Enhanced Apiaceous Potyvirus Phylogeny, Novel Viruses, and New Country and Host Records from Sequencing Samples.

The family Apiaceae comprises approximately 3700 species of herbaceous plants, including important crops, aromatic herbs and field weeds. Here we report a study of 10 preserved historical or recent virus samples of apiaceous plants collected in the United Kingdom (UK) import interceptions from the Mediterranean region (Egypt, Israel and Cyprus) or during surveys of Australian apiaceous crops. Seven complete new genomic sequences and one partial sequence, of the apiaceous potyviruses apium virus Y (ApVY), carrot thin leaf virus (CaTLV), carrot virus Y (CarVY) and celery mosaic virus (CeMV) were obtained.

Integrating High throughput Sequencing into Survey Design Reveals Turnip Yellows Virus and Soybean Dwarf Virus in Pea () in the United Kingdom.

There is only limited knowledge of the presence and incidence of viruses in peas within the United Kingdom, therefore high-throughput sequencing (HTS) in combination with a bulk sampling strategy and targeted testing was used to determine the virome in cultivated pea crops. Bulks of 120 leaves collected from twenty fields from around the UK were initially tested by HTS, and presence and incidence of virus was then determined using specific real-time reverse-transcription PCR assays by testing smaller mixed-bulk size samples. This study presents the first finding of turnip yellows virus (TuYV) in peas in the UK and the first finding of soybean dwarf virus (SbDV) in the UK.

A novel high-throughput sequencing approach reveals the presence of a new virus infecting Rosa: rosa ilarvirus-1 (RIV-1).

Roses are one of the most valuable ornamental flowering shrubs grown worldwide. Despite the widespread of rose viruses and their impact on cultivation, they have not been studied in detail in the United Kingdom (UK) since the 1980's. As part of a survey of rose viruses entering the UK, 35 samples were collected at Heathrow Airport (London, UK) and were tested by RT-qPCR for different common rose viruses.

Phylogenetics and Evolution of Potato Virus V: Another Potyvirus that Originated in the Andes.

Potato virus V (PVV) causes a disease of potato () in South and Central America, Europe, and the Middle East. We report here the complete genomic sequences of 42 new PVV isolates from the potato's Andean domestication center in Peru and of eight historical or recent isolates from Europe. When the principal open reading frames of these genomic sequences together with those of nine previously published genomic sequences were analyzed, only two from Peru and one from Iran were found to be recombinant.

Potato Virus Y Biological Strain Group Y: Hypersensitive Resistance Genes Elicited and Phylogenetic Placement.

Potato virus Y (PVY) disrupts healthy seed potato production and causes tuber yield and quality losses globally. Its subdivisions consist of strain groups defined by potato hypersensitive resistance (HR) genes and whether necrosis occurs in tobacco, and phylogroups defined by sequencing. When PVY isolate PP was inoculated to potato cultivar differentials with HR genes, the HR phenotype pattern obtained resembled that caused by strain group PVY isolate KIP1.

The Phylogeography of Potato Virus X Shows the Fingerprints of Its Human Vector.

Potato virus X (PVX) occurs worldwide and causes an important potato disease. Complete PVX genomes were obtained from 326 new isolates from Peru, which is within the potato crop's main domestication center, 10 from historical PVX isolates from the Andes (Bolivia, Peru) or Europe (UK), and three from Africa (Burundi). Concatenated open reading frames (ORFs) from these genomes plus 49 published genomic sequences were analyzed.

Plant pest surveillance: from satellites to molecules.

Plant pests and diseases impact both food security and natural ecosystems, and the impact has been accelerated in recent years due to several confounding factors. The globalisation of trade has moved pests out of natural ranges, creating damaging epidemics in new regions. Climate change has extended the range of pests and the pathogens they vector.

Potato Virus A Isolates from Three Continents: Their Biological Properties, Phylogenetics, and Prehistory.

Forty-seven potato virus A (PVA) isolates from Europe, Australia, and South America's Andean region were subjected to high-throughput sequencing, and 46 complete genomes from Europe ( = 9), Australia ( = 2), and the Andes ( = 35) obtained. These and 17 other genomes gave alignments of 63 open reading frames 9,180 nucleotides long; 9 were recombinants. The nonrecombinants formed three tightly clustered, almost equidistant phylogroups; A comprised 14 Peruvian potato isolates; W comprised 37 from potato in Peru, Argentina, and elsewhere in the world; and T contained three from tamarillo in New Zealand.

Identification and full genomic sequence of nerine yellow stripe virus.

This study reports the first complete genome sequence of nerine yellow stripe virus (NeYSV, GenBank MT396083). The genome consists of 10,165 nucleotides, excluding the 3'-terminal poly(A) tail. A single open reading frame encodes a large polyprotein of 3294 amino acids with typical potyvirus features.

Changes in Faecal Microbiota Profiles Associated With Performance and Birthweight of Piglets.

The gastrointestinal tract microbiota interacts with the host to modulate metabolic phenotype. This interaction could provide insights into why some low birthweight pigs can exhibit compensatory growth whilst others remain stunted. This study aimed to identify microbiota markers associated with birthweight [low birthweight ( = 13) or normal birthweight pigs ( = 13)] and performance ["good" or "poor" average daily gain (ADG) class].

Complete Coding Sequence of from a 40-Year-Old Sample from Peru.

A complete coding sequence of the type strain of from Peru (isolate Lm) was obtained. Comparison of its RNA1 and RNA2 sequences with variants of this virus isolated in Brazil revealed RNA1 and RNA2 nucleotide identities of 81 to 83% and 70 to 71%, respectively.

