In Silico Identification of Cassava Genome-Encoded MicroRNAs with Predicted Potential for Targeting the ICMV-Kerala Begomoviral Pathogen of Cassava

文献类型： 外文期刊

第一作者： Ashraf, Muhammad Aleem

作者： Ashraf, Muhammad Aleem;Yu, Naitong;Ashraf, Muhammad Aleem;Ali, Babar;Brown, Judith K.;Shahid, Imran

作者机构：

关键词： begomovirus; computational miRNA algorithms; Indian cassava mosaic virus-Kerala; non-coding RNA; RNA interference; R-language; virus resistance

期刊名称：VIRUSES-BASEL （ 影响因子：4.7； 五年影响因子：4.8 ）

ISSN：

年卷期： 2023 年 15 卷 2 期

页码：

收录情况： SCI

摘要： Cassava mosaic disease (CMD) is caused by several divergent species belonging to the genus Begomovirus (Geminiviridae) transmitted by the whitefly Bemisia tabaci cryptic species group. In India and other parts of Asia, the Indian cassava mosaic virus-Kerala (ICMV-Ker) is an emergent begomovirus of cassava causing damage that results in reduced yield loss and tuber quality. Double-stranded RNA-mediated interference (RNAi) is an evolutionary conserved mechanism in eukaryotes and highly effective, innate defense system to inhibit plant viral replication and/or translation. The objective of this study was to identify and characterize cassava genome-encoded microRNAs (mes-miRNA) that are predicted to target ICMV-Ker ssDNA-encoded mRNAs, based on four in silico algorithms: miRanda, RNA22, Tapirhybrid, and psRNA. The goal is to deploy the predicted miRNAs to trigger RNAi and develop cassava plants with resistance to ICMV-Ker. Experimentally validated mature cassava miRNA sequences (n = 175) were downloaded from the miRBase biological database and aligned with the ICMV-Ker genome. The miRNAs were evaluated for base-pairing with the cassava miRNA seed regions and to complementary binding sites within target viral mRNAs. Among the 175 locus-derived mes-miRNAs evaluated, one cassava miRNA homolog, mes-miR1446a, was identified to have a predicted miRNA target binding site, at position 2053 of the ICMV-Ker genome. To predict whether the cassava miRNA might bind predicted ICMV-Ker mRNA target(s) that could disrupt viral infection of cassava plants, a cassava locus-derived miRNA-mRNA regulatory network was constructed using Circos software. The in silico-predicted cassava locus-derived mes-miRNA-mRNA network corroborated interactions between cassava mature miRNAs and the ICMV-Ker genome that warrant in vivo analysis, which could lead to the development of ICMV-Ker resistant cassava plants.

分类号：

  • 相关文献
作者其他论文 更多>>
  • Identification and Characterization of the Stimulator of Interferon Genes (STING) in Chinese Giant Salamander Andrias davidianus

    作者：Chen, Zhongyuan;Wang, Ronghua;Wang, Ruisong;Yang, Pinhong;Yu, Naitong

    关键词：stimulator of interferon genes (STING); Chinese giant salamander; Andrias davidianus ranavirus (ADRV); antiviral activity; innate immunity

  • In Silico Apple Genome-Encoded MicroRNA Target Binding Sites Targeting Apple Chlorotic Leaf Spot Virus

    作者：Ashraf, Muhammad Aleem;Yu, Naitong;Ashraf, Muhammad Aleem;Murtaza, Nimra;Brown, Judith K. K.

    关键词：Trichovirus; in silico tools; apple chlorotic leaf spot virus; miRNA; RNA interference

  • Computational Biology and Machine Learning Approaches Identify Rubber Tree (Hevea brasiliensis Muell. Arg.) Genome Encoded MicroRNAs Targeting Rubber Tree Virus 1

    作者：Ashraf, Muhammad Aleem;Zou, Zhi;Ashraf, Muhammad Aleem;Tariq, Hafiza Kashaf;Hu, Xiao-Wen;Khan, Jallat

    关键词：rubber tree capillovirus 1; microRNAs; plant-virus interaction; RNAi; computational algorithms; gene silencing; minimum free energy

  • In silico identification of sugarcane (Saccharum officinarum L.) genome encoded microRNAs targeting sugarcane bacilliform virus

