Sequence diversity and potential recombination events in the coat protein gene of Apple stem pitting virus

Komorowska, B.; Siedlecki, Paweł; Kaczanowski, Szymon; Hasiów‐Jaroszewska, Beata; Malinowski, Tadeusz

doi:10.1016/j.virusres.2011.03.003

Cited by 23 publications

(31 citation statements)

References 38 publications

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“…The estimation of selection pressure on the ACLSV genome fragments revealed that they undergo the strong negative selection. Studies conducted in different countries showed that purifying selection dominates in the cases of viruses infecting apple trees, but individual nucleotides or viral genome regions may be under positive selection (Komorowska et al 2011;Liebenberg et al 2012;Liu et al 2014;Yoon et al 2014). Perhaps, the negative selection pressure can be explained by the participation of a single viral protein in numerous processes.…”

Section: Resultsmentioning

confidence: 99%

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Molecular variability of Apple chlorotic leaf spot virus isolated in Belarus

Kuzmitskaya¹,

Титок²,

Anoshenko³

et al. 2016

EEB

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Apple chlorotic leaf spot virus (ACLSV) is a harmful latent pathogen distributed worldwide in apple orchards. To evaluate the genetic diversity of this virus in Belarusian apple orchards, 850 bp genome fragments coding parts of replicase and movement protein open reading frames from five viral isolates from apple in Belarus were sequenced. High genetic variability was detected among isolates studied. The potential sites of recombination were identified in the partial sequences of the replicase and movement protein genes of ASLSV. The estimation of selection pressure revealed strong negative selection on the genome fragments obtained in this study and homologous to them ACLSV sequences from the GenBank database. Relationships between the geographic origin and the nucleotide identity of the fragments of ACLSV were not found.

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Section: Resultsmentioning

confidence: 99%

“…Perhaps, such a pattern is formed by the action of strong purifying selection which is typical for plant viruses. Similarity between isolates from the same host plant is observed much more frequently, although it is not always (Komorowska et al 2011;Liebenberg et al 2012;Liu et al 2014;Valasevich et al 2015).…”

Section: Resultsmentioning

confidence: 99%

Molecular variability of Apple chlorotic leaf spot virus isolated in Belarus

Kuzmitskaya¹,

Титок²,

Anoshenko³

et al. 2016

EEB

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“…Однако четкой картины распределения образцов в зависимости от места отбора пробы выявить не удалось, несмотря на значительную вариабельность вирусных геномов (Liebenberg et al, 2012;Liu et al, 2014). Кластеризация изолятов в зависимости от растения-хозяина наблюдается чаще, хотя и она не является абсолютной (Komorowska et al, 2011;Liebenberg et al, 2012;Liu et al, 2014). Выявленная нами генетическая дифференциация вирусов ACLSV, ASPV и ASGV также не связана непосредственно с реги-оном их распространения (см.…”

Section: Discussionunclassified

“…Результаты других исследований также свидетельствуют о значитель-ном генетическом разнообразии этих вирусов. Степень идентичности генов, кодирующих белок оболочки ASPV у изолятов, полученных в Польше, составляла 70,7-93,5 % (Komorowska et al, 2011). Последовательности двух геномов ACLSV, выделенных на территории Китая, имели степень идентичности 95,1 % (Niu et al, 2012).…”

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“…Исследования, проведенные в разных странах, свидетельствуют о доминировании от-рицательной селекции в эволюции вирусов, поражающих яблоню. Однако отдельные нуклеотиды или регионы ге-номов вирусов могут находиться под влиянием положи-тельной селекции (Komorowska et al, 2011;Liebenberg et al, 2012;Liu et al, 2014;Yoon et al, 2014). Возможно, такое селективное давление обусловлено участием одного вирусного белка в множестве процессов.…”

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Distribution and genetic diversity of three apple viruses in Belarus

