In Silico Apple Genome-Encoded MicroRNA Target Binding Sites Targeting Apple Chlorotic Leaf Spot Virus
<i>Apple chlorotic leaf spot virus</i> (ACLSV) (genus, <i>Trichovirus</i>; family, <i>Betaflexiviridae</i>) is a widespread, deleterious, and the most damaging pathogen of pome and fruit trees including domesticated apple (<i>Malus</i> × <i>domes...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-07-01
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| Series: | Horticulturae |
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| Online Access: | https://www.mdpi.com/2311-7524/9/7/808 |
| _version_ | 1797406233948323840 |
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| author | Muhammad Aleem Ashraf Nimra Murtaza Judith K. Brown Naitong Yu |
| author_facet | Muhammad Aleem Ashraf Nimra Murtaza Judith K. Brown Naitong Yu |
| author_sort | Muhammad Aleem Ashraf |
| collection | DOAJ |
| description | <i>Apple chlorotic leaf spot virus</i> (ACLSV) (genus, <i>Trichovirus</i>; family, <i>Betaflexiviridae</i>) is a widespread, deleterious, and the most damaging pathogen of pome and fruit trees including domesticated apple (<i>Malus</i> × <i>domestica</i> Borkh.), to which it is transmitted by grafting and pruning. The positive-sense, single-stranded RNA virus is 600–700 nm long and has a genome of 74.7–7.56 kbp in size, minus the poly-A tail and 3′- and 5′-untranslated regions. The genome has three overlapping open reading frames (ORFs) that encode a replication-associated protein (Rep), movement protein (MP), and coat protein (CP). RNA interference (RNAi)-mediated antiviral defense in eukaryotes has evolved to control infections in plant viruses. The objective of this study was to analyze locus-derived microRNAs (mdm-miRNAs) in the apple genome with potential for targeting ACLSV +ssRNA-encoded mRNAs, using a predictive approach that involves four algorithms. The goal is to mobilize the in silico-predicted endogenous mdm-miRNAs and trigger the RNAi pathway experimentally in apple trees to evaluate antiviral resistance to ACLSV. Experimentally validated apple (2<i>n</i> = 2<i>X</i> = 34) mdm-miRNAs (<i>n</i> = 322) were obtained from the miRBase database and aligned to the ACLSV genome (KU870525). Of the 322 targeting mature locus-derived mdm-miRNAs analyzed, nine apple mdm-miRNA homologs (mdm-miR395k, mdm-miR5225c, and mdm-miR7121 (a, b, c, d, e, f, g, h) were predicted by all “four algorithms”, whereas fifty-eight mdm-miRNAs were identified as consensus binding sites by the combined results of two algorithms. The miRanda, RNA22, and TAPIR algorithms predicted binding of mdm-miR395k at nucleotide position 4691 and identified it as the most effective interacting mdm-miRNA targeting the virus ORF1 sequence. An integrated Circos plot was generated to validate the accuracy of target prediction and determine if apple mdm-miRNAs could bind to the predicted ACLSV mRNA target(s). A genome-wide in silico-predicted miRNA-mediated target gene regulatory network was implicated to validate interactions necessary to warrant in vivo analysis. The availability of validated locus-derived microRNAs (mdm-miRNAs) with predicted potential to target ACLSV in infected apple trees represents the first step toward development of ACLSV-resistant apple trees. |
| first_indexed | 2024-03-09T03:22:25Z |
| format | Article |
| id | doaj.art-5a4eae1d8091484596e3c38766c85a8f |
| institution | Directory Open Access Journal |
| issn | 2311-7524 |
| language | English |
| last_indexed | 2024-03-09T03:22:25Z |
| publishDate | 2023-07-01 |
| publisher | MDPI AG |
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| series | Horticulturae |
