scholarly journals Genome Size Doubling Arises From the Differential Repetitive DNA Dynamics in the Genus Heloniopsis (Melanthiaceae)

2021 ◽  
Vol 12 ◽  
Author(s):  
Jaume Pellicer ◽  
Pol Fernández ◽  
Michael F. Fay ◽  
Ester Michálková ◽  
Ilia J. Leitch
Keyword(s):  
Genome Size ◽  
Repetitive Dna ◽  
High Throughput Sequencing ◽  
Evolutionary Dynamics ◽  
Dna Dynamics ◽  
Closely Related Species ◽  
Sequencing Technologies ◽  
Genomic Landscape ◽  
Evolutionary Changes ◽  
Low Coverage

Plant genomes are highly diverse in size and repetitive DNA composition. In the absence of polyploidy, the dynamics of repetitive elements, which make up the bulk of the genome in many species, are the main drivers underpinning changes in genome size and the overall evolution of the genomic landscape. The advent of high-throughput sequencing technologies has enabled investigation of genome evolutionary dynamics beyond model plants to provide exciting new insights in species across the biodiversity of life. Here we analyze the evolution of repetitive DNA in two closely related species of Heloniopsis (Melanthiaceae), which despite having the same chromosome number differ nearly twofold in genome size [i.e., H. umbellata (1C = 4,680 Mb), and H. koreana (1C = 2,480 Mb)]. Low-coverage genome skimming and the RepeatExplorer2 pipeline were used to identify the main repeat families responsible for the significant differences in genome sizes. Patterns of repeat evolution were found to correlate with genome size with the main classes of transposable elements identified being twice as abundant in the larger genome of H. umbellata compared with H. koreana. In addition, among the satellite DNA families recovered, a single shared satellite (HeloSAT) was shown to have contributed significantly to the genome expansion of H. umbellata. Evolutionary changes in repetitive DNA composition and genome size indicate that the differences in genome size between these species have been underpinned by the activity of several distinct repeat lineages.

scholarly journals Recent Insights into Mechanisms of Genome Size Change in Plants

2010 ◽  
Vol 2010 ◽  
pp. 1-8 ◽  
Author(s):  
Corrinne E. Grover ◽  
Jonathan F. Wendel
Keyword(s):  
Genome Size ◽  
Related Species ◽  
Evolutionary Dynamics ◽  
Higher Order ◽  
Size Change ◽  
Closely Related Species ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Recent Developments

Genome sizes vary considerably across all eukaryotes and even among closely related species. The genesis and evolutionary dynamics of that variation have generated considerable interest, as have the patterns of variation themselves. Here we review recent developments in our understanding of genome size evolution in plants, drawing attention to the higher order processes that can influence the mechanisms generating changing genome size.

scholarly journals Comparative Analysis of Transposable Elements in Genus Calliptamus Grasshoppers Revealed That Satellite DNA Contributes to Genome Size Variation

Insects ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 837
Author(s):  
Muhammad Majid ◽  
Huang Yuan
Keyword(s):  
Comparative Analysis ◽  
Transposable Elements ◽  
Genome Size ◽  
Structural Changes ◽  
Evolutionary Dynamics ◽  
Size Variation ◽  
Genome Size Variation ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Low Coverage

Transposable elements (TEs) play a significant role in both eukaryotes and prokaryotes genome size evolution, structural changes, duplication, and functional variabilities. However, the large number of different repetitive DNA has hindered the process of assembling reference genomes, and the genus level TEs diversification of the grasshopper massive genomes is still under investigation. The genus Calliptamus diverged from Peripolus around 17 mya and its species divergence dated back about 8.5 mya, but their genome size shows rather large differences. Here, we used low-coverage Illumina unassembled short reads to investigate the effects of evolutionary dynamics of satDNAs and TEs on genome size variations. The Repeatexplorer2 analysis with 0.5X data resulted in 52%, 56%, and 55% as repetitive elements in the genomes of Calliptamus barbarus, Calliptamus italicus, and Calliptamus abbreviatus, respectively. The LINE and Ty3-gypsy LTR retrotransposons and TcMar-Tc1 dominated the repeatomes of all genomes, accounting for 16–35% of the total genomes of these species. Comparative analysis unveiled that most of the transposable elements (TEs) except satDNAs were highly conserved across three genomes in the genus Calliptamus grasshoppers. Out of a total of 20 satDNA families, 17 satDNA families were commonly shared with minor variations in abundance and divergence between three genomes, and 3 were Calliptamus barbarus specific. Our findings suggest that there is a significant amplification or contraction of satDNAs at genus phylogeny which is the main cause that made genome size different.

