Characterization of ovine Toll-like receptor 9 protein coding region, comparative analysis, detection of mutations and maedi visna infection

2011 ◽  
Vol 35 (2) ◽  
pp. 182-192 ◽  
Author(s):  
Ivan Mikula ◽  
Ivan Mikula
Keyword(s):  
Comparative Analysis ◽  
Toll Like Receptor ◽  
Coding Region ◽  
Protein Coding ◽  
Detection Of Mutations

scholarly journals Characterization of Tomato Necrotic Spot Virus, a Subgroup 1 Ilarvirus Causing Necrotic Foliar, Stem, and Fruit Symptoms in Tomatoes in the United States

Plant Disease ◽  
2019 ◽  
Vol 103 (6) ◽  
pp. 1391-1396 ◽  
Author(s):  
Sara A. Bratsch ◽  
Samuel Grinstead ◽  
Tom C. Creswell ◽  
Gail E. Ruhl ◽  
Dimitre Mollov
Keyword(s):  
Genomic Sequence ◽  
The United States ◽  
Amino Acid Identity ◽  
Necrotic Spot ◽  
Coding Region ◽  
Spot Virus ◽  
Protein Coding ◽  
Serological Characterization ◽  
Necrotic Spots

The genomic, biological, and serological characterization of tomato necrotic spot virus (ToNSV), a virus first described infecting tomato in California, was completed. The complete genomic sequence identified ToNSV as a new subgroup 1 ilarvirus distinct from the previously described tomato-infecting ilarviruses. We identified ToNSV in Indiana in 2017 and 2018 and in Ohio in 2018. The coat protein coding region of the isolates from California, Indiana, and Ohio have 94 to 98% identity, while the same isolates had 99% amino acid identity. ToNSV is serologically related to TSV, a subgroup 1 ilarvirus, and shows no serological relationship to ilarviruses in the other subgroups. In tomato, ToNSV caused symptoms of necrotic spots and flecks on leaves, necrotic streaking on stems, and necrotic spots and circular patterns on fruit resulting in a yield loss of 1 to 13%. These results indicate that ToNSV is a proposed new subgroup 1 ilarvirus causing a necrotic spotting disease of tomato observed in California, Indiana, and Ohio.

scholarly journals Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa

2018 ◽  
Vol 22 (5) ◽  
pp. 524-530 ◽  
Author(s):  
M. A. Filyushin ◽  
A. M. Mazur ◽  
A. V. Shchennikova ◽  
Е. Z. Kochieva
Keyword(s):  
Comparative Analysis ◽  
Rrna Genes ◽  
Trna Genes ◽  
Vegetable Crops ◽  
Structural Elements ◽  
Protein Coding ◽  
Plastid Genomes ◽  
Plastome Evolution ◽  
Taxonomic Studies

Sequencing and comparative characterization of plant plastid genomes, or plastomes, is an important tool for modern phylogenetic and taxonomic studies, as well as for understanding the plastome evolution. The genusAlliumL. (family Amaryllidaceae) incorporates more than 900 species, includes economically signifi­cant vegetable crops such as garlicA. sativum, onionA. cepa, leekA. porrum, etc. In this work, the plastome of garlicA. sativumhas been completely sequenced. TheA. sativumplastome is 153172 bp in size. It consists of a large unique (LSC, 82035 bp) and small unique (SSC, 18015 bp) copies, separated by inverted repeats (IRa and IRb) of 26561 bp each. In the garlic plastome, 134 genes have been annotated: 82 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and 6 pseudogenes. Comparative analysis ofA. sativumandA. cepaplastomes reveals differences in the sizes of structural elements and spacers at the inverted repeat bound­aries. The total numbers of genes inA. sativumandA. cepaare the same, but the gene composition is dif­ferent: therpl22gene is functional inA. sativum, being a pseudogene inA. cepa; conversely, therps16gene is a pseudogene inA. sativumand a protein-coding gene inA. cepa. In theA. sativumandA. cepaplastomes, 32 SSR sequences have been identified. More than half of them are dinucleotides, and the remaining are tetra-, penta-, and hexanucleotides at the same time, trinucleotides were absent. The compared plastomes differ in the numbers of certain SSRs, and some are present in only one of the species.

