through download or through a webserver we have implemented.ConclusionThese phylogenies will be useful for any cichlid researchers trying to predict biological and protein function for a given cichlid gene, understanding the evolutionary history of a given cichlid gene, identifying recently duplicated cichlid genes, or performing genome-wide analysis in cichlids that relies on using databases generated from other species.

scholarly journals Superior ab initio Identification, Annotation and Characterisation of TEs and Segmental Duplications from Genome Assemblies

2017 ◽  
Author(s):  
Lu Zeng ◽  
R. Daniel Kortschak ◽  
Joy M. Raison ◽  
Terry Bertozzi ◽  
David L. Adelson
Keyword(s):  
Transposable Elements ◽  
Ab Initio ◽  
Dna Sequences ◽  
Repetitive Elements ◽  
Segmental Duplications ◽  
Evolutionary Analysis ◽  
Mobile Dna ◽  
Consensus Sequences ◽  
New Genes ◽  
Genome Assemblies

AbstractTransposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for ab initio repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our ab initio repeat annotations for 7 genome assemblies (1 unpublished) to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package.Author summaryTransposable elements (TEs) are interspersed repetitive DNA sequences, also known as ‘jumping genes’, because of their ability to replicate in to new genomic locations. TEs account for a significant proportion of all eukaryotic genomes. Previous studies have found that TE insertions have contributed to new genes, coding sequences and regulatory regions. They also play an important role in genome evolution. Therefore, we developed a novel, ab initio approach for identifying and annotating repetitive elements. The idea is simple: define a “repeat” as any sequence that occurs at least twice in the genome. Our ab initio method is able to identify species-specific TEs with high sensitivity and accuracy including both TEs and segmental duplications. Because of the high degree of sequence identity used in our method, the TEs we find are less diverged and may still be active. We also retain all the information that links identified repeat consensus sequences to their genome intervals, permiting direct evolutionary analysis of the TE families we identify.

scholarly journals The complete mitochondrial genome of Gyps coprotheres (Aves, Accipitridae, Accipitriformes): phylogenetic analysis of mitogenome among raptors

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10034
Author(s):  
Emmanuel Oluwasegun Adawaren ◽  
Morne Du Plessis ◽  
Essa Suleman ◽  
Duodane Kindler ◽  
Almero O. Oosthuizen ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Trees ◽  
Complete Mitochondrial Genome ◽  
Evolutionary Relationship ◽  
Species Sensitivity ◽  
Model Species ◽  
Cathartes Aura ◽  
Old World ◽  
A Genome ◽  
Generation Sequencing

Three species of Old World vultures on the Asian peninsula are slowly recovering from the lethal consequences of diclofenac. At present the reason for species sensitivity to diclofenac is unknown. Furthermore, it has since been demonstrated that other Old World vultures like the Cape (Gyps coprotheres; CGV) and griffon (G. fulvus) vultures are also susceptible to diclofenac toxicity. Oddly, the New World Turkey vulture (Cathartes aura) and pied crow (Corvus albus) are not susceptible to diclofenac toxicity. As a result of the latter, we postulate an evolutionary link to toxicity. As a first step in understanding the susceptibility to diclofenac toxicity, we use the CGV as a model species for phylogenetic evaluations, by comparing the relatedness of various raptor species known to be susceptible, non-susceptible and suspected by their relationship to the Cape vulture mitogenome. This was achieved by next generation sequencing and assembly. The Cape vulture mitogenome had a genome size of 16,908 bp. The mitogenome phylogenetic analysis indicated a close evolutionary relationship between Old World vultures and other members of the Accipitridae as indicated by bootstrap value of 100% on the phylogenetic trees. Based on this, we postulate that the other species could also be sensitive to the toxic effects of diclofenac. This warrants further investigations.

scholarly journals Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Mohanad A. Ibrahim ◽  
Badr M. Al-Shomrani ◽  
Mathew Simenc ◽  
Sultan N. Alharbi ◽  
Fahad H. Alqahtani ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Transposable Elements ◽  
Genome Evolution ◽  
De Novo ◽  
Endogenous Retroviruses ◽  
Similar Proportion ◽  
Copy Numbers ◽  
Genome Wide ◽  
Vicugna Pacos ◽  
A Genome

Abstract Background Transposable elements (TEs) are common features in eukaryotic genomes that are known to affect genome evolution critically and to play roles in gene regulation. Vertebrate genomes are dominated by TEs, which can reach copy numbers in the hundreds of thousands. To date, details regarding the presence and characteristics of TEs in camelid genomes have not been made available. Results We conducted a genome-wide comparative analysis of camelid TEs, focusing on the identification of TEs and elucidation of transposition histories in four species: Camelus dromedarius, C. bactrianus, C. ferus, and Vicugna pacos. Our TE library was created using both de novo structure-based and homology-based searching strategies (https://github.com/kacst-bioinfo-lab/TE_ideintification_pipeline). Annotation results indicated a similar proportion of each genomes comprising TEs (35–36%). Class I LTR retrotransposons comprised 16–20% of genomes, and mostly consisted of the endogenous retroviruses (ERVs) groups ERVL, ERVL-MaLR, ERV_classI, and ERV_classII. Non-LTR elements comprised about 12% of genomes and consisted of SINEs (MIRs) and the LINE superfamilies LINE1, LINE2, L3/CR1, and RTE clades. Least represented were the Class II DNA transposons (2%), consisting of hAT-Charlie, TcMar-Tigger, and Helitron elements and comprising about 1–2% of each genome. Conclusions The findings of the present study revealed that the distribution of transposable elements across camelid genomes is approximately similar. This investigation presents a characterization of TE content in four camelid to contribute to developing a better understanding of camelid genome architecture and evolution.

scholarly journals Potential Vaccine Targets for COVID-19 and Phylogenetic Analysis Based on the Nucleocapsid Phosphoprotein of Indonesian SARS-CoV-2 Isolates

2021 ◽  
pp. 328-337
Author(s):  
Muhammad Aldino ◽  
Renadya Maulani ◽  
Rasyadan Probojati ◽  
Viol Dhea Karisma ◽  
Arif Nur Muhammad Ansori ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Vaccine Candidate ◽  
Peptide Vaccine ◽  
Evolutionary Relationship ◽  
Nucleocapsid Proteins ◽  
N Protein ◽  
The World ◽  
Potential Vaccine ◽  
The One ◽  
Relationship Of

Recently, the world is facing the outbreaks of severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2 and the number of infected patients is increasing every day. Researchers are doing their best to find the most effective treatment to tackle this deathly virus. Several approaches had been proposed to be tested in the lab for the efficacy but none of them are qualified to be use as the treatment of the COVID-19. Therefore, the aim of this study is to design a vaccine based on epitope, which were obtained from the nucleocapsid phosphoprotein (N protein). In addition, 38 samples of SARS-CoV-2 Isolates were being retrieved from the GISAID Database and NCBI GenBank. Later on, these samples will be used for checking the evolutionary relationship of the SARS-CoV-2 and also, to determine whether this nucleocapsid proteins are well-conserved (less or even no mutations occur at all) and whether there was any evolutionary relationship between the recent coronavirus with the previous coronavirus by conducting the phylogenetic analysis. Then, we wanted to see the molecular interaction between the human BCR/FAB receptor with the predicted peptides through the molecular docking process. All of the peptides were generated by the IEDB analysis tools and have already been tested for the antigenicity, so the one that was being docked are the peptide that has antigen properties. Based on the analysis that had been done, we would like to recommend the PEP1 as an epitope-based peptide vaccine candidate to deal with the SARS-CoV-2 outbreaks.

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