Small RNA and transcriptome sequencing of a symptomatic peony plant reveals mixed infections with novel viruses

Plant Disease ◽  
2021 ◽  
Author(s):  
Anning Jia ◽  
Chenge Yan ◽  
Hang Yin ◽  
Rui Sun ◽  
Fei Xia ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Small Rna ◽  
High Throughput Sequencing ◽  
Viral Infections ◽  
Triple Gene Block ◽  
Field Investigation ◽  
Mixed Infections ◽  
Species Classification ◽  
Gene Block ◽  
Sequence Identity

To identify the viruses in tree peony plants associated with the symptoms of yellowing, leaf rolling, stunted growth, and decline, high-throughput sequencing of small RNA and mRNA was conducted from a single symptomatic plant. Bioinformatic analyses and reconstruction of viral genomes indicated mixed viral infections involving cycas necrotic stunt virus (CNSV), apple stem grooving virus (ASGV), lychnis mottle virus (LycMoV), grapevine line pattern virus (GLPV), and three new viruses designated as peony yellowing-associated citrivirus (PYaCV, Citrivirus in Betaflexiviridae), peony betaflexivirus 1 (PeV1, unclassified in Betaflexiviridae), and peony leafroll-associated virus (PLRaV, Ampelovirus in Closteroviridae). PYaCV was 8,666 nucleaotides (nt) in length, comprising three open reading frames (ORFs) and shared 63.8–75.9% nucleotide sequence identity with citrus leaf blotch virus (CLBV) isolates. However, the ORF encoding the replication-associated protein (REP) shared 57% and 52% sequence identities at the nt and amino acid (aa) level, respectively, with other reported CLBV isolates, which were below the criterion for species classification within the family Betaflexiviridae. Recombination analysis identified putative recombination sites in PYaCV, which originated from CLBV. PeV1, only identified from the transcriptome data, was 8,124 nt in length with five ORFs encoding the REP (ORF1), triple gene block (TGB, ORF2–4) and coat protein (CP, ORF5) proteins. Phylogenetic analysis and sequence comparison showed that PeV1 clustered with an unassigned member, the garlic yellow mosaic-associated virus (GYMaV) within the Betaflexiviridae family, into a separate clade. Partial genome sequence analysis of PLRaV (12,545 nt) showed it contained seven ORFs encoding the partial polyprotein 1a, the RNA-dependent RNA polymerase (RdRp), two small hydrophobic proteins p11 and p6, HSP70h, p55, and a CP duplicate, which shared low aa sequence identity with Closteroviridae family members. Phylogenetic analysis based on the aa sequences of RdRp or HSP70h indicated that PLRaV clustered with grapevine leafroll-associated virus 1 (GLRaV-1) and GLRaV-13 in the Ampelovirus genus. Field investigation confirmed the wide distribution of these viruses, causing mixed infections of peony plants in Beijing.

scholarly journals Genomic Analyses of Cherry Rusty Mottle Group and Cherry Twisted Leaf-Associated Viruses Reveal a Possible New Genus Within the FamilyBetaflexiviridae

2015 ◽  
Vol 105 (3) ◽  
pp. 399-408 ◽  
Author(s):  
D. E. V. Villamor ◽  
J. Susaimuthu ◽  
K. C. Eastwell
Keyword(s):  
New Genus ◽  
High Throughput Sequencing ◽  
Prunus Avium ◽  
Triple Gene Block ◽  
Mottle Virus ◽  
Virus Species ◽  
Gene Block ◽  
Green Ring ◽  
The Family ◽  
Prunus Spp

