Rai Richa, Anand Yumlembam Rupert, Monteshori Sapam, Diksha Damini, Dubey Saurabh Kumar, Baranwal Virendra Kumar, Sharma Susheel Kumar
Advanced Center for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India.
ICAR Research Complex for NEH Region, Manipur Centre, Lamphelpat, Imphal, 795004 India.
3 Biotech. 2024 Nov;14(11):277. doi: 10.1007/s13205-024-04113-4. Epub 2024 Oct 23.
Divergent banana streak viruses (BSV) were characterized from banana plants exhibiting diverse symptoms in the Northeast region (NER) of India. Using rolling circle amplification (RCA), the complete genome sequences of seven episomal banana streak MY virus (BSMYV) isolates, including two novel variants, and two new banana streak IM virus (BSIMV) isolates were characterized. The novel BSMYV genetic variants were associated with conspicuous necrosis on newly emerged leaves, peduncle distortion, pseudostem internal necrosis, in addition to common streak symptoms. For complete genome nucleotide sequences, BSMYV-IN4 and IN5 shared 77-79% identity with other BSMYVs, while BSMYV-IN7 and IN8 exhibited identities of 77-97%. This study reports for the first time, the complete genomes of two banana streak IM virus (BSIMV-IN1 and -IN2) infecting triploid banana hybrids exhibiting leaf distortion, stunted rosette-like growth, and necrosis, sharing 87% sequence identity with reference BSIMV genome (GenBank accession no. HQ593112). Phylogenetic inference based on complete genomes revealed the distinct and congruent placement of BSMYV-IN4 and IN5 within the BSMYV cluster. Pairwise sequence comparisons of the conserved RT/RNase H nucleotide (nt) sequences revealed that the BSMYV-IN7 and IN4 isolates showed 85% and 97% identity to BSMYV (AY805074), respectively, which shared highest nt identity with BSMYV-IN6, IN9, and IN10, at 100%. The RT/RNase H nt sequences of BSIMV-IN1 and IN2 had 98% identity with the BSIMV (HQ593112), but were characterized as novel variants of BSIMV based on complete genomes. An analysis of relative synonymous codon usage (RSCU) pattern in the ORFIII polyprotein of BSMYV and BSIMV isolates revealed AGA and AGG (arginine) as the most frequently overrepresented codons (>1.5), evolutionary conserved in the genome of both species. A total of 14 recombination events were detected among the 36 BSV genomes, with recombination breakpoints mainly located in the ORFI, III, and IGR genomic regions. A novel phylogenetic cluster, comprised of BSMYV-IN4 and IN5 within the clade I was probably derived from heterologous recombination between parents resembling banana streak VN virus (BSVNV; AY750155) and banana streak GF virus (BSGFV; KJ013507) isolates. The present study conclusively reports the infection of genetically and symptomatically distinct variants of BSMYV and BSIMV infecting banana hybrids in NER India.
从印度东北地区（NER）表现出不同症状的香蕉植株中鉴定出了不同的香蕉条纹病毒（BSV）。利用滚环扩增（RCA）技术，对7个附加型香蕉条纹MY病毒（BSMYV）分离株（包括2个新变体）和2个新的香蕉条纹IM病毒（BSIMV）分离株的完整基因组序列进行了鉴定。这些新的BSMYV基因变体除了具有常见的条纹症状外，还与新长出叶片上明显的坏死、果梗扭曲、假茎内部坏死有关。对于完整基因组核苷酸序列，BSMYV-IN4和IN5与其他BSMYV的序列同一性为77%-79%，而BSMYV-IN7和IN8的序列同一性为77%-97%。本研究首次报道了感染三倍体香蕉杂交种的两种香蕉条纹IM病毒（BSIMV-IN1和-IN2）的完整基因组，这些杂交种表现出叶片扭曲、莲座状生长受阻和坏死症状，与参考BSIMV基因组（GenBank登录号HQ593112）的序列同一性为87%。基于完整基因组的系统发育推断显示，BSMYV-IN4和IN5在BSMYV簇中具有独特且一致的位置。对保守的RT/RNase H核苷酸（nt）序列进行成对序列比较发现，BSMYV-IN7和IN4分离株与BSMYV（AY805074）的序列同一性分别为85%和97%，后者与BSMYV-IN6、IN9和IN10的nt同一性最高，为100%。BSIMV-IN1和IN2的RT/RNase H nt序列与BSIMV（HQ593112）的序列同一性为98%，但基于完整基因组被鉴定为BSIMV的新变体。对BSMYV和BSIMV分离株的ORFIII多聚蛋白中相对同义密码子使用（RSCU）模式的分析表明，AGA和AGG（精氨酸）是最常出现的高表达密码子（>1.5），在两个物种的基因组中具有进化保守性。在36个BSV基因组中总共检测到14个重组事件，重组断点主要位于ORFI、III和IGR基因组区域。一个新的系统发育簇，由进化枝I中的BSMYV-IN4和IN5组成，可能源自类似于香蕉条纹VN病毒（BSVNV；AY750155）和香蕉条纹GF病毒（BSGFV；KJ013507）分离株的亲本之间的异源重组。本研究最终报道了在印度东北地区感染香蕉杂交种的BSMYV和BSIMV在遗传和症状上不同的变体。
