scholarly journals High global diversity of cycloviruses amongst dragonflies

2013 ◽  
Vol 94 (8) ◽  
pp. 1827-1840 ◽  
Author(s):  
Anisha Dayaram ◽  
Kristen A. Potter ◽  
Angela B. Moline ◽  
Dana Drake Rosenstein ◽  
Milen Marinov ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Genome Structure ◽  
Sister Group ◽  
Regulatory Elements ◽  
Intergenic Regions ◽  
The Usa ◽  
Circular Ssdna ◽  
Insect Populations ◽  
Ssdna Viruses

Members of the family Circoviridae, specifically the genus Circovirus, were thought to infect only vertebrates; however, members of a sister group under the same family, the proposed genus Cyclovirus, have been detected recently in insects. In an effort to explore the diversity of cycloviruses and better understand the evolution of these novel ssDNA viruses, here we present five cycloviruses isolated from three dragonfly species (Orthetrum sabina, Xanthocnemis zealandica and Rhionaeschna multicolor) collected in Australia, New Zealand and the USA, respectively. The genomes of these five viruses share similar genome structure to other cycloviruses, with a circular ~1.7 kb genome and two major bidirectionally transcribed ORFs. The genomic sequence data gathered during this study were combined with all cyclovirus genomes available in public databases to identify conserved motifs and regulatory elements in the intergenic regions, as well as determine diversity and recombinant regions within their genomes. The genomes reported here represent four different cyclovirus species, three of which are novel. Our results confirm that cycloviruses circulate widely in winged-insect populations; in eight different cyclovirus species identified in dragonflies to date, some of these exhibit a broad geographical distribution. Recombination analysis revealed both intra- and inter-species recombination events amongst cycloviruses, including genomes recovered from disparate sources (e.g. goat meat and human faeces). Similar to other well-characterized circular ssDNA viruses, recombination may play an important role in cyclovirus evolution.

scholarly journals Reconstructing the phylogeny of new world monkeys (platyrrhini): evidence from multiple non-coding loci

2018 ◽  
Vol 65 (5) ◽  
pp. 579-588 ◽  
Author(s):  
Xiaoping Wang ◽  
Burton K Lim ◽  
Nelson Ting ◽  
Jingyang Hu ◽  
Yunpeng Liang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
New World ◽  
Sequence Data ◽  
Sister Group ◽  
New World Monkeys ◽  
Independent Sequence ◽  
Tree Inference ◽  
Intergenic Regions ◽  
Group Relationships ◽  
Rapid Radiations

Abstract Among mammalian phylogenies, those characterized by rapid radiations are particularly problematic. The New World monkeys (NWMs, Platyrrhini) comprise 3 families and 7 subfamilies, which radiated within a relatively short time period. Accordingly, their phylogenetic relationships are still largely disputed. In the present study, 56 nuclear non-coding loci, including 33 introns (INs) and 23 intergenic regions (IGs), from 20 NWM individuals representing 18 species were used to investigate phylogenetic relationships among families and subfamilies. Of the 56 loci, 43 have not been used in previous NWM phylogenetics. We applied concatenation and coalescence tree-inference methods, and a recently proposed question-specific approach to address NWM phylogeny. Our results indicate incongruence between concatenation and coalescence methods for the IN and IG datasets. However, a consensus was reached with a single tree topology from all analyses of combined INs and IGs as well as all analyses of question-specific loci using both concatenation and coalescence methods, albeit with varying degrees of statistical support. In detail, our results indicated the sister-group relationships between the families Atelidae and Pitheciidae, and between the subfamilies Aotinae and Callithrichinae among Cebidae. Our study provides insights into the disputed phylogenetic relationships among NWM families and subfamilies from the perspective of multiple non-coding loci and various tree-inference approaches. However, the present phylogenetic framework needs further evaluation by adding more independent sequence data and a deeper taxonomic sampling. Overall, our work has important implications for phylogenetic studies dealing with rapid radiations.

scholarly journals Diverse circular ssDNA viruses discovered in dragonflies (Odonata: Epiprocta)

2012 ◽  
Vol 93 (12) ◽  
pp. 2668-2681 ◽  
Author(s):  
Karyna Rosario ◽  
Anisha Dayaram ◽  
Milen Marinov ◽  
Jessica Ware ◽  
Simona Kraberger ◽  
...  
Keyword(s):  
Rolling Circle Amplification ◽  
Molecular Techniques ◽  
Limited Information ◽  
Dna Viruses ◽  
Rolling Circle ◽  
Viral Genomes ◽  
Initiator Protein ◽  
Circular Ssdna ◽  
Insect Populations ◽  
Ssdna Viruses