    作者：Ashraf, Muhammad Aleem;Feng, Xiaoyan;Ashraf, Fakiha;Shen, Linbo;Zhang, Shuzhen;Ashraf, Muhammad Aleem;Hu, Xiaowen;Iqbal, Muhammad Shahzad

    关键词：

  • 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales (Aug, 10.1007/s00705-021-05143-6, 2021)

    作者：Kuhn, Jens H.;Wada, Jiro;Adkins, Scott;Al Kubrusli, Rim;Buettner, Carmen;Gaskin, Thomas;Huettner, Florian;von Bargen, Susanne;Alkhovsky, Sergey V.;Amarasinghe, Gaya K.;Avsic-Zupanc, Tatjana;Ayllon, Maria A.;Bahl, Justin;Balkema-Buschmann, Anne;Ballinger, Matthew J.;Basler, Christopher F.;Bavari, Sina;Beer, Martin;Bejerman, Nicolas;Bennett, Andrew J.;Bente, Dennis A.;Bergeron, Eric;Bird, Brian H.;Blair, Carol D.;Blasdell, Kim R.;Agwanda, Bernard R.;Blystad, Dag-Ragnar;Bojko, Jamie;Borth, Wayne B.;Hu, John S.;Kawate, Michael;Olmedo-Velarde, Alejandro;Park, Adam C.;Sugano, Jari;Uchida, Janice;Bradfute, Steven;Breyta, Rachel;Briese, Thomas;Briese, Thomas;Brown, Paul A.;Brown, Judith K.;Buchholz, Ursula J.;Buchmeier, Michael J.;Bukreyev, Alexander;Burt, Felicity;Burt, Felicity;Calisher, Charles H.;Cao, Mengji;Zhang, Song;Casas, Inmaculada;Chandran, Kartik;Charrel, Remi N.;de Lamballerie, Xavier;Cheng, Qi;Hu, Tao;Wang, Yaqin;Wu, Jiangxiang;Chiaki, Yuya;Chiapello, Marco;Ciuffo, Marina;Peracchio, Carlotta;Vaira, Anna Maria;Vallino, Marta;Choi, Il-Ryong;Choi, Il-Ryong;Clegg, J. Christopher S.;Crozier, Ian;Dal Bo, Elena;de la Torre, Juan Carlos;de Swart, Rik L.;Debat, Humberto;Dheilly, Nolwenn M.;Di Cicco, Emiliano;Di Paola, Nicholas;Dye, John M.;Gago-Zachert, Selma;Garrison, Aura R.;Palacios, Gustavo;Di Serio, Francesco;Dietzgen, Ralf G.;Digiaro, Michele;Dolnik, Olga;Drebot, Michael A.;Drexler, J. Felix;Junglen, Sandra;Marklewitz, Marco;Paraskevopoulou, Sofia;Drexler, J. Felix;Junglen, Sandra;Marklewitz, Marco;Paraskevopoulou, Sofia;Drexler, J. Felix;Junglen, Sandra;Marklewitz, Marco;Paraskevopoulou, Sofia;Dundon, William G.;Duprex, W. Paul;Durrwald, Ralf;Easton, Andrew J.;Ebihara, Hideki;Elbeaino, Toufic;Ergunay, Koray;Fooks, Anthony R.;Forgia, Marco;Formenty, Pierre B. H.;Franova, Jana;Koloniuk, Igor;Freitas-Astua, Juliana;Fu, Jingjing;Han, Tong;Yang, Caixia;Furl, Stephanie;Garcia, Maria Laura;Garcia-Sastre, Adolfo;Gaskin, Thomas;Gonzalez, Jean-Paul J.;Griffiths, Anthony;Muehlberger, Elke;Griffiths, Anthony;Muehlberger, Elke;Goldberg, Tony L.;Groschup, Martin H.;Guenther, Stephan;Hall, Roy A.;Hammond, John;Hepojoki, Jussi;Hewson, Roger;Hong, Jiang;Hong, Ni;Li, Longhui;Liu, Huazhen;Wang, Guoping;Wang, Yanxiang;Wen, Shaohua;Yang, Zuokun;Zhang, Zhe;Horie, Masayuki;Hughes, Holly R.;Lambert, Amy