Post by jontrip247 on Aug 24, 2015 13:27:55 GMT -6
Virus on interest: Tomato spotted wilt virus (TSWV)
RefSeq: TSWV yields 2947 entries in the NCBI nt database. If we go to RefSeq, we only see 3. This occurs because the RefSeq database is composed of fully annotated and curated nucleotide datasets. This data is the most reliable sequence data there is for a particular organism and is used as a reference source when comparing other sequences.
BioProject: This link will take us to the detailed breakdown of the particular sequence we are interested in. It provides links to the protein AA sequence and reference articles that were published on obtaining the sequence. Additionally, we can find the fully assembled genome or shotgun sequences. We can also find the date of sequence registration, which might be of value. For example: a sequence that is very old my not be as reliable due to mutations or errors that might have occurred in early sequencing.
For TSWV there is sequence homology with other Bunyaviridae viruses among the proteins encoded by the L, M, & S RNA which is why Tospoviruses-TSWV is categorized as such. Additionally, the fact that this virus has an ambisense genome, which is one where both the sense and anti-sense strands code for proteins, and due to coding for a hairpin to stop translation, also places it in the family Bunyaviridae. Using BioProject links takes us to additional links where we find 5 proteins including RNA polymerase (2875 aa), 2 non-structure prot fragments (255 aa & 464aa), nucleocapsid (258 aa), and G1 (1135 aa). See below for more details. After reading through the abstracts, it would seem the primary factor in sequencing this virus was to understand where it should be placed taxonomically; however, this particular genus infects just about every crop, making it of great importance to IPM and other scientific and industry stakeholders.
L RNA (4,821 bp): Has 1 ORF | encodes a RNA polymerase
M RNA (8,897 bp): Has 2 ORFs | One ORF is sense and encodes a protein?? the other is complementary sense and encodes precursors for G1/G2 glycoproteins | ***Both ORFs are expressed via subgenomic mRNAs and are terminated at a hairpin
S RNA (2,916): Has 2 ORFs | One ORF in the sense that encodes a protein?
and another complementary sense that encodes the nucleocapsid protein | ***Both are expressed via subgenomic translation and terminate at the hairpin | There structure is very similar to arthropod-borne phleboviruses that infect animals
RefSeq: TSWV yields 2947 entries in the NCBI nt database. If we go to RefSeq, we only see 3. This occurs because the RefSeq database is composed of fully annotated and curated nucleotide datasets. This data is the most reliable sequence data there is for a particular organism and is used as a reference source when comparing other sequences.
BioProject: This link will take us to the detailed breakdown of the particular sequence we are interested in. It provides links to the protein AA sequence and reference articles that were published on obtaining the sequence. Additionally, we can find the fully assembled genome or shotgun sequences. We can also find the date of sequence registration, which might be of value. For example: a sequence that is very old my not be as reliable due to mutations or errors that might have occurred in early sequencing.
For TSWV there is sequence homology with other Bunyaviridae viruses among the proteins encoded by the L, M, & S RNA which is why Tospoviruses-TSWV is categorized as such. Additionally, the fact that this virus has an ambisense genome, which is one where both the sense and anti-sense strands code for proteins, and due to coding for a hairpin to stop translation, also places it in the family Bunyaviridae. Using BioProject links takes us to additional links where we find 5 proteins including RNA polymerase (2875 aa), 2 non-structure prot fragments (255 aa & 464aa), nucleocapsid (258 aa), and G1 (1135 aa). See below for more details. After reading through the abstracts, it would seem the primary factor in sequencing this virus was to understand where it should be placed taxonomically; however, this particular genus infects just about every crop, making it of great importance to IPM and other scientific and industry stakeholders.
L RNA (4,821 bp): Has 1 ORF | encodes a RNA polymerase
M RNA (8,897 bp): Has 2 ORFs | One ORF is sense and encodes a protein?? the other is complementary sense and encodes precursors for G1/G2 glycoproteins | ***Both ORFs are expressed via subgenomic mRNAs and are terminated at a hairpin
S RNA (2,916): Has 2 ORFs | One ORF in the sense that encodes a protein?
and another complementary sense that encodes the nucleocapsid protein | ***Both are expressed via subgenomic translation and terminate at the hairpin | There structure is very similar to arthropod-borne phleboviruses that infect animals- The nucleotide sequence of the M RNA segment of tomato spotted wilt virus, a bunyavirus with two ambisense RNA segments. Kormelink R, et al. J Gen Virol 1992 Nov
- Tomato spotted wilt virus L RNA encodes a putative RNA polymerase. de Haan P, et al. J Gen Virol 1991 Sep
- The S RNA segment of tomato spotted wilt virus has an ambisense character. de Haan P, et al. J Gen Virol 1990 May
