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ویژگی‌های بیولوژیکی و مولکولی چهار جدایه ویروس وای سیب‌زمینی (PVY) براساس بخشی از ناحیه ژنی رمزکننده پروتئین پوششی

نوع مقاله : مقاله پژوهشی

نویسندگان

1 گروه گیاهپزشکی، دانشکده کشاورزی، دانشکدگان کشاورزی و منابع طبیعی، دانشگاه تهران، کرج، ایران

2 گروه گیاهپزشکی، دانشکده کشاورزی، دانشکدگان کشاورزی و منابع طبیعی، دانشگاه تهران، کرج، ایران.

3 بخش تحقیقات گیاهپزشکی، مرکز تحقیقات و آموزش کشاورزی و منابع طبیعی استان گلستان، گرگان، ایران.

4 گروه گیاهپزشکی دانشکده کشاورزی دانشگاه تهران. کرج. ایران

5 عضو هیأت علمی گروه گیاهپزشکی، دانشکده کشاورزی، دانشگاه رازی، کرمانشاه، ایران

چکیده

ویروس وای سیب‌زمینی (Potato virus Y, PVY) یکی از ویروس‌های محدودکننده تولید توتون و سیب‌زمینی در دنیا می‌باشد. به منظور بررسی خصوصیات بیولوژیکی و مولکولی جدایه‌های میزبانی ویروس وای سیب‌زمینی، طی سال‌های 1389 و 1390، در مجموع 1178 نمونه از گیاهان توتون، سیب‌زمینی، فلفل و علف هرز عروسک پشت پرده که دارای علائم موزائیک بودند از هشت شهرستان مختلف کشور شامل کرج، ارومیه، رشت، سنندج، شیراز، قزوین، ورامین و همدان جمع‌آوری شد. آلودگی نمونه‌ها به PVY با آزمون سرولوژیکی ساندویچ دو طرفه الیزا (double antibody sandwich enzyme-linked immunosorbent assay, DAS-ELISA) بررسی و میزان آلودگی در بین نمونه‌های توتون، سیب‌زمینی، عروسک‌پشت‌پرده و فلفل به ترتیب 2/27، 4/20، 75/18 و صفر درصد برآورد گردید. دامنه میزبانی ‌آزمایشی چهار جدایه منتخب ویروس وای سیب‌زمینی (Po2، Po5، Tob2 و Ph1) روی 12 گونه گیاه محک در شرایط گلخانه تفاوت‌های جزئی داشت. پس از تکثیر انتهای 3' ژنوم جدایه‌ها به اندازه 1200 جفت باز، درخت تبارزائی براساس توالی نوکلئوتیدی یک سوم بالادست ناحیه ژنی رمزکننده پروتئین پوششی بازسازی شد که جدایه‌های Tob2، Ph1 و Po5 در کلاد PVYN/NTN و جدایه Po2 در کلاد PVYO قرار گرفتند. نتایج IC-RT-PCR با استفاده از آغازگرهای اختصاصی سویه، و مقایسه توالی‌های نوکلئوتیدی و بررسی موتیف‌های اختصاصی سویه در همردیف‌های توالی آمینواسیدی پیش بینی شده انتهای آمینی پروتئین پوششی، نتایج واکاوی تبارزائی را تایید کردند. این اولین گزارش از آلودگی گونه Physalis divaricata به سویه PVYN/NTN در دنیا می‌باشد.

کلیدواژه‌ها


عنوان مقاله [English]

Biological and molecular characteristics of four potato virus Y (PVY) isolates based on partial coat protein gene

نویسندگان [English]

  • Prastoo Poursharifi 1
  • Akbar Dizadji 2
  • Parisa sharifinezamabad 3
  • Mina Koohi Habibi 4
  • Hadi Khateri 5
1 Department of Plant Protection, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
2 Department of Plant Protection, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.
3 Department of Plant Protection, Agricultural and Natural Resources and Research Center of Golestan province, Gorgan, Iran.
4 Department of Herbal Medicine, Faculty of Agriculture, University of Tehran. Karaj. Iran
5 Department of Plant Protection, College of Agriculture, Razi University, Kermanshah, Iran
چکیده [English]

