Complete nucleotide sequences of attenuated and severe isolates of Leek yellow stripe virus from garlic in northern Japan: identification of three distinct virus types in garlic and leek world-wide

Host-specific adaptation drove the coevolution of leek yellow stripe virus and Allium plants

Host adaptation plays a crucial role in virus evolution and is a consequence of long-term interactions between virus and host in a complex arms race between host RNA silencing and viral RNA silencing suppressor (RSS) as counterdefense. Leek yellow stripe virus (LYSV), a potyvirus causing yield loss of garlic, infects several species of Allium plants. The unexpected discovery of an interspecific hybrid of garlic, leek, and great-headed (GH) garlic motivated us to explore the host-adaptive evolution of LYSV. Here, using Bayesian phylogenetic comparative methods and a functional assay of viral RSS activity, we show that the evolutionary context of LYSV has been shaped by the host adaptation of the virus during its coevolution with Allium plants. Our phylogenetic analysis revealed that LYSV isolates from leek and their taxonomic relatives (Allium ampeloprasum complex; AAC) formed a distinct monophyletic clade separate from garlic isolates and are likely to be uniquely adapted to AAC. Our comparative studies on viral accumulation indicated that LYSV accumulated at a low level in leek, whereas LYSVs were abundant in other Allium species such as garlic and its relatives. When RSS activity of the viral P1 and HC-Pro of leek LYSV isolate was analyzed, significant synergism in RSS activity between the two proteins was observed in leek but not in other species, suggesting that viral RSS activity may be important for the viral host-specific adaptation. We thus consider that LYSV may have undergone host-specific evolution at least in leek, which must be driven by speciation of its Allium hosts. IMPORTANCE Potyviruses are the most abundant plant RNA viruses and are extremely diversified in terms of their wide host range. Due to frequent host switching during their evolution, host-specific adaptation of potyviruses may have been shaped by numerous host factors. However, any critical determinants for viral host range remain largely unknown, possibly because of the repeated gain and loss of virus infectivity of plants. Leek yellow stripe virus (LYSV) is a species of the genus Potyvirus, which has a relatively narrow host range, generally limited to hosts in the genus Allium. Our investigations on leek and leek relatives (Allium ampeloprasum complex), which must have been generated through interspecies hybridization, revealed that LYSV accumulation remained low in leek as a result of viral host adaptation in competition with host resistance such as RNA silencing. This study presents LYSV as an ideal model to study the process of host-adaptive evolution and virus-host coevolution.

Phylogenetic and diversity analyses revealed that leek yellow stripe virus population consists of three types: S, L, and N

Phylogenetic and evolutionary analyses were performed on the P1 and CP genes of global isolates to clarify the phylogrouping of leek yellow stripe virus (LYSV, genus Potyvirus), a pathogen affecting Allium spp. worldwide, into different types based on genetic variation and host species. The constructed phylogenetic trees divided the isolates into three major groups: S, L, and N. Low nucleotide (nt) and amino acid (aa) percent identities among the three groups were observed on full ORF (75.4-99.0 and 79.1-99.0), P1 (59.1-98.3 and 36.8-98.3), and CP (76.6-100 and 75.7-100) coding regions. The dN/dS values of P1 and CP confirmed that both genes are under strong negative (purifying) selection pressure. Neutrality tests on Eastern Asian isolates suggested that the ancestors of current LYSV isolates evolved with garlic while they were in Asia before spreading to other world regions through garlic propagative materials. Genetic differentiation and gene flow analysis showed extremely frequent gene flow from S group to L and N groups, and these phylogroups differentiated from each other over time. Host differences, inconsistent serological test results, substantial nt and aa variation, and phylogenetic and diversity analyses in this study supported previous reports that LYSV can be separated into three major evolutionary lineages: S, L, and N types.