scholarly journals Corrigendum: Genome Size Doubling Arises From the Differential Repetitive DNA Dynamics in the Genus Heloniopsis (Melanthiaceae)

2021 ◽  
Vol 12 ◽  
Author(s):  
Jaume Pellicer ◽  
Pol Fernández ◽  
Michael F. Fay ◽  
Ester Michálková ◽  
Ilia J. Leitch
Keyword(s):  
Genome Size ◽  
Repetitive Dna ◽  
Dna Dynamics

scholarly journals The Tritryps comparative repeatome: insights on repetitive element evolution in Trypanosomatid pathogens

2018 ◽  
Author(s):  
Sebastián Pita ◽  
Florencia Díaz-Viraqué ◽  
Gregorio Iraola ◽  
Carlos Robello
Keyword(s):  
Repetitive Dna ◽  
Leishmania Major ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Low Cost ◽  
Repetitive Sequences ◽  
Human Pathogens ◽  
Genome Wide ◽  
Low Coverage

AbstractThe major human pathogens Trypanosoma cruzi, Trypanosoma brucei and Leishmania major are collectively known as the Tritryps. The initial comparative analysis of their genomes has uncovered that Tritryps share a great number of genes, but repetitive DNA seems to be extremely variable between them. However, the in-depth characterization of repetitive DNA in these pathogens has been in part neglected, mainly due to the well-known technical challenges of studying repetitive sequences from de novo assemblies using short reads. Here, we compared the repetitive DNA repertories between the Tritryps genomes using genome-wide, low-coverage Illumina sequencing coupled to RepeatExplorer analysis. Our work demonstrates that this extensively implemented approach for studying higher eukaryote repeatomes is also useful for protozoan parasites like trypanosomatids, as we recovered previously observed differences in the presence and amount of repetitive DNA families. Additionally, our estimations of repetitive DNA abundance were comparable to those obtained from enhanced-quality assemblies using longer reads. Importantly, our methodology allowed us to describe a previously unknown transposable element in Leishmania major (TATE family), highlighting its potential to accurately recover distinctive features from poorly characterized repeatomes. Together, our results support the application of this low-cost, low-coverage sequencing approach for the extensive characterization of repetitive DNA evolutionary dynamics in trypanosomatid and other protozooan genomes.

scholarly journals Reassortment of Genome Segments Creates Stable Lineages Among Strains of Orchid Fleck Virus Infecting Citrus in Mexico

2020 ◽  
Vol 110 (1) ◽  
pp. 106-120 ◽  
Author(s):  
Avijit Roy ◽  
Andrew L. Stone ◽  
Gabriel Otero-Colina ◽  
Gang Wei ◽  
Ronald H. Brlansky ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sensu Stricto ◽  
Genome Segment ◽  
Rt Pcr ◽  
Sequence Comparisons ◽  
Orchid Fleck Virus ◽  
Reverse Transcription Pcr ◽  
Sequencing Technologies ◽  
Negative Sense

The genus Dichorhavirus contains viruses with bipartite, negative-sense, single-stranded RNA genomes that are transmitted by flat mites to hosts that include orchids, coffee, the genus Clerodendrum, and citrus. A dichorhavirus infecting citrus in Mexico is classified as a citrus strain of orchid fleck virus (OFV-Cit). We previously used RNA sequencing technologies on OFV-Cit samples from Mexico to develop an OFV-Cit–specific reverse transcription PCR (RT-PCR) assay. During assay validation, OFV-Cit–specific RT-PCR failed to produce an amplicon from some samples with clear symptoms of OFV-Cit. Characterization of this virus revealed that dichorhavirus-like particles were found in the nucleus. High-throughput sequencing of small RNAs from these citrus plants revealed a novel citrus strain of OFV, OFV-Cit2. Sequence comparisons with known orchid and citrus strains of OFV showed variation in the protein products encoded by genome segment 1 (RNA1). Strains of OFV clustered together based on host of origin, whether orchid or citrus, and were clearly separated from other dichorhaviruses described from infected citrus in Brazil. The variation in RNA1 between the original (now OFV-Cit1) and the new (OFV-Cit2) strain was not observed with genome segment 2 (RNA2), but instead, a common RNA2 molecule was shared among strains of OFV-Cit1 and -Cit2, a situation strikingly similar to OFV infecting orchids. We also collected mites at the affected groves, identified them as Brevipalpus californicus sensu stricto, and confirmed that they were infected by OFV-Cit1 or with both OFV-Cit1 and -Cit2. OFV-Cit1 and -Cit2 have coexisted at the same site in Toliman, Queretaro, Mexico since 2012. OFV strain-specific diagnostic tests were developed.