It is demonstrated that closely related viruses within the family Betaflexiviridae are associated with a number of diseases that affect sweet cherry (Prunus avium) and other Prunus spp. Cherry rusty mottle-associated virus (CRMaV) is correlated with the appearance of cherry rusty mottle disease (CRMD), and Cherry twisted leaf-associated virus (CTLaV) is linked to cherry twisted leaf disease (CTLD) and apricot ringpox disease (ARPD). Comprehensive analysis of previously reported full genomic sequences plus those determined in this study representing isolates of CTLaV, CRMaV, Cherry green ring mottle virus, and Cherry necrotic rusty mottle virus revealed segregation of sequences into four clades corresponding to distinct virus species. High-throughput sequencing of RNA from representative source trees for CRMD, CTLD, and ARPD did not reveal additional unique virus sequences that might be associated with these diseases, thereby further substantiating the association of CRMaV and CTLaV with CRMD and CTLD or ARPD, respectively. Based on comparison of the nucleotide and amino acid sequence identity values, phylogenetic relationships with other triple-gene block-coding viruses within the family Betaflexiviridae, genome organization, and natural host range, a new genus (Robigovirus) is suggested.

scholarly journals A Virus in American Blackcurrant (Ribes americanum) with Distinct Genome Features Reshapes Classification in the Tymovirales

2018 ◽  
Author(s):  
Thanuja Thekke-Veetil ◽  
Thien Ho ◽  
Joseph D. Postman ◽  
Robert R. Martin ◽  
Ioannis E. Tzanetakis
Keyword(s):  
Genome Organization ◽  
High Throughput Sequencing ◽  
Triple Gene Block ◽  
Open Reading Frames ◽  
Methyl Transferase ◽  
Gene Block ◽  
New Family ◽  
Molecular Features ◽  
Genome Features ◽  
Novel Virus

A novel virus with distinct genome features was discovered by high throughput sequencing in a symptomatic blackcurrant plant. The virus tentatively named as blackcurrant virus A (BCVA) has distinct genome organization and molecular features bridging genera in the order Tymovirales. The genome consists of 7106 nucleotides excluding the poly(A) tail. Five open reading frames were identified with the first encoding a putative viral replicase with methyl transferase (MTR), AlkB, helicase and RNA dependent RNA polymerase (RdRp) domains. The other four putative proteins exhibit no significant homology to other virus proteins. The genome organization downstream of the replicase resembles that of members of the order Tymovirales with an unconventional triple gene block (TGB) movement protein arrangement. Phylogenetic analysis using replicase conserved motifs loosely placed BCVA within the Betaflexiviridae whereas it was evolutionarily distant to existing members of the family when using the putative TGBp 1-like and coat protein sequences. Our analysis strongly suggests that BCVA is a novel virus that should be classified as a species in a new genus in the Betaflexiviridae or a new family in the order Tymovirales.

scholarly journals High Throughput Sequencing-Aided Survey Reveals Widespread Mixed Infections of Whitefly-Transmitted Viruses in Cucurbits in Georgia, USA

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 988
Author(s):  
Saritha Raman Kavalappara ◽  
Hayley Milner ◽  
Naga Charan Konakalla ◽  
Kaelyn Morgan ◽  
Alton N. Sparks ◽  
...  
Keyword(s):  
Small Rna ◽  
High Throughput Sequencing ◽  
Mixed Infections ◽  
Genome Sequences ◽  
Rna Sequences ◽  
Southeastern Usa ◽  
Coding Regions ◽  
The Usa ◽  
Cucurbit Leaf Crumple Virus ◽  
Cucurbit Chlorotic Yellows Virus

Viruses transmitted by the sweet potato whitefly (Bemisia tabaci) have been detrimental to the sustainable production of cucurbits in the southeastern USA. Surveys were conducted in the fall of 2019 and 2020 in Georgia, a major cucurbit-producing state of the USA, to identify the viruses infecting cucurbits and their distribution. Symptomatic samples were collected and small RNA libraries were prepared and sequenced from three cantaloupes, four cucumbers, and two yellow squash samples. An analysis of the sequences revealed the presence of the criniviruses cucurbit chlorotic yellows virus (CCYV), cucurbit yellow stunting disorder virus (CYSDV), and the begomovirus cucurbit leaf crumple virus (CuLCrV). CuLCrV was detected in 76%, CCYV in 60%, and CYSDV in 43% of the total samples (n = 820) tested. The level of mixed infections was high in all the cucurbits, with most plants tested being infected with at least two of these viruses. Near-complete genome sequences of two criniviruses, CCYV and CYSDV, were assembled from the small RNA sequences. An analysis of the coding regions showed low genetic variability among isolates from different hosts. In phylogenetic analysis, the CCYV isolates from Georgia clustered with Asian isolates, while CYSDV isolates clustered with European and USA isolates. This work enhances our understanding of the distribution of viruses on cucurbits in South Georgia and will be useful to develop strategies for managing the complex of whitefly-transmitted viruses in the region.

