The nucleotide sequence of parsnip yellow fleck virus: a plant picorna-like virus

Abstract

The complete sequence of 9871 nucleotides (nts) of parsnip yellow fleck virus (PYFV; isolate P-121) was determined from cDNA clones and by direct sequencing of viral RNA. The RNA contains a large open reading frame between nts 279 and 9362 which encodes a polyprotein of 3027 amino acids with a calculated Mr of 336212 (336K). A PYFV polyclonal antiserum reacted with the proteins expressed from phage carrying cDNA clones from the 5' half of the PYFV genome. Comparison of the polyprotein sequence of PYFV with other viral polyprotein sequences reveals similarities to the putative NTP-binding and RNA polymerase domains of cowpea mosaic comovirus, tomato black ring nepovirus and several animal picornaviruses. The 3' untranslated region of PYFV RNA is 509 nts long and does not have a poly(A) tail. The Y-terminal 121 nts may form a stem-loop structure which resembles that formed in the genomic RNA of mosquito-borne flaviviruses.

Nucleotide sequence and taxonomy of maize chlorotic dwarf virus within the family Sequiviridae.

“…Until now, the distinction has been based only on differences between the RTSV and PYFV genomes. The MCDV-TN genome is more similar to RTSV than PYFV in size (" 12 kb vs " 10 kb) and in the presence of a 3h poly(A) tail, which is absent in PYFV (Turnbull-Ross et al, 1992). MCDV-TN is also similar to RTSV in that it contains a small ORF at the 3h end of the genome that might code for a small protein of 65 amino acids.…”

“…A region with similarities to picorna-like viral proteinases was identified in MCDV-TN (Shen et al, 1993 ;Turnbull-Ross et al, 1992 (Fig. 2).…”

“…Nucleotide sequence of MCDV Nucleotide sequence of MCDV (Figs 1 and 2) (Turnbull-Ross et al, 1992). A comparison of the amino acid sequence of the NTP-binding region of MCDV-TN with other picorna-like viruses found significant identities to MCDV-OH (86 %), RTSV (69 %), PYFV (37 %), cowpea mosaic virus (CPMV ; Lomonossoff & Shanks, 1983) (32 %) and poliovirus (PV ; Nomoto et al, 1982) (24 %) ( Table 1).…”

“…The nucleotide and protein sequences of MCDV-TN are compared with the published sequences of an isolate of MCDV from Ohio (MCDV-OH) (Roth et al, 1994), RTSV (Shen et al, 1993), parsnip yellow fleck virus (PYFV) (Turnbull-Ross et al, 1992Reavy et al, 1993) and other picorna-like viruses. We discuss the genome organization of MDCV-TN in relation to the taxonomy of the Sequiviridae and other picorna-like virus groups.…”

The novel genome organization of the insect picorna-like virus Drosophila C virus suggests this virus belongs to a previously undescribed virus family.

“…The overall similarity between the protease domains is low (data not shown). Najarian et al (1985) ; TBRV (tomato black ring virus), Greif et al (1988) ; CPMV (cowpea mosaic virus), Lomonossoff & Shanks (1983) ; RTSV (rice tungro spherical virus), Shen et al (1993) ; PYFV (parsnip yellow fleck virus), Turnbull-Ross et al (1992). Residues identical in at least four viruses are shaded.…”