Potato virus Y (PVY) is one of the viruses limiting tobacco and potato production in the world. To investigate the biological and molecular characteristics of PVY isolates, during 2010-2011, a total of 1178 symptomatic leaf samples of tobacco, potato, pepper and grand cherry (Physalis divaricata) plants were collected from eight different cities including Karaj, Urmia, Sanandaj, Shiraz, Qazvin, Varamin and Hamedan of Iran. The samples were tested serologically by double-antibody sandwich enzyme-linked immunosorbent assays (DAS-ELISA) and PVY was detected in tobacco (27.27 %), potato (20.4 %) and grand cherry
(18.75 %) samples, with no infection in pepper samples. Four biologically purified PVY isolates (Po2, Po5, Tob2 and Ph1) revealed few differences in experimental host range studies among 12 test plant species. After amplification of the 3´ genomic end of four PVY isolates with the expected size of 1200 bp, phylogenetic analysis based on the nucleotide sequences of partial coat protein gene (encoding N- terminal region of coat protein) revealed that Tob2, Po5 and Ph1 isolates grouped into PVYN/NTN clade, while only isolate Po2 grouped into PVYO clade. The results of IC-RT-PCR using strain-specific primers and further pairwise nucleotide sequence comparisons and strain-specific motifs analysis in the predicted amino acid sequences of the N-terminal region of coat protein confirmed the results of phylogenetic analysis. This is the first report of Physalis divaricata infection with PVYN/NTN strain in the world.

کلیدواژه‌ها [English]

  • Phylogeny
  • strain
  • serology
  • Physalis

Extended Abstract

Introduction

Potato virus Y (PVY, genus Potyvirus, family Potyviridae), one of the top 10 most important plant viruses (Scholthof et al., 2011), is a serious problem in solanaceous crops worldwide (Green et al., 2017a; Kerlan, 2006; Quenouille et al., 2013). Currently, five non-recombinant (PVYO, PVYEu-N, PVYNA-N, PVYC, and PVYO-O5) and nine recombinant strains (PVYN:O, PVYN-Wi, PVYNTNa, PVYNTNb, PVY-NE11, PVYE, and PVY-SYR-I, -II, and -III) have been defined (Galvino-Costa et al., 2012; Green et al., 2017b; Karasev & Gray, 2013). Molecular studies are useful tools to shed light on the molecular basis of virus geographical spread and adaptation to new hosts and for designing appropriate epidemic control strategies (Elena et al., 2011; Jones, 2009). PVY has been reported in several regions of Iran (Hosseini et al., 2011; Pourrahim & Farzadfar, 2016; Pourrahim et al., 2007; Sadeghi et al., 2008; Shamsaddin Saeed et al., 2008; Toosi et al., 2004). In this study, biological, serological and molecular analysis of four PVY isolates was performed based on the C-terminal of the coat protein genomic region.

 

Materials and Methods

A total of 1178 symptomatic leaf samples of pepper, potato, tobacco and physalis were collected from the fields in Karaj, Urmia, Sanandaj, Shiraz, Qazvin, Varamin and Hamedan counties during 2010-2011. The samples were tested serologically by double-antibody sandwich enzyme-linked immunosorbent assays (DAS-ELISA) as described by Clark and Adams (1977) using PVY-specific polyclonal antibodies (DSMZ, AS-0137).

Four ELISA-positive samples were biologically purified by serial single local lesion transfers and propagated on Nicotiana glutinosa, then mechanically inoculated on a number of indicator plants. Total RNA was extracted from infected N. glutinosa leaves by RNeasy Plant Mini Kit (Qiagen, Hilden Germany) and subjected to RT-PCR using CPUTR-F/CPUTR-R primer pair to amplify the virus genomic 3' end (Bukovinszki et al., 2007). Amplified fragments were extracted from the gel using a GF-1 Gel DNA recovery kit (Vivantis, Malaysia) then sequenced directly in both directions (Macrogen Inc., South Korea).

