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Navarro B.,CNR Institute of Neuroscience | Aboughanem-Sabanadzovic N.,Institute for Genomics | Ragozzino A.,University of Naples Federico II | Ragozzino E.,University of Naples Federico II | Di Serio F.,CNR Institute of Neuroscience
Molecular Plant Pathology | Year: 2016

A novel virus has been identified by next-generation sequencing (NGS) in privet (Ligustrum japonicum L.) affected by a graft-transmissible disease characterized by leaf blotch symptoms resembling infectious variegation, a virus-like privet disease with an unclear aetiology. This virus, which has been tentatively named 'privet leaf blotch-associated virus' (PrLBaV), was absent in non-symptomatic privet plants, as revealed by NGS and reverse transcription-polymerase chain reaction (RT-PCR). Molecular characterization of PrLBaV showed that it has a segmented genome composed of two positive single-stranded RNAs, one of which (RNA1) is monocistronic and codes for the viral replicase, whereas the other (RNA2) contains two open reading frames (ORFs), ORF2a and ORF2b, coding for the putative movement (p38) and coat (p30) proteins, respectively. ORF2b is very probably expressed through a subgenomic RNA starting with six nucleotides (AUAUCU) that closely resemble those found in the 5′-terminal end of genomic RNA1 and RNA2 (AUAUUU and AUAUAU, respectively). The molecular signatures identified in the PrLBaV RNAs and proteins resemble those of Raspberry bushy dwarf virus (RBDV), currently the only member of the genus Idaeovirus. These data, together with phylogenetic analyses, are consistent with the proposal of considering PrLBaV as a representative of the second species in the genus Idaeovirus. Transient expression of a recombinant PrLBaV p38 fused to green fluorescent protein in leaves of Nicotiana benthamiana, coupled with confocal laser scanning microscopy assays, showed that it localizes at cell plasmodesmata, strongly supporting its involvement in viral movement/trafficking and providing the first functional characterization of an idaeovirus encoded protein. © 2016 BSPP AND JOHN WILEY & SONS LTD.


Lavoie C.A.,Institute for Genomics | Platt R.N.,Institute for Genomics | Novick P.A.,York College | Ray D.A.,Institute for Genomics | Ray D.A.,Texas Tech University
Mobile DNA | Year: 2013

Abstract. Background: Transposable elements (TEs) have the potential to impact genome structure, function and evolution in profound ways. In order to understand the contribution of transposable elements (TEs) to Heliconius melpomene, we queried the H. melpomene draft sequence to identify repetitive sequences. Results: We determined that TEs comprise ∼25% of the genome. The predominant class of TEs (∼12% of the genome) was the non-long terminal repeat (non-LTR) retrotransposons, including a novel SINE family. However, this was only slightly higher than content derived from DNA transposons, which are diverse, with several families having mobilized in the recent past. Compared to the only other well-studied lepidopteran genome, Bombyx mori, H. melpomene exhibits a higher DNA transposon content and a distinct repertoire of retrotransposons. We also found that H. melpomene exhibits a high rate of TE turnover with few older elements accumulating in the genome. Conclusions: Our analysis represents the first complete, de novo characterization of TE content in a butterfly genome and suggests that, while TEs are able to invade and multiply, TEs have an overall deleterious effect and/or that maintaining a small genome is advantageous. Our results also hint that analysis of additional lepidopteran genomes will reveal substantial TE diversity within the group. © 2013 Lavoie et al.; licensee BioMed Central Ltd.


Sabanadzovic S.,Mississippi State University | Wintermantel W.M.,U.S. Department of Agriculture | Valverde R.A.,Louisiana State University | McCreight J.D.,U.S. Department of Agriculture | Aboughanem-Sabanadzovic N.,Institute for Genomics
Virus Research | Year: 2016

A high molecular weight dsRNA was isolated from a Cucumis melo L. plant (referred to as 'CL01') of an unknown cultivar and completely sequenced. Sequence analyses showed that dsRNA is associated with an endornavirus for which a name Cucumis melo endornavirus (CmEV) is proposed. The genome of CmEV-CL01 consists of 15,078 nt, contains a single, 4939 codons-long ORF and terminates with a stretch of 10 cytosine residues. Comparisons of the putative CmEV-encoded polyprotein with available references in protein databases revealed a unique genome organization characterized by the presence of the following domains: viral helicase Superfamily 1 (Hel-1), three glucosyltransferases (doublet of putative capsular polysaccharide synthesis proteins and a putative C_28_Glycosyltransferase), and an RNA-dependent RNA polymerase (RdRp). The presence of three glycome-related domains of different origin makes the genome organization of CmEV unique among endornaviruses. Phylogenetic analyses of viral RdRp domains showed that CmEV belongs to a specific lineage within the family Endornaviridae made exclusively of plant-infecting endornaviruses. An RT-PCR based survey demonstrated high incidence of CmEV among melon germplasm accession (>87% of tested samples). Analyses of partial genome sequences of CmEV isolates from 26 different melon genotypes suggest fine-tuned virus adaptation and co-divergence with the host. Finally, results of the present study revealed that CmEV is present in plants belonging to three different genera in the family Cucurbitaceae. Such diverse host range is unreported for known endornaviruses and suggests a long history of CmEV association with cucurbits predating their speciation. © 2016 Elsevier B.V..