J.;Hyndman, Timothy H.;Ilyas, M.;Jalkanen, Risto;Jiang, Daohong;Jonson, Gilda B.;Junglen, Sandra;Marklewitz, Marco;Paraskevopoulou, Sofia;Kadono, Fujio;Tsuda, Shinya;Kaukinen, Karia H.;Miller, Kristina M.;Tabata, Amy;Klempa, Boris;Klingstrom, Jonas;Kondo, Hideki;Koonin, Eugene V.;Wolf, Yuri I.;Krupovic, Mart;Kubota, Kenji;Usugi, Tomio;Kurath, Gael;Laenen, Lies;Maes, Piet;Langevin, Stanley L.;Lee, Benhur;Lefkowitz, Elliot J.;Leroy, Eric M.;Li, Shaorong;Liu, Jianrong;Lukashevich, Igor S.;Lukashevich, Igor S.;de Souza, William Marciel;Marshall, Sergio H.;Marzano, Shin-Yi L.;Massart, Sebastien;McCauley, John W.;Melzer, Michael;Mielke-Ehret, Nicole;Muehlbach, Hans-Peter;Ming, Tobi J.;Mirazimi, Ali;Mordecai, Gideon J.;Naidu, Rayapati;Natsuaki, Tomohide;Navarro, Jose A.;Netesov, Sergey V.;Neumann, Gabriele;Nowotny, Norbert;Pallas, Vicente;Palyi, Bernadett;Papa, Anna;Parrish, Colin R.;Patterson, David A.;Pauvolid-Correa, Alex;Pauvolid-Correa, Alex;Paweska, Janusz T.;Payne, Susan;Perez, Daniel R.;Postler, Thomas S.;Qi, Liying;Xu, Lei;Radoshitzky, Sheli R.;Resende, Renato O.;Reyes, Carina A.;Luna, Gabriel Robles;Rima, Bertus K.;Romanowski, Victor;Rubbenstroth, Dennis;Rubino, Luisa;Runstadler, Jonathan A.;Sabanadzovic, Sead;Salvato, Maria S.;Sang, Rosemary;Tchouassi, David P.;Torto, Baldwyn;Sasaya, Takahide;Schulze, Angela D.;Schwemmle, Martin;Shi, Mang;Shi, Xiaohong;Shi, Zhengli;Shimomoto, Yoshifumi;Shirako, Yukio;Siddell, Stuart G.;Simmonds, Peter;Sironi, Manuela;Smagghe, Guy;Smither, Sophie;Song, Jin-Won;Spann, Kirsten;Spengler, Jessica R.;Stenglein, Mark D.;Stone, David M.;Suttle, Curtis A.;Suttle, Curtis A.;Suttle, Curtis A.;Suttle, Curtis A.;Suttle, Curtis A.;Takada, Ayato;Takeuchi, Shigeharu;Teffer, Amy;Tesh, Robert B.;Vasilakis, Nikos;Thornburg, Natalie J.;Tomitaka, Yasuhiro;Tomonaga, Keizo;Tordo, Noel;Towner, Jonathan S.;Tu, Changchun;Turina, Massimo;Tzanetakis, Ioannis E.;van den Hoogen, Bernadette;Varsani, Arvind;Verbeek, Martin;Wahl, Victoria;Walker, Peter J.;Wang, Lin-Fa;Waqas, Muhammad;Wei, Taiyun;Whitfield, Anna E.;Williams, John V.;Yanagisawa, Hironobu;Zerbini, F. Murilo;Zhai, Lifeng;Zhang, Jinguo;Zhou, Xueping;Towner, Jonathan S.;Ayllon, Maria A.;Bojko, Jamie;Breyta, Rachel;Debat, Humberto;Gonzalez, Jean-Paul J.;Hepojoki, Jussi;Horie, Masayuki;Junglen, Sandra;Laenen, Lies;Marklewitz, Marco;Nowotny, Norbert;Park, Adam C.;Pauvolid-Correa, Alex;Varsani, Arvind;Agwanda, Bernard R.;Agwanda, Bernard R.;Ferguson, Hugh W.;Gao, George Fu;Hongo, Seiji;Kobinger, Gary;Nunes, Marcio R. T.;Rota, Paul;Sall, Amadou Alpha;Zhang, Yong-Zhen;Zhang, Yong-Zhen;Zhang, Yong-Zhen