Immunocapture-RT-PCR (IC-RT-PCR) was performed by using strain-specific primers as described by Boonham et al. (2002).

The nucleotide sequences of Iranian isolates were compared against the online NCBI nt database using BLASTn, then aligned to a set of PVY sequences available in GenBank. Pairwise nucleotide identities  were obtained by SDT v. 1.2 (Muhire et al., 2014), phylogenetic tree reconstruction was done by MEGA X (Kumar et al., 2018).

 

Results and Discussion

PVY was detected by DAS-ELISA in samples of tobacco (27.27 %), potato (20.4 %) and physalis (18.75 %). Interestingly, although a large number of pepper samples were tested, none of them were infected by PVY. Four biologically purified PVY isolates (Po2, Po5, Tob2 and Ph1), obtained from potato, tobacco and physalis caused local lesions on Chenopodium amaranticolor and systemic symptoms on Capsicum annuum, Datura metel, Solanum lycopersicum, Nicotiana debneyi, N. glutinosa and N. rustica, with minor differences in experimental host range. RT-PCR resulted in the amplification of the 3´ genomic end of PVY isolates with the expected size of 1200 bp. Phylogenetic analysis based on nucleotide sequences of partial coat protein gene (encoding N- terminal region of coat protein) of four PVY Po2, Ph1, Po5 and Tob2 isolates in this study (with NCBI GenBank accession numbers of PP195788, PP195789, PP195790 and PP195791, respectively) with other PVY sequences available in GenBank revealed that Ph1, Po5 and Tob2 isolates grouped into PVYN/NTN clade, while only Po2 grouped into PVYO clade. Pairwise nucleotide sequence comparisons of 55 PVY genomes (for 51 isolates previously reported and the 4 isolates reported in this study) using SDT revealed that Tob2, Po5 and Ph1 isolates have >94- 100% and Po2 has >99% identity with PVYN/NTN and PVYO isolates, respectively. Immunocapture-RT-PCR (IC-RT-PCR) by using the strain-specific primers resulted in the amplification of a cDNA fragment with the expected size of 545 bp in Tob2, Po5 and Ph1 isolates and of 609 bp in Po2 one, which confirmed the phylogenetic results. No recombination event was detected in the partial cp gene between 55 PVY isolates.

The information obtained can be a key element in future research to develop improved control strategies for potato virus diseases in Iran.

 

Conclusion

The present study showed the occurrence of PVYN/NTN and PVYO in different hosts based on biological characteristics and molecular analyses of the partial cp gene nucleotide sequence. To our knowledge, this is the first report of the occurrence of PVYN/NTN on Physalis divaricata, while whole genome sequencing of this isolate is needed.

شریفی نظام آباد، پریسا؛ نصراله نژاد، سعید؛ آقاجانی، محمدعلی؛ دیزجی، اکبر و ندیمی احمد (1398). بررسی شاخص های مهم مرتبط با بیماری ویروسی وای سیب زمینی (Potato virus Y) در مزارع توتون استان گلستان. آفات و بیماری های گیاهی، 87 (2)، 227- 240.
شمس الدین سعید، فاطمه؛ معصومی، حسین؛ حسینی، عاطفه؛ حسنی پور، اکبر؛ حیدرنژاد، جهانگیر؛ شعبانیان، مهدی و میرتاج‌الدینی، منصور (1387). معرفی چند میزبان جدید ویروس Y سیب‌زمینی(PVY)  در استان کرمان. هجدهمین کنگره گیاهپزشکی ایران، همدان، ایران.
طوسی، نفیسه؛ آهون منش، علی؛ پوررحیم، رضا و بهار، مسعود (1383). شناسائی نژادهای C و N ویروس Y سیب زمینی با استفاده از Reverse Transcriptase- Polymerase Chain Reaction ( RT- PCR) و Restriction Fragment Lenth Polymorphism (RFLP). شانزدهمین کنگره گیاه‌پزشکی ایران، تبریز، ایران.
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