Coevolution of a Persistent Plant Virus and Its Pepper Hosts

There are many nonpathogenic viruses that are maintained in a persistent lifestyle in plants. Plant persistent viruses are widespread, replicating in their hosts for many generations. So far, Endornaviridae is the only family of plant persistent viruses with a single-stranded RNA genome, containing one large open reading frame. Bell pepper endornavirus (BPEV), Hot pepper endornavirus, Capsicum frutescens endornavirus 1 (CFEV 1) have been identified from peppers. Peppers are native to Central and South America and, as domesticated plants, human selection accelerated their evolution. We investigated the evolution of these endornaviruses in different peppers including Capsicum annuum, C. chacoense, C. chinense, C. frutescens, C. baccutum, and C. pubescens using two fragments from the viral helicase (Hel) and RNA dependent RNA polymerase (RdRp) domains. In addition, using single nucleotide polymorphisms, we analyzed the pepper host populations and phylogenies. The endornaviruses phylogeny was correlated with its Capsicum species host. In this study, BPEV was limited to C. annuum species, and the RdRp and Hel phylogenies identified two clades that correlated with the host pungency. No C. annuum infected with CFEV 1 was found in this study, but the CFEV 1 RdRp fragment was recovered from C. chinense, C. frutescens, C. baccutum, and C. pubescens. Hence, during pepper speciation, the ancestor of CFEV 1 may have evolved as a new endornavirus, BPEV, in C. annuum peppers.

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Molecular Cloning, Expression Profiling, and Marker Validation of the Chicken Myoz3 Gene

BioMed Research International ◽

10.1155/2017/5930918 ◽

2017 ◽

Vol 2017 ◽

pp. 1-10 ◽

Cited By ~ 1

Author(s):

Maosen Ye ◽

Fei Ye ◽

Liutao He ◽

Yiping Liu ◽

Xiaoling Zhao ◽

...

Keyword(s):

Expression Profiling ◽

Fiber Type ◽

Breast Muscle ◽

Nucleotide Polymorphisms ◽

Amino Acid Sequence Analysis ◽

Single Nucleotide ◽

Reading Frame ◽

Marker Validation ◽

Basic Characteristics ◽

Fiber Type Differentiation

Myozenin3 (Myoz3) has been reported to bind multiple Z-disc proteins and hence play a key role in signal transduction and muscle fiber type differentiation. The purpose of current study is to better understand the basic characteristics of Myoz3. Firstly, we cloned the ORF (open reading frame) of the Myoz3 gene. AA (amino acid) sequence analysis revealed that the Myoz3 gene encodes a 26 kDa protein which have 97% identities with that of turkey. Expression profiling showed that Myoz3 mRNA is mainly expressed in leg muscle and breast muscle. Furthermore, we investigated Myoz3 gene polymorphisms in two broiler breeds, the Yellow Bantam (YB) and the Avian. Five SNPs (single nucleotide polymorphisms) were identified in the YB breed and 3 were identified in the Avian breed. Genotypes and haplotype were constructed and their associations with carcass traits were analyzed. In the YB breed, c.516 C>T had a strong effect on both shank bone length and the L⁎ value of breast muscle, and the H1H3 diplotype had the highest FC compared to other diplotypes. The markers identified in this study may serve as useful targets for the marker-assisted selection (MAS) of growth and meat quality traits in chickens.

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An exploration of ambigrammatic sequences in narnaviruses

10.1101/761890 ◽

2019 ◽

Author(s):

Joseph L. DeRisi ◽

Greg Huber ◽

Amy Kistler ◽

Hanna Retallack ◽

Michael Wilkinson ◽

...

Keyword(s):

De Novo ◽

Rna Viruses ◽

Nucleotide Substitutions ◽

Rna Dependent Rna Polymerase ◽

Single Nucleotide ◽

Reading Frame ◽

Reverse Complement ◽

Positive Sense ◽

Reverse Strand ◽

Coding Strategy

ABSTRACTNarnaviruses have been described as positive-sense RNA viruses with a remarkably simple genome of ∼ 3 kb, encoding only a highly conserved RNA-dependent RNA polymerase (RdRp). Many narnaviruses, however, are ‘ambigrammatic’ and harbour an additional uninterrupted open reading frame (ORF) covering almost the entire length of the reverse complement strand. No function has been described for this ORF, yet the absence of stops is conserved across diverse narnaviruses, and in every case the codons in the reverse ORF and the RdRp are aligned. The > 3 kb ORF overlap on opposite strands, unprecedented among RNA viruses, motivates an exploration of the constraints imposed or alleviated by the codon alignment. Here, we show that only when the codon frames are aligned can all stop codons be eliminated from the reverse strand by synonymous single-nucleotide substitutions in the RdRp gene, suggesting a mechanism for de novo gene creation within a strongly conserved amino-acid sequence. It will be fascinating to explore what implications this coding strategy has for other aspects of narnavirus biology. Beyond narnaviruses, our rapidly expanding catalogue of viral diversity may yet reveal additional examples of this broadly-extensible principle for ambigrammatic-sequence development.