    关键词：

  • 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

    作者：Kuhn, Jens H.;Wada, Jiro;Adkins, Scott;Al Kubrusli, Rim;Buettner, Carmen;Gaskin, Thomas;Huettner, Florian;von Bargen, Susanne;Alkhovsky, Sergey V.;Amarasinghe, Gaya K.;Avsic-Zupanc, Tatjana;Ayllon, Maria A.;Bahl, Justin;Balkema-Buschmann, Anne;Ballinger, Matthew J.;Basler, Christopher F.;Bavari, Sina;Beer, Martin;Rubbenstroth, Dennis;Bejerman, Nicolas;Bennett, Andrew J.;Bente, Dennis A.;Bergeron, Eric;Bird, Brian H.;Blair, Carol D.;Blasdell, Kim R.;Blystad, Dag-Ragnar;Bojko, Jamie;Borth, Wayne B.;Hu, John S.;Kawate, Michael;Olmedo-Velarde, Alejandro;Park, Adam C.;Sugano, Jari;Uchida, Janice;Bradfute, Steven;Breyta, Rachel;Briese, Thomas;Briese, Thomas;Brown, Paul A.;Brown, Judith K.;Buchholz, Ursula J.;Buchmeier, Michael J.;Bukreyev, Alexander;Burt, Felicity;Burt, Felicity;Calisher, Charles H.;Cao, Mengji;Zhang, Song;Casas, Inmaculada;Chandran, Kartik;Charrel, Remi N.;de Lamballerie, Xavier;Cheng, Qi;Hu, Tao;Wang, Yaqin;Wu, Jiangxiang;Chiaki, Yuya;Chiapello, Marco;Ciuffo, Marina;Peracchio, Carlotta;Vaira, Anna Maria;Vallino, Marta;Choi, Il-Ryong;Choi, Il-Ryong;Crozier, Ian;Dal Bo, Elena;de la Torre, Juan Carlos;de Swart, Rik L.;Debat, Humberto;Dheilly, Nolwenn M.;Di Cicco, Emiliano;Di Paola, Nicholas;Dye, John M.;Garrison, Aura R.;Palacios, Gustavo;Di Serio, Francesco;Rubino, Luisa;Dietzgen, Ralf G.;Digiaro, Michele;Dolnik, Olga;Drebot, Michael A.;Drexler, J. Felix;Junglen, Sandra;Marklewitz, Marco;Paraskevopoulou, Sofia;Drexler, J. Felix;Junglen, Sandra;Marklewitz, Marco;Paraskevopoulou, Sofia;Drexler, J. Felix;Junglen, Sandra;Marklewitz, Marco;Paraskevopoulou, Sofia;Dundon, William G.;Duprex, W. Paul;Durrwald, Ralf;Easton, Andrew J.;Ebihara, Hideki;Elbeaino, Toufic;Ergunay, Koray;Fooks, Anthony R.;Forgia, Marco;Formenty, Pierre B. H.;Koloniuk, Igor;Freitas-Astua, Juliana;Fu, Jingjing;Han, Tong;Yang, Caixia;Fuerl, Stephanie;Gago-Zachert, Selma;Garcia, Maria Laura;Garcia-Sastre, Adolfo;Gaskin, Thomas;Gonzalez, Jean-Paul J.;Griffiths, Anthony;Muehlberger, Elke;Griffiths, Anthony;Muehlberger, Elke;Goldberg, Tony L.;Groschup, Martin H.;Guenther, Stephan;Hall, Roy A.;Hammond, John;Hepojoki, Jussi;Hewson, Roger;Hong, Jiang;Hong, Ni;Li, Longhui;Liu, Huazhen;Wang, Guoping;Wang, Yanxiang;Wen, Shaohua;Yang, Zuokun;Zhang, Zhe;Horie, Masayuki;Hughes, Holly R.;Lambert, Amy J.;Hyndman, Timothy H.;Ilyas, M.;Jalkanen, Risto;Jiang, Daohong;Jiang, Daohong;Junglen, Sandra;Marklewitz, Marco;Paraskevopoulou, Sofia;Kadono, Fujio;Tsuda, Shinya;Kaukinen, Karia H.;Li, Shaorong;Miller, Kristina M.;Tabata, Amy;Klempa, Boris;Klingstrom, Jonas;Kondo, Hideki;Koonin, Eugene V.;Wolf, Yuri