Kuzmitskaya¹,

Urbanovich²

2016

Vestn. VOGiS

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Apple chlorotic leaf spot virus (ACLSV), apple stem pitting virus (ASPV), and apple stem grooving virus (ASGV) are common in all apple cultivating countries including Belarus. The aim of this investigation was to study the genetic diversity of the apple-tree viruses in Belarus. Virus-infected apple trees were identified by RT-PCR in modern horticultural plantations and were not found among old trees aged more than 50 years. The genome fragments of the ACLSV, ASPV, and ASGV viruses detected were cloned and sequenced. The analysis of their nucleotide sequences gives evidence of high molecular variability generated mostly by single nucleotide substitutions and rarely by single nucleotide deletions and insertions. Recombination processes could also make some contribution to the existing genetic diversity of the virus populations studied. Estimates of selective pressure on the genome fragments of ACLSV, ASPV and ASGV obtained in this study as well as homologous sequences from the GenBank database indicate negative selection, except for one codon in the sequence of the ACLSV coat protein, which is under positive selection. The study of phylogenetic relationships between viruses isolated in different countries did not reveal any clear-cut relationship between their geographical origin and the degree of similarity of virus genome fragments.Keywords: RT-PCR; ACLSV; ASGV; ASPV; genetic diversity; selection pressure.Вирус хлоротической пятнистости листьев яблони (ACLSV), вирус ямчатости древесины яблони (ASPV) и вирус бороздчатости дре-весины яблони (ASGV) распространены во всех странах, где воз-делывается яблоня. В данной работе исследовалось генетическое разнообразие этих патогенов на территории Беларуси. Заражен-ные различными вирусными инфекциями деревья были обна-ружены с помощью метода ОТ-ПЦР в современных садовых насаж дениях. Среди старых деревьев, возрастом более 50 лет, заражен ных не выявлено. Фрагменты геномов вирусов ACLSV, ASPV и ASGV были клонированы и секвенированы. Анализ их нуклеотидных последовательностей свидетельствует о высокой молекулярной вариабельности, сформированной за счет одно-нуклеотидных замен, реже -однонуклеотидных делеций и инсер-ций. Некоторый вклад в существующее генетическое разнообра-зие популяции вирусов также могли вносить и рекомбинацион-ные процессы. Оценка селекционного давления на фрагменты геномов ACLSV, ASPV и ASGV, полученные в настоящем исследова-нии, а также гомологичные последовательности из базы данных GenBank свидетельствует о том, что они находятся под воздей-ствием отрицательной селекции, за исключением одного кодона в последовательности белка оболочки ACLSV, находящегося под воздействием положительной селекции. При исследовании филогенетических взаимоотношений изолятов вирусов, выделен-ных в разных странах, четкой зависимости между географическим происхождением и степенью идентичности фрагментов геномов вирусов выявлено не было. Ключевые

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Identification and complete genome analysis of a virus variant or putative new foveavirus associated with apple green crinkle disease

et al. 2013

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A virus identified as "apple green crinkle associated virus" (AGCaV) was isolated from Aurora Golden Gala apple showing severe symptoms of green crinkle disease. Evidence was obtained of a potential causal relationship to the disease. The viral genome consists of 9266 nucleotides, excluding the poly(A) tail at the 3'-terminus. It has a genome organization similar to that of members of the species Apple stem pitting virus (ASPV), the type species of the genus Foveavirus, family Betaflexiviridae. ORF1 of AGCaV encodes a replicase-complex polyprotein with a molecular mass of 247 kDa; the proteins of ORFs 2, 3, and 4 (TGB proteins) are estimated to be 25.1 kDa, 12.8 kDa, and 7.4 kDa, respectively; and ORF5 encodes the CP, with an estimated molecular mass of 43.3 kDa. Interestingly, AGCaV utilizes different stop codons for ORF1, ORF3, and ORF5 compared to the ASPV type isolate PA66, and between the two viruses, six distinct indel events were observed within ORF5. AGCaV has four non-coding regions (NCRs), including a 5'-NCR (60 nt), a 3'-NCR (134 nt), and two intergenic (IG) NCRs: IG-NCR1 (69 nt) and IG-NCR2 (91 nt). A conserved stable hairpin structure was identified in the variable 5'-NCR of members of the genus Foveavirus. AGCaV may be a variant or strain of ASPV with unique biological properties, but there is evidence that it may be a distinct putative foveavirus.

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Sequence diversity and potential recombination events in the coat protein gene of Apple stem pitting virus

Cited by 23 publications

References 38 publications

Molecular variability of Apple chlorotic leaf spot virus isolated in Belarus

Molecular variability of Apple chlorotic leaf spot virus isolated in Belarus

Distribution and genetic diversity of three apple viruses in Belarus

Identification and complete genome analysis of a virus variant or putative new foveavirus associated with apple green crinkle disease

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