Genomic sequence and host range studies reveal considerable variation within the species Arracacha virus B.

Arracacha virus B type (AVB-T) and oca (AVB-O) strains from arracacha (Arracacia xanthorrhiza) and oca (Oxalis tuberosa) samples collected in 1975 and two additional isolates obtained from arracacha (AVB-PX) and potato (AVB-6A) in Peru in 1976 and 1978, respectively, were studied. In its host responses and serological properties, AVB-PX most resembled AVB-T, whereas AVB-6A most resembled AVB-O. Complete genomic sequences of the RNA-1 and RNA-2 of each isolate were obtained following high-throughput sequencing of RNA extracts from isolates preserved for 38 (AVB-PX) or 32 (the other 3 isolates) years, and compared with a genomic sequence of AVB-O obtained previously (PV-0082).

Biological and Molecular Properties of Isolates from Pepino ().

In 1976, a virus with flexuous, filamentous virions typical of the family was isolated from symptomatic pepino () plants growing in two valleys in Peru's coastal desert region. In 2014, a virus with similar-shaped virions was isolated from asymptomatic fruits obtained from pepino plants growing in six coastal valleys and a valley in Peru's Andean highlands. Both were identified subsequently as (WPMV) by serology or high-throughput sequencing (HTS).

The Biology and Phylogenetics of Potato virus S Isolates from the Andean Region of South America.

Biological characteristics of 11 Potato virus S (PVS) isolates from three cultivated potato species (Solanum spp.) growing in five Andean countries and 1 from Scotland differed in virulence depending on isolate and host species. Nine isolates infected Chenopodium quinoa systemically but two others and the Scottish isolate remained restricted to inoculated leaves; therefore, they belonged to biologically defined strains PVS and PVS, respectively.

A 33-Year-Old Plant Sample Contributes the First Complete Genomic Sequence of .

A isolate detected in a Peruvian potato sample collected in 1977 produced the first genome sequence of this virus. When this genome sequence was compared with those of other nepoviruses, the amino acid sequences of RNA1 and RNA2 were most similar to those of subgroup C nepoviruses.

Full-Genome Sequencing of a Virus from a 33-Year-Old Sample Demonstrates that Is Synonymous with .

We describe here the first genome sequence of Arracacha virus Y (ArVY) derived from an arracacha (Arracacia xanthorrhiza) sample originally collected in 1976 in Peru and compare it with other potyvirus genome sequences. It had a 79% nucleotide identity with a 2013 Brazilian Arracacha mottle virus (AMoV) sequence, suggesting that AMoV is ArVY.

Complete Genome Sequence of from Bolivia, Obtained from a 33-Year-Old Sample.

We present the complete genomic sequence of a (PVT) isolate originally obtained from a Bolivian potato sample collected in 1976, and we compare it with the genome of the PVT type isolate from Peru. There is an 81% nucleotide identity between the two genomes of this Andean potato virus.

Complete Genomic Sequence of the Potyvirus , Obtained from a 33-Year-Old Mashua () Sample.

We present the complete genomic sequence of a new potyvirus we tentatively call (MasVY), first isolated in 1984 from a plant of the Andean tuber crop mashua (, family ). There was a 70% nucleotide identity between MasVY and a genomic sequence of .

Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt ().

Environmental DNA (eDNA) analysis is a rapid, cost-effective, non-invasive biodiversity monitoring tool which utilises DNA left behind in the environment by organisms for species detection. The method is used as a species-specific survey tool for rare or invasive species across a broad range of ecosystems. Recently, eDNA and "metabarcoding" have been combined to describe whole communities rather than focusing on single target species.

First Complete Genome Sequence of Isolated from a 38-Year-Old Sample from Peru.

We present here the first complete genomic sequence of from a Peruvian arracacha sample collected in 1975 and compare it with the genomes of other nepoviruses. Its RNA1 and RNA2 both had greatest amino acid identities with those of the subgroup A nepovirus .

Carrot yellow leaf virus is associated with carrot internal necrosis.

Internal necrosis of carrot has been observed in UK carrots for at least 10 years, and has been anecdotally linked to virus infection. In the 2009 growing season some growers had up to 10% of yield with these symptoms. Traditional diagnostic methods are targeted towards specific pathogens.

Detection of honey bee (Apis mellifera) viruses with an oligonucleotide microarray.

In recent years, declines in honey bee (Apis mellifera L.) colonies have been observed to varying degrees worldwide with the worst losses in the USA being termed Colony Collapse Disorder (CCD). Pathogen load and the prevalence of honey bee viruses have been implicated in these losses and many diseased hives have multiple viruses present.

Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology.

A novel, unbiased approach to plant viral disease diagnosis has been developed which requires no a priori knowledge of the host or pathogen. Next-generation sequencing coupled with metagenomic analysis was used to produce large quantities of cDNA sequence in a model system of tomato infected with Pepino mosaic virus. The method was then applied to a sample of Gomphrena globosa infected with an unknown pathogen originally isolated from the flowering plant Liatris spicata.

Malic enzyme: the controlling activity for lipid production? Overexpression of malic enzyme in Mucor circinelloides leads to a 2.5-fold increase in lipid accumulation.

Malic enzyme (ME; NADP(+)-dependent; EC 1 . 1 . 1 .

Cloning and characterization of a gene encoding a malic enzyme involved in anaerobic growth in Mucor circinelloides.

A 3193 bp contiguous sequence has been cloned from the oleaginous fungus Mucor circinelloides, that contains a full-length gene encoding a putative NADP+: dependent malic enzyme (EC. 1.1.