Abstract
Marigold plants with symptoms of mosaic, crinkle, leaf curl and necrosis were observed and small RNA and ribo-depleted total RNA deep sequencing were conducted to identify the associated viruses. Broad bean wilt virus 2, cucumber mosaic virus, turnip mosaic virus, a new potyvirus tentatively named marigold mosaic virus (MMV) and a new partitivirus named as marigold cryptic virus (MCV) were finally identified. Complete genome sequence analysis showed MMV was 9811 nt in length, encoding a large polyprotein with highest aa sequence identity (57%) with the putative potyvirus polygonatumkingianum virus 1. Phylogenetic analysis with the definite potyviruses based on the polyprotein sequence showed MMV clustered closest to plum pox virus. The complete genome of MCV comprised of dsRNA1 (1583 bp) and dsRNA2 (1459 bp), encoding the RNA-dependent RNA polymerase (RdRp), and coat protein (CP), respectively. MCV RdRp shared the highest (75.7%) aa sequence identity with the unclassified partitivirus ambrosia cryptic virus 2, and 59.0%, 57.1%, 56.1%, 54.5% and 33.7% with the corresponding region of the definite delta-partitiviruses, pepper cryptic virus 2, beet cryptic virus 3, beet cryptic virus 2, pepper cryptic virus 1 and fig cryptic virus, respectively. Phylogenetic analysis based on the RdRp aa sequence showed MCV clustered into the delta-partitivirus group. These findings enriched our knowledge of viruses infecting marigold, but the association of the observed symptom and the identified viruses and the biological characterization of the new viruses should be further investigated.
Highlights
Viral diseases are a major threat to sustainable and productive agriculture worldwide, resulting in economic losses in grain, fruit, vegetable and ornamental plants [1]
After de novo assemble with Velvet 9,495 contigs with sizes ranging between 33 and 791 nt were gained, which were further annotated by BLAST. 263 contigs were identified to be virus originated and related to broad bean wilt virus-2 (BBWV-2) (84 contigs of 8,577nt with 97.8% genome coverage), CMV (34 contigs of 6,821 nt with 77.4% genome coverage), poly-gonatumkingianum virus 1 (PKV1, 27 contigs of 8247nt with 88.1% genome coverage) and ambrosia cryptic virus 2 dsRNA1 (AmCV2, 6 contigs of 454 bp with 28.2% coverage of dsRNA1) (Table 1)
To further characterize the genome sequence of the identified virus related to AmCV2 dsRNA2, ribo-depleted RNA sequencing was conducted
Summary
Viral diseases are a major threat to sustainable and productive agriculture worldwide, resulting in economic losses in grain, fruit, vegetable and ornamental plants [1]. Marigold (Tagetes erecta L.), an annual herbaceous plant from the genus Tagetes and family Asteraceae, is native to Mexico and cultivated commercially as a popular garden ornamental for its wide spectrum flowers with attractive color, shape and size [10]. It is widely cultivated as a dye plant and source of marigold meal [11]. Ageratum enation virus [15], cucumber mosaic virus [16], papaya ringspot virus [17], potato virus Y [18], potato yellow dwarf virus [19], potato yellow vein virus [20], tobacco streak virus [21,22], tomato spotted wilt virus [23,24,25,26] and tomato yellow ring virus [27] have been reported in marigold plants, causing the symptoms of severe stunting, yellowing, mosaic, leaf curl, crinkle and necrosis
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