I.;Krupovic, Mart;Kubota, Kenji;Usugi, Tomio;Kurath, Gael;Laenen, Lies;Maes, Pie;Langevin, Stanley L.;Lee, Benhur;Lefkowitz, Elliot J.;Leroy, Eric M.;Li, Jianrong;Lukashevich, Igor S.;Lukashevich, Igor S.;de Souza, William Marciel;Marshall, Sergio H.;Marzano, Shin-Yi L.;Massart, Sebastien;McCauley, John W.;Melzer, Michael;Mielke-Ehret, Nicole;Muehlbach, Hans-Peter;Ming, Tobi J.;Mirazimi, Ali;Mordecai, Gideon J.;Naidu, Rayapati;Natsuaki, Tomohide;Navarro, Jose A.;Netesov, Sergey V.;Neumann, Gabriele;Nowotny, Norbert;Pallas, Vicente;Palyi, Bernadett;Papa, Anna;Parrish, Colin R.;Patterson, David A.;Pauvolid-Correa, Alex;Pauvolid-Correa, Alex;Paweska, Janusz T.;Payne, Susan;Perez, Daniel R.;Postler, Thomas S.;Qi, Liying;Xu, Lei;Radoshitzky, Sheli R.;Resende, Renato O.;Reyes, Carina A.;Luna, Gabriel Robles;Rima, Bertus K.;Romanowski, Victor;Runstadler, Jonathan A.;Sabanadzovic, Sead;Salvato, Maria S.;Sang, Rosemary;Tchouassi, David P.;Torto, Baldwyn;Sasaya, Takahide;Schulze, Angela D.;Schwemmle, Martin;Shi, Mang;Shi, Xiaohong;Shi, Zhengli;Shimomoto, Yoshifumi;Shirako, Yukio;Siddell, Stuart G.;Simmonds, Peter;Sironi, Manuela;Smagghe, Guy;Smither, Sophie;Song, Jin-Won;Spann, Kirsten;Spengler, Jessica R.;Stenglein, Mark D.;Stone, David M.;Suttle, Curtis A.;Suttle, Curtis A.;Suttle, Curtis A.;Suttle, Curtis A.;Suttle, Curtis A.;Takada, Ayato;Takeuchi, Shigeharu;Teffer, Amy;Tesh, Robert B.;Vasilakis, Nikos;Thornburg, Natalie J.;Tomitaka, Yasuhiro;Tomonaga, Keizo;Tordo, Noel;Towner, Jonathan S.;Tu, Changchun;Turina, Massimo;Tzanetakis, Ioannis E.;van den Hoogen, Bernadette;Varsani, Arvind;Verbeek, Martin;Wahl, Victoria;Walker, Peter J.;Wang, Lin-Fa;Waqas, Muhammad;Wei, Taiyun;Whitfield, Anna E.;Williams, John V.;Yanagisawa, Hironobu;Zerbini, F. Murilo;Zhai, Lifeng;Zhang, Jinguo;Zhou, Xueping;Towner, Jonathan S.;Ayllon, Maria A.;Bojko, Jamie;Breyta, Rachel;Debat, Humberto;Gonzalez, Jean-Paul J.;Hepojoki, Jussi;Horie, Masayuki;Junglen, Sandra;Laenen, Lies;Marklewitz, Marco;Nowotny, Norbert;Park, Adam C.;Pauvolid-Correa, Alex;Varsani, Arvind;Agwanda, Bernard R.;Agwanda, Bernard R.;Ferguson, Hugh W.;Franova, Jana;Gao, George Fu;Hongo, Seiji;Kobinger, Gary;Nunes, Marcio R. T.;Rota, Paul;Sall, Amadou Alpha;Zhang, Yong-Zhen;Zhang, Yong-Zhen;Zhang, Yong-Zhen

    关键词：

  • Potential targets for evaluation of sugarcane yellow leaf virus resistance in sugarcane cultivars: in silico sugarcane miRNA and target network prediction

    作者：Ashraf, Muhammad Aleem;Ashraf, Fakiha;Feng, Xiaoyan;Shen, Linbo;Zhang, Shuzhen;Ashraf, Muhammad Aleem;Feng, Xiaoyan;Zhang, Shuzhen;Hu, Xiaowen;Khan, Jallat

    关键词：Host-virus interaction; RNA interference; Saccharum officinarum; sugarcane yellow leaf virus; target prediction

微信小程序