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Causal Role of Single Nucleotide Polymorphisms within themprFGene of Staphylococcus aureus in Daptomycin Resistance

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01184-13 ◽

2013 ◽

Vol 57 (11) ◽

pp. 5658-5664 ◽

Cited By ~ 48

Author(s):

Soo-Jin Yang ◽

Nagendra N. Mishra ◽

Aileen Rubio ◽

Arnold S. Bayer

Keyword(s):

Staphylococcus Aureus ◽

Single Nucleotide Polymorphisms ◽

Point Mutations ◽

Nucleotide Polymorphisms ◽

Wild Type ◽

Single Nucleotide ◽

Content Type ◽

Reading Frame ◽

A Charge

ABSTRACTSingle nucleotide polymorphisms (SNPs) within themprFopen reading frame (ORF) have been commonly observed in daptomycin-resistant (DAPr)Staphylococcus aureusstrains. Such SNPs are usually associated with a gain-in-function phenotype, in terms of either increased synthesis or enhanced translocation (flipping) of lysyl-phosphatidylglycerol (L-PG). However, it is unclear if suchmprFSNPs are causal in DAPrstrains or are merely a biomarker for this phenotype. In this study, we used an isogenic set ofS. aureusstrains: (i) Newman, (ii) its isogenic ΔmprFmutant, and (iii) several intransplasmid complementation constructs, expressing either a wild-type or point-mutated form of themprFORF cloned from two isogenic DAP-susceptible (DAPs)-DAPrstrain pairs (616-701 and MRSA11/11-REF2145). Complementation of the ΔmprFstrain with singly point-mutatedmprFgenes (mprFS295LormprFT345A) revealed that (i) individual and distinct point mutations within themprFORF can recapitulate phenotypes observed in donor strains (i.e., changes in DAP MICs, positive surface charge, and cell membrane phospholipid profiles) and (ii) these gain-in-function SNPs (i.e., enhanced L-PG synthesis) likely promote reduced DAP binding toS. aureusby a charge repulsion mechanism. Thus, for these two DAPrstrains, the definedmprFSNPs appear to be causally related to this phenotype.

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An exploration of ambigrammatic sequences in narnaviruses

Scientific Reports ◽

10.1038/s41598-019-54181-3 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 10

Author(s):

Joseph L. DeRisi ◽

Greg Huber ◽

Amy Kistler ◽

Hanna Retallack ◽

Michael Wilkinson ◽

...

Keyword(s):

De Novo ◽

Rna Viruses ◽

Nucleotide Substitutions ◽

Rna Dependent Rna Polymerase ◽

Single Nucleotide ◽

Reading Frame ◽

Reverse Complement ◽

Positive Sense ◽

Reverse Strand ◽

Coding Strategy

AbstractNarnaviruses have been described as positive-sense RNA viruses with a remarkably simple genome of ~3 kb, encoding only a highly conserved RNA-dependent RNA polymerase (RdRp). Many narnaviruses, however, are ‘ambigrammatic’ and harbour an additional uninterrupted open reading frame (ORF) covering almost the entire length of the reverse complement strand. No function has been described for this ORF, yet the absence of stops is conserved across diverse narnaviruses, and in every case the codons in the reverse ORF and the RdRp are aligned. The >3 kb ORF overlap on opposite strands, unprecedented among RNA viruses, motivates an exploration of the constraints imposed or alleviated by the codon alignment. Here, we show that only when the codon frames are aligned can all stop codons be eliminated from the reverse strand by synonymous single-nucleotide substitutions in the RdRp gene, suggesting a mechanism for de novo gene creation within a strongly conserved amino-acid sequence. It will be fascinating to explore what implications this coding strategy has for other aspects of narnavirus biology. Beyond narnaviruses, our rapidly expanding catalogue of viral diversity may yet reveal additional examples of this broadly-extensible principle for ambigrammatic-sequence development.

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The First Report of Genetic Polymorphisms of the Equine SPRN Gene in Outbred Horses, Jeju and Halla Horses

Animals ◽

10.3390/ani11092574 ◽

2021 ◽

Vol 11 (9) ◽

pp. 2574

Author(s):

Sae-Young Won ◽

Yong-Chan Kim ◽

Kyoungtag Do ◽

Byung-Hoon Jeong

Keyword(s):

Prion Protein ◽

Prion Disease ◽

Protein Gene ◽

Prion Diseases ◽

Minimum Free Energy ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Reading Frame ◽