Leek Yellow Stripe Virus Can Adjust for Host Adaptation by Trimming the N-Terminal Domain to Allow the P1 Protein to Function as an RNA Silencing Suppressor

In Japan, the P1 protein (S-type) encoded by leek yellow stripe virus (LYSV) isolates detected in Honshu and southward is shorter than the P1 (N-type) of LYSV isolates from garlic grown in Hokkaido due to a large deletion in the N-terminal half. In garlic fields in Hokkaido, two types of LYSV isolate with N- and S-type P1s are sometimes found in mixed infections. In this study, we confirmed that N- and S-type P1 sequences were present in the same plant and that they belong to different evolutionary phylogenetic groups. To investigate how LYSV with S-type P1 (LYSV-S) could have invaded LYSV with N-type P1 (LYSV-N)-infected garlic, we examined wild Allium spp. plants in Hokkaido and found that LYSV was almost undetectable. On the other hand, in Honshu, LYSV-S was detected at a high frequency in Allium spp. other than garlic, suggesting that the LYSV-S can infect a wider host range of Allium spp. compared to LYSV-N. Because P1 proteins of potyviruses have been reported to promote RNA silencing suppressor (RSS) activity of HC-Pro proteins, we analyzed whether the same was true for P1 of LYSV. In onion, contrary to expectation, the P1 protein itself had RSS activity. Moreover, the RSS activity of S-type P1 was considerably stronger than that of N-type P1, suggesting that LYSV P1 may be able to enhance its RSS activity when the deletion is in the N-terminal half and that acquiring S-type P1 may have enabled LYSV to expand its host range.

Occurrence of leek yellow stripe virus and onion yellow dwarf virus from edible Allium plants in the south Marmara region of Turkey

Among edible Allium plants (leek, onion, and garlic), leek yellow stripe (LYSV) and onion yellow dwarf virus (OYDV) are the most common viruses worldwide. While the presence of these two viruses in Turkey has previously been confirmed, only a few studies on their prevalence and genetic diversity have been performed. The aim of this study, conducted in the southern Marmara region of Turkey (SMR), was to identify the presence and genetic diversity of these viruses. Samples were collected from 494 plants exhibiting virus and virus-like symptoms. Samples were tested for the relevant viruses by double-antibody sandwich enzyme-linked immunosorbent assay and reverse transcription polymerase chain reaction (DAS-ELISA and RT-PCR, respectively). Tests revealed the presence of OYDV in 95 samples and LYSV in 52, whereas 33 samples were observed to have a combined infection. To examine the genetic diversity, 10 isolates from each virus were chosen from the infected samples. Using RT-PCR, the complete coat protein (CP) gene for LYSV and a partial sequence region of the nuclear inclusion b + CP gene for OYDV were amplified, cloned, and sequenced from the selected isolates. The sequence data were compared with the isolates in GenBank; it was determined that SMR LYSV and OYDV isolates show similarities over 77% with world isolates at the nucleotide and amino acid levels. Phylogenetic analyses showed that the LYSV and OYDV isolates had some diversity with isolates from different parts of the world, and the host had an important role in the phylogenetic relationships, particularly for LYSV.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03067-1.

Identification of garlic-infecting leek yellow stripe virus through deep-sequencing analyses from Iran

In the study presented here, the first complete genome sequence of Leek yellow stripe virus (LYSV) designated as isolate LYSV-AE65 from Southwest of Iran, was reported. The small RNA deep sequencing analysis showed that, the Iranian isolate has a full RNA genome of 10,142 nucleotide in length (Except for poly (A) tail) and it was shared 77.91-92.16% nucleotide (nt) and 83.62-96.35% amino acid (aa) sequences identities with other known LYSV isolates. The coat protein (CP) region showed 80.21-95.24% nucleotide identity to those of other isolates, while high degrees of nucleotide sequence identity with G77-LYSV isolate (MN059504) from China. Phylogenetic analysis based on full genome sequence of LYSV-AE65, showed the closest relationship with LYSV isolates from China, Australia, Spain and Mexico. Also, phylogenetic analysis of the 5´-untranslated region (UTR)-P1 gene sequences of 44 isolates, confirmed the formation of two main groups, N-type and S-type, in agreement with the previous studies. Isolate LYSV-AE65 was similar to the members of clade S and has two large deletions in P1 gene. Recombination analysis demonstrated that LYSV-AE65 was a recombinant with most part of its genome was derived from already reported LYSV isolates infecting allium species. To the best of our knowledge, this is the first report of complete genome sequencing of LYSV isolate infecting garlic through small RNA deep sequencing method in Iran.

Supplementary Information

The online version contains supplementary material available at (10.1007/s13337-021-00733-z).