scholarly journals Application of Oxford Nanopore Technology to Plant Virus Detection

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1424
Author(s):  
Lia W. Liefting ◽  
David W. Waite ◽  
Jeremy R. Thompson
Keyword(s):  
Plant Virus ◽  
High Throughput Sequencing ◽  
Virus Detection ◽  
Diagnostic Methods ◽  
Plant Virus Detection ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Virus Diagnostics ◽  
Post Entry ◽  
Read Accuracy

The adoption of Oxford Nanopore Technologies (ONT) sequencing as a tool in plant virology has been relatively slow despite its promise in more recent years to yield large quantities of long nucleotide sequences in real time without the need for prior amplification. The portability of the MinION and Flongle platforms combined with lowering costs and continued improvements in read accuracy make ONT an attractive method for both low- and high-scale virus diagnostics. Here, we provide a detailed step-by-step protocol using the ONT Flongle platform that we have developed for the routine application on a range of symptomatic post-entry quarantine and domestic surveillance plant samples. The aim of this methods paper is to highlight ONT’s feasibility as a valuable component to the diagnostician’s toolkit and to hopefully stimulate other laboratories towards the eventual goal of integrating high-throughput sequencing technologies as validated plant virus diagnostic methods in their own right.

scholarly journals A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Shan-Shan Zhou ◽  
Xue-Mei Yan ◽  
Kai-Fu Zhang ◽  
Hui Liu ◽  
Jie Xu ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Age Determination ◽  
Genome Plasticity ◽  
Ltr Retrotransposons ◽  
Functional Variation ◽  
Plant Genomes ◽  
Sequencing Technologies ◽  
Plant Groups ◽  
Functional Implications ◽  
Classification Information

AbstractLTR retrotransposons (LTR-RTs) are ubiquitous and represent the dominant repeat element in plant genomes, playing important roles in functional variation, genome plasticity and evolution. With the advent of new sequencing technologies, a growing number of whole-genome sequences have been made publicly available, making it possible to carry out systematic analyses of LTR-RTs. However, a comprehensive and unified annotation of LTR-RTs in plant groups is still lacking. Here, we constructed a plant intact LTR-RTs dataset, which is designed to classify and annotate intact LTR-RTs with a standardized procedure. The dataset currently comprises a total of 2,593,685 intact LTR-RTs from genomes of 300 plant species representing 93 families of 46 orders. The dataset is accompanied by sequence, diverse structural and functional annotation, age determination and classification information associated with the LTR-RTs. This dataset will contribute valuable resources for investigating the evolutionary dynamics and functional implications of LTR-RTs in plant genomes.

scholarly journals Assessing genotyping errors in mammalian museum study skins using high-throughput genotyping-by-sequencing

2021 ◽  
Author(s):  
Stella C. Yuan ◽  
Eric Malekos ◽  
Melissa T. R. Hawkins
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Museum Specimens ◽  
Museum Specimen ◽  
Genotyping Errors ◽  
Allelic Dropout ◽  
Parallel Sequencing ◽  
Sequencing Technologies

AbstractThe use of museum specimens held in natural history repositories for population and conservation genetic research is increasing in tandem with the use of massively parallel sequencing technologies. Short Tandem Repeats (STRs), or microsatellite loci, are commonly used genetic markers in wildlife and population genetic studies. However, they traditionally suffered from a host of issues including length homoplasy, high costs, low throughput, and difficulties in reproducibility across laboratories. Massively parallel sequencing technologies can address these problems, but the incorporation of museum specimen derived DNA suffers from significant fragmentation and exogenous DNA contamination. Combatting these issues requires extra measures of stringency in the lab and during data analysis, yet there have not been any high-throughput sequencing studies evaluating microsatellite allelic dropout from museum specimen extracted DNA. In this study, we evaluate genotyping errors derived from mammalian museum skin DNA extracts for previously characterized microsatellites across PCR replicates utilizing high-throughput sequencing. We found it useful to classify samples based on DNA concentration, which determined the rate by which genotypes were accurately recovered. Longer microsatellites performed worse in all museum specimens. Allelic dropout rates across loci were dependent on sample quantity, with high concentration museum specimens performing as well and recovering quality metrics nearly as high as the frozen tissue sample. Based on our results, we provide a set of best practices for quality assurance and incorporation of reliable genotypes from museum specimens.

Sign in / Sign up

Export Citation Format

Share Document