PubMed | Institute for Genomics, Louisiana State University, U.S. Department of Agriculture and Mississippi State University
Type: | Journal: Virus research | Year: 2016

A high molecular weight dsRNA was isolated from a Cucumis melo L. plant (referred to as CL01) of an unknown cultivar and completely sequenced. Sequence analyses showed that dsRNA is associated with an endornavirus for which a name Cucumis melo endornavirus (CmEV) is proposed. The genome of CmEV-CL01 consists of 15,078 nt, contains a single, 4939 codons-long ORF and terminates with a stretch of 10 cytosine residues. Comparisons of the putative CmEV-encoded polyprotein with available references in protein databases revealed a unique genome organization characterized by the presence of the following domains: viral helicase Superfamily 1 (Hel-1), three glucosyltransferases (doublet of putative capsular polysaccharide synthesis proteins and a putative C_28_Glycosyltransferase), and an RNA-dependent RNA polymerase (RdRp). The presence of three glycome-related domains of different origin makes the genome organization of CmEV unique among endornaviruses. Phylogenetic analyses of viral RdRp domains showed that CmEV belongs to a specific lineage within the family Endornaviridae made exclusively of plant-infecting endornaviruses. An RT-PCR based survey demonstrated high incidence of CmEV among melon germplasm accession (>87% of tested samples). Analyses of partial genome sequences of CmEV isolates from 26 different melon genotypes suggest fine-tuned virus adaptation and co-divergence with the host. Finally, results of the present study revealed that CmEV is present in plants belonging to three different genera in the family Cucurbitaceae. Such diverse host range is unreported for known endornaviruses and suggests a long history of CmEV association with cucurbits predating their speciation.


Aboughanem-Sabanadzovic N.,Institute for Genomics | Tzanetakis I.E.,University of Arkansas | Lawrence A.,Mississippi State University | Stephenson R.C.,Mississippi State University | Sabanadzovic S.,Mississippi State University
Phytopathology | Year: 2016

Necrotic ringspot disease (NRSD) is a graft-transmissible disorder of privet (synonym ligustrum), originally reported from Florida and Louisiana more than 50 years ago. In this communication we report an isometric virus isolated from Japanese privet (Ligustrum japonicum) collected in the southern United States displaying symptoms resembling those of NRSD. In mechanical transmission tests, the virus induced systemic infections in several herbaceous hosts. Double-stranded RNA analysis showed a pattern resembling replicative forms of members of the family Bromoviridae. The genome organization along with phylogenetic analyses and serological tests revealed that the virus belongs to subgroup 1 of the genus Ilarvirus. Pairwise comparisons with recognized ilarviruses indicated that the virus is a distinct, and as yet, undescribed member in the taxon, for which we propose the name Privet ringspot virus (PrRSV). Furthermore, the nearperfect association of PrRSV infections with symptoms, and apparent absence of any other virus(es) in studied samples, strongly suggest an important role of this virus in the etiology of NRSD of privet in the southeastern United States. © 2016 The American Phytopathological Society.


Liu W.,Mississippi State University | Thummasuwan S.,Mississippi State University | Sehgal S.K.,Kansas State University | Chouvarine P.,Mississippi State University | And 3 more authors.
BMC Genomics | Year: 2011