Direct Dna Sequencing ◽

Thoroughbred Horses

Prion disease is a fatal infectious disease caused by the accumulation of pathogenic prion protein (PrPSc) in several mammals. However, to date, prion disease has not been reported in horses. The Sho protein encoded by the shadow of the prion protein gene (SPRN) plays an essential role in the pathomechanism of prion diseases. To date, the only genetic study of the equine SPRN gene has been reported in the inbred horse, Thoroughbred horse. We first discovered four SPRN single nucleotide polymorphisms (SNPs) in 141 Jeju and 88 Halla horses by direct DNA sequencing. In addition, we found that the genotype, allele and haplotype frequencies of these SNPs of Jeju horses were significantly different from those of Halla and Thoroughbred horses, this latter breed is also included in this study. Furthermore, we observed that the minimum free energy and mRNA secondary structure were significantly different according to haplotypes of equine SPRN polymorphisms by the RNAsnp program. Finally, we compared the SNPs in the coding sequence (CDS) of the SPRN gene between horses and prion disease-susceptible species. Notably, prion disease-susceptible animals had polymorphisms that cause amino acid changes in the open reading frame (ORF) of the SPRN gene, while these polymorphisms were not found in horses.

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Single nucleotide polymorphisms in the open reading frame of the stearoyl-CoA desaturase gene and resulting genetic variants in Canadian Holstein and Jersey cows

DNA Sequence ◽

10.1080/10425170701291921 ◽

2007 ◽

Vol 18 (5) ◽

pp. 357-362 ◽

Cited By ~ 15

Author(s):

Patrick M. Kgwatalala ◽

Eveline M. Ibeagha-Awemu ◽

Patrick M. Kgwatalala ◽

Eveline M. Ibeagha-Awemu ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Genetic Variants ◽

Open Reading Frame ◽

Nucleotide Polymorphisms ◽

Desaturase Gene ◽

Single Nucleotide ◽

Reading Frame ◽

Stearoyl Coa Desaturase ◽

Jersey Cows

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Molecular characterisation of the buffalo SCAP gene and its association with milk production traits in water buffaloes

Journal of Dairy Research ◽

10.1017/s0022029918000195 ◽

2018 ◽

Vol 85 (2) ◽

pp. 133-137

Author(s):

Tingxian Deng ◽

Xiaoya Ma ◽

Chunying Pang ◽

Shasha Liang ◽

Xingrong Lu ◽

...

Keyword(s):

Milk Production ◽

Gene Expression Analysis ◽

Open Reading Frame ◽

Molecular Characterisation ◽

Early Lactation ◽

Nucleotide Polymorphisms ◽

Production Traits ◽

Milk Production Traits ◽

Single Nucleotide ◽

Reading Frame

The study reported in this Research Communication was conducted to investigate the molecular characterisation of buffalo SCAP gene, expression analysis, and the association between single nucleotide polymorphisms and milk production traits in 384 buffaloes. Sequence analysis revealed the SCAP gene had an open reading frame of 3837 bp encoding 1279 amino acids. A ubiquitous expression profile of SCAP gene was detected in various tissues with extreme predominance in the mammary gland during early lactation. Moreover, eleven SNPs in buffalo SCAP gene were identified, six of them (g.1717600A>G, g.1757922C>T, g.1758953G>A, g.1759142C>T, g.1760740G>A, and g.1766036T>C) were found to be significantly associated with 305-day milk yield. Thus, buffalo SCAP could sever as a candidate gene affecting milk production traits in buffalo and the identified SNPs might potentially be genetic markers.

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The Complete Chloroplast Genome of Two Important Annual Clover Species, Trifolium alexandrinum and T. resupinatum: Genome Structure, Comparative Analyses and Phylogenetic Relationships with Relatives in Leguminosae

Plants ◽

10.3390/plants9040478 ◽

2020 ◽

Vol 9 (4) ◽

pp. 478 ◽

Cited By ~ 1

Author(s):

Yanli Xiong ◽

Yi Xiong ◽

Jun He ◽

Qingqing Yu ◽

Junming Zhao ◽

...

Keyword(s):

Repetitive Sequences ◽

Genome Structure ◽

Divergence Time ◽

Global Alignment ◽

Trifolium Alexandrinum ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Reading Frame ◽

Annual Grasses ◽

Cp Genome

Trifolium L., which belongs to the IR lacking clade (IRLC), is one of the largest genera in the Leguminosae and contains several economically important fodder species. Here, we present whole chloroplast (cp) genome sequencing and annotation of two important annual grasses, Trifolium alexandrinum (Egyptian clover) and T. resupinatum (Persian clover). Abundant single nucleotide polymorphisms (SNPs) and insertions/deletions (In/Dels) were discovered between those two species. Global alignment of T. alexandrinum and T. resupinatum to a further thirteen Trifolium species revealed a large amount of rearrangement and repetitive events in these fifteen species. As hypothetical cp open reading frame (ORF) and RNA polymerase subunits, ycf1 and rpoC2 in the cp genomes both contain vast repetitive sequences and observed high Pi values (0.7008, 0.3982) between T. alexandrinum and T. resupinatum. Thus they could be considered as the candidate genes for phylogenetic analysis of Trifolium species. In addition, the divergence time of those IR lacking Trifolium species ranged from 84.8505 Mya to 4.7720 Mya. This study will provide insight into the evolution of Trifolium species.

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