scholarly journals A Virus in American Blackcurrant (Ribes americanum) with Distinct Genome Features Reshapes Classification in the Tymovirales

Viruses ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 406 ◽  
Author(s):  
Thanuja Thekke-Veetil ◽  
Thien Ho ◽  
Joseph Postman ◽  
Robert Martin ◽  
Ioannis Tzanetakis
Keyword(s):  
Genome Organization ◽  
High Throughput Sequencing ◽  
Triple Gene Block ◽  
Open Reading Frames ◽  
Methyl Transferase ◽  
Gene Block ◽  
New Family ◽  
Molecular Features ◽  
Genome Features ◽  
Novel Virus

A novel virus with distinct genome features was discovered by high throughput sequencing in a symptomatic blackcurrant plant. The virus, tentatively named Ribes americanum virus A (RAVA), has distinct genome organization and molecular features bridging genera in the order Tymovirales. The genome consists of 7106 nucleotides excluding the poly(A) tail. Five open reading frames were identified, with the first encoding a putative viral replicase with methyl transferase (MTR), AlkB, helicase, and RNA dependent RNA polymerase (RdRp) domains. The genome organization downstream of the replicase resembles that of members of the order Tymovirales with an unconventional triple gene block (TGB) movement protein arrangement with none of the other four putative proteins exhibiting significant homology to viral proteins. Phylogenetic analysis using replicase conserved motifs loosely placed RAVA within the Betaflexiviridae. Data strongly suggest that RAVA is a novel virus that should be classified as a species in a new genus in the Betaflexiviridae or a new family within the order Tymovirales.

scholarly journals Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing

Plants ◽  
2019 ◽  
Vol 8 (6) ◽  
pp. 167 ◽  
Author(s):  
Gonçalo Silva ◽  
Moritz Bömer ◽  
Ajith I. Rathnayake ◽  
Steven O. Sewe ◽  
Paul Visendi ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Triple Gene Block ◽  
Open Reading Frames ◽  
Virus Species ◽  
Gene Block ◽  
Full Diversity ◽  
Putative Coat Protein ◽  
The Family ◽  
International Distribution

To date, several viruses of different genera have been reported to infect yam (Dioscorea spp.). The full diversity of viruses infecting yam, however, remains to be explored. High-throughput sequencing (HTS) methods are increasingly being used in the discovery of new plant viral genomes. In this study, we employed HTS on yam to determine whether any undiscovered viruses were present that would restrict the international distribution of yam germplasm. We discovered a new virus sequence present in 31 yam samples tested and have tentatively named this virus “yam virus Y” (YVY). Twenty-three of the samples in which YVY was detected showed mosaic and chlorotic leaf symptoms, but Yam mosaic virus was also detected in these samples. Complete genome sequences of two YVY viral isolates were assembled and found to contain five open reading frames (ORFs). ORF1 encodes a large replication-associated protein, ORF2, ORF3 and ORF4 constitute the putative triple gene block proteins, and ORF5 encodes a putative coat protein. Considering the species demarcation criteria of the family Betaflexiviridae, YVY should be considered as a novel virus species in the family Betaflexiviridae. Further work is needed to understand the association of this new virus with any symptoms and yield loss and its implication on virus-free seed yam production.