Detection and Distribution of Viruses Infecting Garlic Crops in Australia

The distribution of viruses in eastern Australian field garlic was evaluated. Detection assays were developed that involved generic RT-PCR for viruses in the Allexivirus, Carlavirus and Potyvirus genera followed by virus-specific colorimetric dot-blot hybridization. Assays targeted the potyviruses (onion yellow dwarf virus (OYDV), shallot yellow stripe virus (SYSV), and leek yellow stripe virus (LYSV)), the carlaviruses (garlic common latent virus (GCLV) and shallot latent virus (SLV)), and the allexiviruses (garlic viruses A, B, C, X (GarVA, -B, -C, -X) and shallot virus X (ShVX)). Virus incidence in crops was consistently high, with most plants infected with at least one virus from each genus. OYDV, LYSV, SLV, and GCLV were commonly detected. Three of the four allexiviruses were in all districts surveyed but varied in incidence, whereas ShVX and SYSV were not detected. There was no association between virus species complement and bulb size, indicating size is not a good predictor of the virus status of planting material. The variation of virus incidence across different Australian growing districts and in different cultivars implies multiple introductions of viruses rather than spread within the country. The genetic diversity observed within coat protein sequences of some virus species also supports multiple separate introductions.

Distinct intraspecific variations of garlic (Allium sativum L.) revealed by the exon-intron sequences of the alliinase gene

Garlic (Allium sativum L.) has been used worldwide as a food and for medicinal purposes since early times. Garlic cultivars exhibit considerable morphological diversity despite the fact that they are mostly sterile and are grown only by vegetative propagation of cloves. Considerable recombination occurs in garlic genomes, including the genes involved in secondary metabolites. We examined the genomic DNAs (gDNAs) from garlic, encoding alliinase, a key enzyme involved in organosulfur metabolism in Allium plants. The 1.7-kb gDNA fragments, covering three exons (2, 3, and 4) and all four introns, were amplified from total DNAs prepared from garlic samples produced in Asia and Europe, leading to 73 sequences in total: Japan (JPN), China (CHN), India (IND), Spain (ESP), and France (FRA). The exon sequences were highly conserved among all the sequences, probably reflecting the fully functional alliinase associated with the flavor quality. Distinct intraspecific variations were detected for all four intron sequences, leading to the haplotype classifications. A close relationship between JPN and CHN was observed for all four introns, whereas IND showed a more divergent distribution. ESP and FRA afforded clearly different variants compared with those from Asian sequences. The present study provides information that could be useful in the development of an additional molecular marker for garlic authentication and quality control.

Variability in the P1 gene helps to refine phylogenetic relationships among leek yellow stripe virus isolates from garlic

Nucleotide sequences from the P1 gene and the 5' untranslated region of leek yellow stripe virus (LYSV), collected from several locations, were used to refine the phylogenetic relationships among the isolates. Multiple alignments revealed three distinct regions of insertions and deletions to classify LYSVs. In our phylogenetic analyses, the LYSV isolates separated into two major groups (N-type and S-type). S-type viruses had two large deletions compared to N-type viruses. Considering that the outgroup, onion yellow dwarf virus (OYDV) also has the sequences corresponding to the deletions in the S-type viruses, our study shows that the sequences missing in the S-type were present in the common ancestor of the N-type and S-type. In the phylogenetic trees, we found three distinct clades of isolates, from Uruguay (U), Okinawa (O) and Spain (Sp), suggesting that LYSVs have unique evolutionary histories depending on their garlic origins. The P1 gene of LYSV is thus quite suited to reflecting viral evolution, as recently suggested for other potyviruses.

The complete nucleotide sequence of attenuated onion yellow dwarf virus: a natural potyvirus deletion mutant lacking the N-terminal 92 amino acids of HC-Pro

The complete nucleotide sequence of a severe isolate of Onion yellow dwarf virus contains 10,459 nucleotides encoding 3,403 amino acids, while that of an attenuated isolate contains 10,183 nucleotides encoding 3,311 amino acids. The sequence coding for the N-terminal 92 amino acids of HC-Pro was missing in the attenuated isolate. Interestingly, garlic plants growing in commercial gardens were co-infected with isolates of both types. This is the first report of a natural potyvirus deletion mutant lacking the N-terminal region of HC-Pro.