Background: Bald cypress (Taxodium distichum var. distichum) is a coniferous tree of tremendous ecological and economic importance. It is a member of the family Cupressaceae which also includes cypresses, redwoods, sequoias, thujas, and junipers. While the bald cypress genome is more than three times the size of the human genome, its 1C DNA content is amongst the smallest of any conifer. To learn more about the genome of bald cypress and gain insight into the evolution of Cupressaceae genomes, we performed a Cot analysis and used Cot filtration to study Taxodium DNA. Additionally, we constructed a 6.7 genome-equivalent BAC library that we screened with known Taxodium genes and select repeats.Results: The bald cypress genome is composed of 90% repetitive DNA with most sequences being found in low to mid copy numbers. The most abundant repeats are found in fewer than 25,000 copies per genome. Approximately 7.4% of the genome is single/low-copy DNA (i.e., sequences found in 1 to 5 copies). Sequencing of highly repetitive Cot clones indicates that most Taxodium repeats are highly diverged from previously characterized plant repeat sequences. The bald cypress BAC library consists of 606,336 clones (average insert size of 113 kb) and collectively provides 6.7-fold genome equivalent coverage of the bald cypress genome. Macroarray screening with known genes produced, on average, about 1.5 positive clones per probe per genome-equivalent. Library screening with Cot-1 DNA revealed that approximately 83% of BAC clones contain repetitive sequences iterated 103to 104times per genome.Conclusions: The BAC library for bald cypress is the first to be generated for a conifer species outside of the family Pinaceae. The Taxodium BAC library was shown to be useful in gene isolation and genome characterization and should be an important tool in gymnosperm comparative genomics, physical mapping, genome sequencing, and gene/polymorphism discovery. The single/low-copy (SL) component of bald cypress is 4.6 times the size of the Arabidopsis genome. As suggested for other gymnosperms, the large amount of SL DNA in Taxodium is likely the result of divergence among ancient repeat copies and gene/pseudogene duplication. © 2011 Liu et al; licensee BioMed Central Ltd.


News Article | March 23, 2016
Site: www.scientificcomputing.com

A research team has released a new version of MEGA (Molecular Evolutionary Genomics Analysis) software, one of the most highly downloaded and widely used tools used by scientists worldwide to harness large-scale DNA sets for comparative studies. At its core, MEGA is a powerful bioinformatics tool designed to help researchers identify key patterns among the diversity and complexity of life on Earth, and unravel the mysteries of human evolution, health and disease coded within the genome. The MEGA7 edition, developed by Temple University professor Sudhir Kumar, Glen Stecher and Tokyo Metropolitan University professor Koichiro Tamura, represents the most sophisticated, powerful and advanced version yet, designed to extend its use to ever more complex and large DNA analysis datasets. "We've done a significant upgrade of MEGA, which was necessary to speed up the data-crunching time and memory usage with 64 bit processors, and much larger memory space to handle gigabytes of data, so now people can analyze an ever larger amount of sequences," said Kumar, who directs the Institute for Genomics and Evolutionary Medicine at Temple. For Kumar, making the software freely available to the scientific community is a key to propelling worldwide evolutionary discoveries. "MEGA has been freely available for over 20 years for any use, spanning research, teaching and industry. We enable people throughout the world, including developing nations, to use fundamental technologies that are needed to address these burgeoning sequence databases. "Everyone in the world should be able to use evolutionary and genomics tools to analyze the wealth of information that is being produced relating the genomes of humans to pathogens, to disease to traits, to uncover our similarities and differences. It will take all of our global efforts to do so. The most important thing is to develop user-friendly, sophisticated software for use by all." MEGA has one of the largest user-bases, and has been downloaded more than 1.1 million times across 184 countries. The latest improvements are only likely to increase its usage in the scientific community, MEGA is cited in more than 10,000 publications annually, making it one of the most cited bioinformatics tools in teaching and research for those uncovering the secrets of the complex, four-billion-year evolutionary history of life on Earth.


At its core, MEGA is a powerful bioinformatics tool designed to help researchers identify key patterns among the diversity and complexity of life on Earth, and unravel the mysteries of human evolution, health and disease coded within the genome. The MEGA7 edition, developed by Temple University professor Sudhir Kumar, Glen Stecher and Tokyo Metropolitan University professor Koichiro Tamura, represents the most sophisticated, powerful and advanced version yet, designed to extend its use to ever more complex and large DNA analysis datasets. "We've done a significant upgrade of MEGA, which was necessary to speed up the data-crunching time and memory usage with 64 bit processors, and much larger memory space to handle gigabytes of data, so now people can analyze an ever larger amount of sequences," said Kumar, who directs the Institute for Genomics and Evolutionary Medicine at Temple. For Kumar, making the software freely available to the scientific community is a key to propelling worldwide evolutionary discoveries. "MEGA has been freely available for over 20 years for any use, spanning research, teaching and industry. We enable people throughout the world, including developing nations, to use fundamental technologies that are needed to address these burgeoning sequence databases. "Everyone in the world should be able to use evolutionary and genomics tools to analyze the wealth of information that is being produced relating the genomes of humans to pathogens, to disease to traits, to uncover our similarities and differences. It will take all of our global efforts to do so. The most important thing is to develop user-friendly, sophisticated software for use by all." MEGA has one of the largest user-bases, and has been downloaded more than 1.1 million times across 184 countries. The latest improvements are only likely to increase its usage in the scientific community, MEGA is cited in more than 10,000 publications annually, making it one of the most cited bioinformatics tools in teaching and research for those uncovering the secrets of the complex, 4 billion year evolutionary history of life on Earth. Explore further: Professor uses evolution, informatics to uncover secrets of the genome

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