| spelling | doaj.art-5a4eae1d8091484596e3c38766c85a8f2023-12-03T15:06:44ZengMDPI AGHorticulturae2311-75242023-07-019780810.3390/horticulturae9070808In Silico Apple Genome-Encoded MicroRNA Target Binding Sites Targeting Apple Chlorotic Leaf Spot VirusMuhammad Aleem Ashraf0Nimra Murtaza1Judith K. Brown2Naitong Yu3Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, ChinaInstitute of Biological Sciences, Faculty of Natural and Applied Sciences, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan 64200, PakistanSchool of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USAInstitute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China<i>Apple chlorotic leaf spot virus</i> (ACLSV) (genus, <i>Trichovirus</i>; family, <i>Betaflexiviridae</i>) is a widespread, deleterious, and the most damaging pathogen of pome and fruit trees including domesticated apple (<i>Malus</i> × <i>domestica</i> Borkh.), to which it is transmitted by grafting and pruning. The positive-sense, single-stranded RNA virus is 600–700 nm long and has a genome of 74.7–7.56 kbp in size, minus the poly-A tail and 3′- and 5′-untranslated regions. The genome has three overlapping open reading frames (ORFs) that encode a replication-associated protein (Rep), movement protein (MP), and coat protein (CP). RNA interference (RNAi)-mediated antiviral defense in eukaryotes has evolved to control infections in plant viruses. The objective of this study was to analyze locus-derived microRNAs (mdm-miRNAs) in the apple genome with potential for targeting ACLSV +ssRNA-encoded mRNAs, using a predictive approach that involves four algorithms. The goal is to mobilize the in silico-predicted endogenous mdm-miRNAs and trigger the RNAi pathway experimentally in apple trees to evaluate antiviral resistance to ACLSV. Experimentally validated apple (2<i>n</i> = 2<i>X</i> = 34) mdm-miRNAs (<i>n</i> = 322) were obtained from the miRBase database and aligned to the ACLSV genome (KU870525). Of the 322 targeting mature locus-derived mdm-miRNAs analyzed, nine apple mdm-miRNA homologs (mdm-miR395k, mdm-miR5225c, and mdm-miR7121 (a, b, c, d, e, f, g, h) were predicted by all “four algorithms”, whereas fifty-eight mdm-miRNAs were identified as consensus binding sites by the combined results of two algorithms. The miRanda, RNA22, and TAPIR algorithms predicted binding of mdm-miR395k at nucleotide position 4691 and identified it as the most effective interacting mdm-miRNA targeting the virus ORF1 sequence. An integrated Circos plot was generated to validate the accuracy of target prediction and determine if apple mdm-miRNAs could bind to the predicted ACLSV mRNA target(s). A genome-wide in silico-predicted miRNA-mediated target gene regulatory network was implicated to validate interactions necessary to warrant in vivo analysis. The availability of validated locus-derived microRNAs (mdm-miRNAs) with predicted potential to target ACLSV in infected apple trees represents the first step toward development of ACLSV-resistant apple trees.https://www.mdpi.com/2311-7524/9/7/808<i>Trichovirus</i>in silico tools<i>apple chlorotic leaf spot virus</i>miRNARNA interference |
| spellingShingle | Muhammad Aleem Ashraf Nimra Murtaza Judith K. Brown Naitong Yu In Silico Apple Genome-Encoded MicroRNA Target Binding Sites Targeting Apple Chlorotic Leaf Spot Virus Horticulturae <i>Trichovirus</i> in silico tools <i>apple chlorotic leaf spot virus</i> miRNA RNA interference |
| title | In Silico Apple Genome-Encoded MicroRNA Target Binding Sites Targeting Apple Chlorotic Leaf Spot Virus |
| title_full | In Silico Apple Genome-Encoded MicroRNA Target Binding Sites Targeting Apple Chlorotic Leaf Spot Virus |
| title_fullStr | In Silico Apple Genome-Encoded MicroRNA Target Binding Sites Targeting Apple Chlorotic Leaf Spot Virus |
| title_full_unstemmed | In Silico Apple Genome-Encoded MicroRNA Target Binding Sites Targeting Apple Chlorotic Leaf Spot Virus |
| title_short | In Silico Apple Genome-Encoded MicroRNA Target Binding Sites Targeting Apple Chlorotic Leaf Spot Virus |
| title_sort | in silico apple genome encoded microrna target binding sites targeting apple chlorotic leaf spot virus |
| topic | <i>Trichovirus</i> in silico tools <i>apple chlorotic leaf spot virus</i> miRNA RNA interference |
| url | https://www.mdpi.com/2311-7524/9/7/808 |
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