Heteroplasmy due to coexistence of mtCOI haplotypes from different lineages of the Thrips tabaci cryptic species group.

Heteroplasmy is the existence of multiple mitochondrial DNA haplotypes within the cell. Although the number of reports of heteroplasmy is increasing for arthropods, the occurrence, number of variants, and origins are not well studied. In this research, the occurrence of heteroplasmy was investigated in Thrips tabaci, a putative species complex whose lineages can be distinguished by their mitochondrial DNA haplotypes. The results from this study showed that heteroplasmy was due to the occurrence of mitochondrial cytochrome oxydase I (mtCOI) haplotypes from two different T. tabaci lineages. An assay using flow cytometry and quantitative real-time PCR was then used to quantify the per cell copy number of the two mtCOI haplotypes present in individuals exhibiting heteroplasmy from nine geographically distant populations in India. All of the T. tabaci individuals in this study were found to exhibit heteroplasmy, and in every individual the per cell copy number of mtCOI from lineage 3 comprised 75-98% of the haplotypes detected and was variable among individuals tested. There was no evidence to suggest that the presense of lineage-specific haplotypes was due to nuclear introgression; however, further studies are needed to investigate nuclear introgression and paternal leakage during rare interbreeding between individuals from lineages 2 and 3.

Sequence analysis of Indian iris yellow spot virus ambisense genome segments: evidence of interspecies RNA recombination.

The nucleotide sequence of M- and S-RNA segments of an Indian iris yellow spot virus (IYSV) were determined. Sequence comparisons showed that both of these sequences shared less than 95 % identity with those other known IYSV isolates. Phylogenetic analysis revealed that the S- and M-RNA sequences of known IYSV isolates clustered with those of the tospoviruses, tomato yellow ring virus, polygonum ringspot virus and hippeastrum chlorotic ringspot virus. Further, multiple recombination detection methods detected inter- and intra-species recombination events that clustered primarily within the intergenic regions of S- and M-RNA, suggesting that these are possibly recombination hotspots in IYSV and closely related tospoviruses.

First Report of Iris yellow spot virus Infecting Allium tuberosum in India.

Allium tuberosum L., commonly known as garlic chives, is an important spice in northeastern India as well as in many other parts of the world. Iris yellow spot virus (IYSV; genus Tospovirus, family Bunyaviridae) is an important pathogen of onion (4) and other related Alliums such as garlic (3) and leek (2). During April 2013, symptoms potentially induced by IYSV such as chlorotic and straw-colored spindle-like lesions were observed on leaves of A. tuberosum accession Hanzong Winter (CGN 20779) plants in the wild species garden at the Directorate of Onion and Garlic Research (DOGR), Rajgurunagar, Pune, Maharashtra, India. Ten plant samples of A. tuberosum were randomly collected from the wild species garden and the upper, middle, and lower portions of the leaves were pooled and tested by double-antibody sandwich (DAS)-ELISA using a commercially available kit (Agdia Inc., Elkhart, IN) for IYSV. All of them showed positive results for IYSV incidence. Total RNA from the ELISA positive leaf samples of A. tuberosum was extracted using the RNeasy Plant Mini kit (Qiagen GmbH, Hilden, Germany). The primer pair IYSV-F (5'-TCAGAAATCGAGAAACTT-3') and IYSV-R (5'-TAATTATATCTATCTTTCTTGG-3') (1) was used for RT-PCR. The primer pair was specific to amplify 797 bp of the nucleocapsid (N) gene of IYSV. The amplified product derived from A. tuberosum isolate was purified by QIAquick PCR Purification Kit (Qiagen) and cloned using the vector pDrive (Qiagen). The recombinant clone was sequenced (Accession No. KF624624). Sequence analysis performed on CLC Main Workbench Version 6.8.4 confirmed that the fragment was of IYSV. Nucleotide sequence comparison of our virus with other IYSV isolates revealed that the highest nucleotide identity (99%) was with the IYSV garlic isolate (HM173691) from India. Further, maximum 96% protein identity was with IYSV onion isolate (ACA09432) and garlic isolate (ADK56108) from India. To our knowledge, this is the first report of IYSV naturally occurring on A. tuberosum in India. It is evident from previous studies that IYSV causes significant losses in onions (1) and from this study, that its symptoms have direct impact on quality of garlic chives. Further detailed studies are required to assess the magnitude of the impact of IYSV infection on yield and quality of A. tuberosum. References: (1) A. Bulajic et al. Plant Dis. 93:976, 2009. (2) M. C. Córdoba-Sellés et al. Plant Dis. 91:1365, 2007. (3) S. J. Gawande et al. Plant Dis. 94:1066, 2010. (4) B. Mandal et al. Plant Dis. 96:468, 2012.

First Report of Leek yellow stripe virus in Allium sativum in Western India.

Garlic (Allium sativum L.) is an important bulbous spice crop in India as well as other parts of world. Garlic is well known for its medicinal properties. Degeneration due to viral infections is one of the important constraints in exploiting its yield potential. Leek yellow stripe virus (LYSV), genus Potyvirus, family Potyviridae, is a prominent virus known to infect garlic worldwide (4). During July 2013, potyvirus-like symptoms such as mosaic, streaking, stunting, mottling of leaves were observed on garlic cv. G-41 and landrace Ranibennur local, collected from Karnataka, India, and maintained at the Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India. The incidence of symptomatic plants was estimated at 70% for Ranibennur local and 68% for cv. G-41. The symptomatic leaves were sampled diagonally from the field. Twenty symptomatic plants per cultivar with each sample was composited from young, middle, and lower (basal) leaves of the plant. These samples were tested by double-antibody sandwich (DAS)-ELISA for LYSV using commercially available kit (Agdia Inc., Elkhart, IN). ELISA-positive plants were further subjected to molecular studies. Total RNA from the infected leaf samples were extracted by RNeasy Plant Mini kit (Qiagen GmbH, Hilden, Germany) and assayed by reverse transcription (RT)-PCR using primer pair LYSV-F 2 (5'-GCACCATACAGTGAATTGAG-3') (1), LYSV-R (5'-GCCTCGCGCGCTCTAA-3') (3) to amplify 874 bases of partial Nib and partial coat protein gene. The amplified product of 874 bp derived from A. sativum isolate was purified (QIAquick PCR Purification Kit, Qiagen) and cloned using vector pDrive (Qiagen). The recombinant clones were sequenced and submitted in NCBI database (GenBank Accession No. KF850539). The sequence analysis performed on CLC Main Workbench Version 6.8.4 gave confirmation of LYSV. Further, phylogenetic analysis of the 874-nt sequence revealed the highest nucleotide identity (80 to 82%) with LYSV isolates (DQ925453, JN127339, AB005611, and JX429965). To the best of our knowledge, this is the first report of natural infection of garlic by LYSV in western India. LYSV is known to cause direct losses in garlic and other related Allium spp. Up to 54% reduction in bulb weight was observed due to single infection of this virus (2). Hence, our first report about this virus has significant impact on garlic production scenario, if this virus found to be widespread in the country. For this, additional surveys and genotype screenings are needed to obtain a better understanding of the potential impact of LYSV on garlic production in India. References: (1) H. Fidan and S. Baloglu. Plant Dis. 93:672, 2009. (2) H. Lot et al. Plant Dis. 82:1381, 1998. (3) P. Lunello et al. J. Virol. Methods. 118:15, 2004. (4) H. R. Pappu et al. Plant Dis. 89:205, 2005.