Viruses with circular ssDNA genomes that encode a replication initiator protein (Rep) are among the smallest viruses known to infect both eukaryotic and prokaryotic organisms. In the past few years an overwhelming diversity of novel circular Rep-encoding ssDNA (CRESS-DNA) viruses has been unearthed from various hosts and environmental sources. Since there is limited information regarding CRESS-DNA viruses in invertebrates, this study explored the diversity of CRESS-DNA viruses circulating among insect populations by targeting dragonflies (Epiprocta), top insect predators that accumulate viruses from their insect prey over space and time. Using degenerate PCR and rolling circle amplification coupled with restriction digestion, 17 CRESS-DNA viral genomes were recovered from eight different dragonfly species collected in tropical and temperate regions. Nine of the genomes are similar to cycloviruses and represent five species within this genus, suggesting that cycloviruses are commonly associated with insects. Three of the CRESS-DNA viruses share conserved genomic features with recently described viruses similar to the mycovirus Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1, leading to the proposal of the genus Gemycircularvirus. The remaining viruses are divergent species representing four novel CRESS-DNA viral genera, including a gokushovirus-like prokaryotic virus (microphage) and three eukaryotic viruses with Reps similar to circoviruses. The novelty of CRESS-DNA viruses identified in dragonflies using simple molecular techniques indicates that there is an unprecedented diversity of ssDNA viruses among insect populations.

scholarly journals Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Brayon J. Fremin ◽  
Ami S. Bhatt
Keyword(s):  
Comparative Genomics ◽  
Large Scale ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Human Microbiome ◽  
Automated Analysis ◽  
Metagenomic Data ◽  
Coding Regions ◽  
Intergenic Regions ◽  
Computationally Intensive

Abstract Background Structured RNAs play varied bioregulatory roles within microbes. To date, hundreds of candidate structured RNAs have been predicted using informatic approaches that search for motif structures in genomic sequence data. The human microbiome contains thousands of species and strains of microbes. Yet, much of the metagenomic data from the human microbiome remains unmined for structured RNA motifs primarily due to computational limitations. Results We sought to apply a large-scale, comparative genomics approach to these organisms to identify candidate structured RNAs. With a carefully constructed, though computationally intensive automated analysis, we identify 3161 conserved candidate structured RNAs in intergenic regions, as well as 2022 additional candidate structured RNAs that may overlap coding regions. We validate the RNA expression of 177 of these candidate structures by analyzing small fragment RNA-seq data from four human fecal samples. Conclusions This approach identifies a wide variety of candidate structured RNAs, including tmRNAs, antitoxins, and likely ribosome protein leaders, from a wide variety of taxa. Overall, our pipeline enables conservative predictions of thousands of novel candidate structured RNAs from human microbiomes.

Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

2019 ◽  
Vol 44 (4) ◽  
pp. 930-942
Author(s):  
Geraldine A. Allen ◽  
Luc Brouillet ◽  
John C. Semple ◽  
Heidi J. Guest ◽  
Robert Underhill
Keyword(s):  
North American ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Morphological Evidence ◽  
South American ◽  
New Combinations ◽  
The North ◽  
Hybridization Event ◽  
Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

PoGB-Pred: Prediction of Antifreeze Proteins Sequences using Amino Acid Composition with Feature Selection followed by a Sequential based Ensemble Approach

2020 ◽  
Vol 15 ◽  
Author(s):  
Affan Alim ◽  
Abdul Rafay ◽  
Imran Naseem
Keyword(s):  
Amino Acid ◽  
Dimension Reduction ◽  
Protein Identification ◽  
Cold Water ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Antifreeze Proteins ◽  
Building Blocks ◽  
Gradient Boosting ◽  
Proposed Model

