Singh Amit Kumar, Mahinghara Birender Kumar, Hallan Vipin, Ram Raja, Zaidi Aijaz Asghar
Plant Virology Lab, Floriculture Division, Institute of Himalayan Bioresource Technology, Palampur 176 061, Himachal Pradesh, India.
Virus Genes. 2008 Apr;36(2):421-7. doi: 10.1007/s11262-008-0197-1. Epub 2008 Jan 18.
The complete genomic nucleotide sequence of an Indian isolate of Lily symptomless virus (LSV) was determined by sequencing 11 overlapping cDNA fragments of different sizes. The genome consisted of 8,394 nucleotides, excluding the poly (A) tail and contained six open reading frames (ORFs) coding protein for ORF1 220 kDa [1,948 amino acid (aa)], ORF2 25 kDa (228 aa), ORF3 12 kDa (106 aa), ORF4 7 kDa (64 aa), ORF5 32 kDa (291 aa) and ORF6 16 kDa (140 aa) from 5' to 3' end. Sequence was analyzed with other previously characterized full genomes of LSV. Phylogenetic analysis on the basis of RNA-dependent RNA polymerase (RdRp), Triple gene block proteins (TGB's), Coat protein (CP), and ORF6 (16 kDa protein) amino acid sequence revealed that Indian isolate is closely related to The Netherlands Isolate (AJ564638). The overall genome of the present LSV isolate shares 97-98% nucleotide sequence homology with the previously characterized isolates. The phylogenetic analysis, sequence alignment studies, and recombination detection program (RDP3) analysis provided evidence for the occurrence of recombination between the present isolate (AM422452) as major parent and The Netherlands Isolate (AJ564638) and Chinese isolate (AM263208) as minor parents in two different independent recombination events. Based on the recombination analysis, it is suggested that the 3' end of the present isolate is involved in recombination with Chinese isolate (AM263208) and gave rise to the Korean isolate. To the best of our knowledge, this is the first report of complete nucleotide sequence from India and also the first evidence of homologous recombination in LSV.
通过对11个不同大小的重叠cDNA片段进行测序，确定了印度分离的百合无症状病毒（LSV）的完整基因组核苷酸序列。该基因组由8394个核苷酸组成，不包括聚（A）尾，包含六个开放阅读框（ORF），从5'到3'端编码ORF1的220 kDa蛋白质[1948个氨基酸（aa）]、ORF2的25 kDa（228 aa）、ORF3的12 kDa（106 aa）、ORF4的7 kDa（64 aa）、ORF5的32 kDa（291 aa）和ORF6的16 kDa（140 aa）。将该序列与其他先前已鉴定的LSV全基因组进行了分析。基于RNA依赖性RNA聚合酶（RdRp）、三基因块蛋白（TGB）、外壳蛋白（CP）和ORF6（16 kDa蛋白）氨基酸序列的系统发育分析表明，印度分离株与荷兰分离株（AJ564638）密切相关。本LSV分离株的整个基因组与先前鉴定的分离株具有97 - 98%的核苷酸序列同源性。系统发育分析、序列比对研究和重组检测程序（RDP3）分析提供了证据，表明在两个不同的独立重组事件中，本分离株（AM422452）作为主要亲本与荷兰分离株（AJ564638）和中国分离株（AM263208）作为次要亲本之间发生了重组。基于重组分析，表明本分离株的3'端与中国分离株（AM263208）参与重组并产生了韩国分离株。据我们所知，这是来自印度的完整核苷酸序列的首次报道，也是LSV中同源重组的首个证据。