scholarly journals Date palm virus A: first plant virus found in date palm trees

2020 ◽  
Author(s):  
Ayoub Maachi ◽  
Tatsuya Nagata ◽  
João Marcos Fagundes Silva
Keyword(s):  
Phylogenetic Analysis ◽  
High Throughput Sequencing ◽  
Date Palm ◽  
Genomic Sequence ◽  
Triple Gene Block ◽  
Gene Organization ◽  
Amino Acid Sequences ◽  
Sequencing Data ◽  
Novel Genus ◽  
The Family

AbstractIn this work, a novel ssRNA (+) viral genomic sequence with gene organization typical of members of the subfamily Quinvirinae (family Betaflexiviridae) was identified using high throughput sequencing data of date palm obtained from the Sequence Read Archive database. The viral genome sequence consists of 7860 nucleotides and contains five ORFs encoding for the replication protein (Rep), triple gene block proteins 1, 2, 3 (TGB 1, 2 and 3) and coat protein (CP). Phylogenetic analysis based on the Rep and the CP amino acid sequences showed the closest relationship to garlic yellow mosaic-associated virus (GYMaV). Based on the demarcation criteria of the family Betaflexiviridae, this new virus, provisionally named date palm virus A (DPVA), could constitute a member of a novel genus. However, considering that DPVA and GYMaV share the same genomic organization and that they cluster together on the Rep phylogenetic analysis, they could also constitute a novel genus together, highlighting the necessity of a revision of the taxonomic criteria of the family Betaflexiviridae.

scholarly journals Independent Expression of the First Two Triple Gene Block Proteins of Beet Necrotic Yellow Vein Virus Complements Virus Defective in the Corresponding Gene but Expression of the Third Protein Inhibits Viral Cell-to-Cell Movement

1997 ◽  
Vol 10 (2) ◽  
pp. 240-246 ◽  
Author(s):  
Claudine Bleykasten-Grosshans ◽  
H. Guilley ◽  
S. Bouzoubaa ◽  
K. E. Richards ◽  
G. Jonard
Keyword(s):  
Triple Gene Block ◽  
Cell Movement ◽  
Viral Rna ◽  
Yellow Vein ◽  
Mixed Infections ◽  
Subgenomic Rna ◽  
Gene Block ◽  
The Third ◽  
Local Lesion Formation ◽  
P15 Gene

Cell-to-cell movement of beet necrotic yellow vein furovirus is controlled by three slightly overlapping genes on RNA 2 called the triple gene block (TGB) encoding, in order, P42, P13, and P15. Synthesis of P42 is directed by subgenomic RNA 2suba while synthesis of both P13 and P15 is probably directed by a dicistronic subgenomic RNA, 2subb. For complementation experiments, each TGB protein gene was inserted into a “replicon” derived from viral RNA 3. In mixed infections, the replicons expressing P42 and P13 complemented RNA 2 mutants defective in the corresponding gene. A P15-containing replicon did not complement a P15-defective RNA 2 but complementation was observed with a dicistronic replicon containing the P15 gene placed behind the P13 gene. In mixed infections with wild-type viral RNAs, the P15-containing replicon did not inhibit viral RNA replication in protoplasts but blocked local lesion formation on leaves. Infection of leaves was also inhibited by an RNA3-derived replicon containing the third TGB gene from another furovirus, peanut clump virus. The results are consistent with a model in which viral cell-to-cell movement requires production of appropriate relative amounts of P13 and P15, and their expression from a dicistronic subgenomic RNA provides a mechanism for coordinating their synthesis.

scholarly journals Small RNA sequencing reveals distinct nuclear microRNAs in pig granulosa cells during ovarian follicle growth

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Derek Toms ◽  
Bo Pan ◽  
Yinshan Bai ◽  
Julang Li
Keyword(s):  
Granulosa Cells ◽  
Small Rna ◽  
High Throughput Sequencing ◽  
Ovarian Function ◽  
Ovarian Follicle ◽  
Small Rna Sequencing ◽  
Cell Fractionation ◽  
Steroid Synthesis ◽  
Non Coding Rna ◽  
Dna Binding Sites