Background: Proteins contribute significantly in every task of cellular life. Their functions encompass the building and repairing of tissues in human bodies and other organisms. Hence they are the building blocks of bones, muscles, cartilage, skin, and blood. Similarly, antifreeze proteins are of prime significance for organisms that live in very cold areas. With the help of these proteins, the cold water organisms can survive below zero temperature and resist the water crystallization process which may cause the rupture in the internal cells and tissues. AFP’s have attracted attention and interest in food industries and cryopreservation. Objective: With the increase in the availability of genomic sequence data of protein, an automated and sophisticated tool for AFP recognition and identification is in dire need. The sequence and structures of AFP are highly distinct, therefore, most of the proposed methods fail to show promising results on different structures. A consolidated method is proposed to produce the competitive performance on highly distinct AFP structure. Methods: In this study, we propose to use machine learning-based algorithms Principal Component Analysis (PCA) followed by Gradient Boosting (GB) for antifreeze protein identification. To analyze the performance and validation of the proposed model, various combinations of two segments composition of amino acid and dipeptide are used. PCA, in particular, is proposed to dimension reduction and high variance retaining of data which is followed by an ensemble method named gradient boosting for modelling and classification. Results: The proposed method obtained the superfluous performance on PDB, Pfam and Uniprot dataset as compared with the RAFP-Pred method. In experiment-3, by utilizing only 150 PCA components a high accuracy of 89.63 was achieved which is superior to the 87.41 utilizing 300 significant features reported for the RAFP-Pred method. Experiment-2 is conducted using two different dataset such that non-AFP from the PISCES server and AFPs from Protein data bank. In this experiment-2, our proposed method attained high sensitivity of 79.16 which is 12.50 better than state-of-the-art the RAFP-pred method. Conclusion: AFPs have a common function with distinct structure. Therefore, the development of a single model for different sequences often fails to AFPs. A robust results have been shown by our proposed model on the diversity of training and testing dataset. The results of the proposed model outperformed compared to the previous AFPs prediction method such as RAFP-Pred. Our model consists of PCA for dimension reduction followed by gradient boosting for classification. Due to simplicity, scalability properties and high performance result our model can be easily extended for analyzing the proteomic and genomic dataset.

scholarly journals Special Issue: Genetic Basis of Phenotypic Variation in Drosophila and Other Insects

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1212
Author(s):  
J. Spencer Johnston ◽  
Carl E. Hjelmen
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Basis ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Complete Genomic Sequence ◽  
Special Issue ◽  
Model Species ◽  
Road Map ◽  
Generation Sequencing ◽  
Complete Genomic

Next-generation sequencing provides a nearly complete genomic sequence for model and non-model species alike; however, this wealth of sequence data includes no road map [...]

scholarly journals Sequence data from isolated lichen-associated melanized fungi enhance delimitation of two new lineages within Chaetothyriomycetidae

2021 ◽  
Vol 20 (7) ◽  
pp. 911-927
Author(s):  
Lucia Muggia ◽  
Yu Quan ◽  
Cécile Gueidan ◽  
Abdullah M. S. Al-Hatmi ◽  
Martin Grube ◽  
...  
Keyword(s):  
Sequence Data ◽  
Single Species ◽  
Sister Group ◽  
Asexual Propagation ◽  
Dna Sequence Data ◽  
Wide Range ◽  
The Family ◽  
Rock Inhabiting Fungi ◽  
Stable Habitat

AbstractLichen thalli provide a long-lived and stable habitat for colonization by a wide range of microorganisms. Increased interest in these lichen-associated microbial communities has revealed an impressive diversity of fungi, including several novel lineages which still await formal taxonomic recognition. Among these, members of the Eurotiomycetes and Dothideomycetes usually occur asymptomatically in the lichen thalli, even if they share ancestry with fungi that may be parasitic on their host. Mycelia of the isolates are characterized by melanized cell walls and the fungi display exclusively asexual propagation. Their taxonomic placement requires, therefore, the use of DNA sequence data. Here, we consider recently published sequence data from lichen-associated fungi and characterize and formally describe two new, individually monophyletic lineages at family, genus, and species levels. The Pleostigmataceae fam. nov. and Melanina gen. nov. both comprise rock-inhabiting fungi that associate with epilithic, crust-forming lichens in subalpine habitats. The phylogenetic placement and the monophyly of Pleostigmataceae lack statistical support, but the family was resolved as sister to the order Verrucariales. This family comprises the species Pleostigma alpinum sp. nov., P. frigidum sp. nov., P. jungermannicola, and P. lichenophilum sp. nov. The placement of the genus Melanina is supported as a lineage within the Chaetothyriales. To date, this genus comprises the single species M. gunde-cimermaniae sp. nov. and forms a sister group to a large lineage including Herpotrichiellaceae, Chaetothyriaceae, Cyphellophoraceae, and Trichomeriaceae. The new phylogenetic analysis of the subclass Chaetothyiomycetidae provides new insight into genus and family level delimitation and classification of this ecologically diverse group of fungi.

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 316-324 ◽  
Author(s):  
Jongsik Chun ◽  
Fred A. Rainey
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Original Research ◽  
Rrna Gene ◽  
New Taxon ◽  
Genome Sequences ◽  
Microbial World ◽  
Content Type ◽  
Link Type ◽  
Type Strains

The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

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