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Phylogenetic analysis and molecular characterization of BBTV DNA-R of wild and cultivated banana isolates from East Java, Indonesia
Análisis filogenético y caracterización molecular de BBTV DNA-R de aislados de banano silvestre y cultivado de Java Oriental, Indonesia
DOI:
https://doi.org/10.15446/rfnam.v76n3.104708Keywords:
Bananas, Genetic variation, Identification, Rep protein, Virus (en)Bananos, Variación genética, Identificación, Proteína Rep, Virus (es)
Banana bunchy top virus (BBTV) molecular detection and understanding its origin are important issues for mitigating future spread. The aim of this study was to molecularly detect BBTV infection and analyze the characteristic also phylogenetic of banana isolates from East Java Indonesia. Two BBTV asymptomatic wild bananas and two BBTV symptomatic banana cultivars were examined. PCR amplifications were accomplished using BBTV DNA-R primers for master replication initiation protein. Sequences evaluations were conducted in SeqScanner. Sequences identification was performed in nucleotide BLAST. Translation of ORFs was determined using ORF Finder server tool. Protein identification was conducted in protein BLAST. Sequences polymorphisms were analyzed using DnaSP6. Phylogenetic analysis was employed using Neighbor-Joining algorithm with Kimura two-parameter (K2P) substitution model in MEGA7. Results showed that BBTV DNA-R components were detected in all isolates and confirmed as Rep protein. The sequences length were varied from 616 to 1,074 bp, low GC content (42.90%) and low conservation (56.47%). Asymptomatic wild bananas generated shorter length and more variable sequences, presumably related to the resistance mechanism. Phylogenetic analysis of BBTV DNA-R East Java with other 38 homolog sequences worldwide were found clustered in Asian Group, closely related to Vietnam, Thailand, and China. Hence, it presumably originated from China mainland via Malay Peninsula route.
La detección molecular virus del cogollo racimoso del banano y la comprensión de su origen son temas importantes para mitigar la propagación futura. El objetivo de este estudio fue detectar molecularmente la infección por BBTV y analizar las características filogenéticas de los aislamientos de banano de Java Oriental, Indonesia. Se examinaron dos cultivares de banano silvestre asintomáticos BBTV y dos cultivares de banano sintomáticos BBTV. Las amplificaciones por PCR se realizaron utilizando cebadores BBTV DNA-R para la proteína maestra de iniciación de la replicación. La evaluación e identificación de las secuencias se realizó en SeqScanner y un análisis nucleótido BLAST, respectivamente. La traducción de los ORF se determinó utilizando la herramienta de servidor ORF Finder. La identificación de proteínas se realizó empleando el programa BLAST. Los polimorfismos de las secuencias se analizaron utilizando DnaSP6. El análisis filogenético se empleó utilizando el algoritmo Neighbor-Joining con el modelo de sustitución Kimura de dos parámetros (K2P) en MEGA7. Los resultados mostraron que los componentes de BBTV DNA-R se detectaron en todos los aislamientos y se confirmaron como proteína Rep. La longitud de las secuencias varió de 616 a 1.074 pb, bajo contenido de GC (42,90%) y baja conservación (56,47%). Los bananos silvestres asintomáticos generaron secuencias más cortas y variables, presumiblemente relacionadas con el mecanismo de resistencia. El análisis filogenético de BBTV DNA-R East Java con otras 38 secuencias homólogas en todo el mundo se encontró agrupado en el Grupo Asiático, estrechamente relacionado con Vietnam, Tailandia y China. Por lo tanto, presumiblemente se originó en China continental a través de la ruta de la Península Malaya.
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