AbstractNuclear small RNAs have emerged as an important subset of non-coding RNA species that are capable of regulating gene expression. A type of small RNA, microRNA (miRNA) have been shown to regulate development of the ovarian follicle via canonical targeting and translational repression. Little has been done to study these molecules at a subcellular level. Using cell fractionation and high throughput sequencing, we surveyed cytoplasmic and nuclear small RNA found in the granulosa cells of the pig ovarian antral preovulatory follicle. Bioinformatics analysis revealed a diverse network of small RNA that differ in their subcellular distribution and implied function. We identified predicted genomic DNA binding sites for nucleus-enriched miRNAs that may potentially be involved in transcriptional regulation. The small nucleolar RNA (snoRNA) SNORA73, known to be involved in steroid synthesis, was also found to be highly enriched in the cytoplasm, suggesting a role for snoRNA species in ovarian function. Taken together, these data provide an important resource to study the small RNAome in ovarian follicles and how they may impact fertility.

scholarly journals Metagenomic Analysis of Marigold: Mixed Infection Including Two New Viruses

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1254
Author(s):  
Hang Yin ◽  
Zheng Dong ◽  
Xulong Wang ◽  
Shuhao Lu ◽  
Fei Xia ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mosaic Virus ◽  
Complete Genome ◽  
Plum Pox Virus ◽  
Cryptic Virus ◽  
Sequence Identity ◽  
Complete Genome Sequence Analysis ◽  
Wilt Virus ◽  
Broad Bean Wilt Virus

Marigold plants with symptoms of mosaic, crinkle, leaf curl and necrosis were observed and small RNA and ribo-depleted total RNA deep sequencing were conducted to identify the associated viruses. Broad bean wilt virus 2, cucumber mosaic virus, turnip mosaic virus, a new potyvirus tentatively named marigold mosaic virus (MMV) and a new partitivirus named as marigold cryptic virus (MCV) were finally identified. Complete genome sequence analysis showed MMV was 9811 nt in length, encoding a large polyprotein with highest aa sequence identity (57%) with the putative potyvirus polygonatumkingianum virus 1. Phylogenetic analysis with the definite potyviruses based on the polyprotein sequence showed MMV clustered closest to plum pox virus. The complete genome of MCV comprised of dsRNA1 (1583 bp) and dsRNA2 (1459 bp), encoding the RNA-dependent RNA polymerase (RdRp), and coat protein (CP), respectively. MCV RdRp shared the highest (75.7%) aa sequence identity with the unclassified partitivirus ambrosia cryptic virus 2, and 59.0%, 57.1%, 56.1%, 54.5% and 33.7% with the corresponding region of the definite delta-partitiviruses, pepper cryptic virus 2, beet cryptic virus 3, beet cryptic virus 2, pepper cryptic virus 1 and fig cryptic virus, respectively. Phylogenetic analysis based on the RdRp aa sequence showed MCV clustered into the delta-partitivirus group. These findings enriched our knowledge of viruses infecting marigold, but the association of the observed symptom and the identified viruses and the biological characterization of the new viruses should be further investigated.

scholarly journals Genetic diversity of cutaneous human papillomaviruses

2007 ◽  
Vol 88 (10) ◽  
pp. 2662-2669 ◽  
Author(s):  
Ola Forslund
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Human Skin ◽  
Human Papillomaviruses ◽  
Sequence Identity ◽  
Hpv Types

Human papillomaviruses (HPVs) of the genera Betapapillomavirus and Gammapapillomavirus are common on human skin. Sequencing of subgenomic amplicons of cutaneous HPVs has revealed a large number of novel putative HPV types within these genera. Phylogenetic analysis based on these amplicons revealed 133 putative HPV types with <90 % sequence identity to any known HPV type or to each other. As there are already 34 characterized HPV types described within the genera Betapapillomavirus and Gammapapillomavirus, they appear to be the most genetically diverse of the HPVs, apparently comprising at least 167 different HPV types.

Sign in / Sign up

Export Citation Format

Share Document