scholarly journals The complete mitochondrial genome of Paragonimus ohirai (Paragonimidae: Trematoda: Platyhelminthes) and its comparison with P. westermani congeners and other trematodes

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7031 ◽  
Author(s):  
Thanh Hoa Le ◽  
Khue Thi Nguyen ◽  
Nga Thi Bich Nguyen ◽  
Huong Thi Thanh Doan ◽  
Takeshi Agatsuma ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Coding Region ◽  
Protein Coding ◽  
Lung Fluke ◽  
Short Tandem

We present the complete mitochondrial genome of Paragonimus ohirai Miyazaki, 1939 and compare its features with those of previously reported mitochondrial genomes of the pathogenic lung-fluke, Paragonimus westermani, and other members of the genus. The circular mitochondrial DNA molecule of the single fully sequenced individual of P. ohirai was 14,818 bp in length, containing 12 protein-coding, two ribosomal RNA and 22 transfer RNA genes. As is common among trematodes, an atp8 gene was absent from the mitogenome of P. ohirai and the 5′ end of nad4 overlapped with the 3′ end of nad4L by 40 bp. Paragonimusohirai and four forms/strains of P. westermani from South Korea and India, exhibited remarkably different base compositions and hence codon usage in protein-coding genes. In the fully sequenced P. ohirai individual, the non-coding region started with two long identical repeats (292 bp each), separated by tRNAGlu. These were followed by an array of six short tandem repeats (STR), 117 bp each. Numbers of the short tandem repeats varied among P. ohirai individuals. A phylogenetic tree inferred from concatenated mitochondrial protein sequences of 50 strains encompassing 42 species of trematodes belonging to 14 families identified a monophyletic Paragonimidae in the class Trematoda. Characterization of additional mitogenomes in the genus Paragonimus will be useful for biomedical studies and development of molecular tools and mitochondrial markers for diagnostic, identification, hybridization and phylogenetic/epidemiological/evolutionary studies.

scholarly journals Characterization of the complete mitochondrial genome of the New Zealand parasitic blowfly Calliphora vicina (Insecta: Diptera: Calliphoridae)

2020 ◽  
Author(s):  
Nikola Palevich ◽  
Luis Carvalho ◽  
Paul Maclean
Keyword(s):  
New Zealand ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Calliphora Vicina ◽  
Coding Region ◽  
Protein Coding ◽  
Transfer Rnas ◽  
Next Generation Sequencing Technology ◽  
Monophyletic Cluster

ABSTRACTIn the present study, the complete mitochondrial genome of the New Zealand parasitic blowfly Calliphora vicina (blue bottle blowfly) field strain NZ_CalVic_NP was generated using next-generation sequencing technology and annotated. The 16,518 bp mitochondrial genome consists of 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a 1,689 bp non-coding region, similar to most metazoan mitochondrial genomes. Phylogenetic analysis showed that C. vicina NZ_CalVic_NP does not form a monophyletic cluster with the remaining three Calliphorinae species. The complete mitochondrial genome sequence of C. vicina NZ_CalVic_NP is a resource to facilitate future species identification research within the Calliphoridae.

scholarly journals The complete mitochondrial genome of a parthenogenetic ant, Monomorium triviale (Hymenoptera: Formicidae)

2021 ◽  
Author(s):  
Naoto Idogawa ◽  
Chih-Chi Lee ◽  
Chin-Cheng Scotty Yang ◽  
Shigeto Dobata
Keyword(s):  
Complete Mitochondrial Genome ◽  
Coding Region ◽  
Protein Coding ◽  
Transfer Rnas ◽  
Phylogenetic Characterization ◽  
Reproductive Division Of Labor ◽  
Reproductive Division ◽  
Rna Genes ◽  
Generation Sequencing

ABSTRACTMonomorium is one of the most species-rich yet taxonomically problematic ant genera. An East Asian species, M. triviale Wheeler, W.M., 1906, reproduces by obligate thelytokous parthenogenesis and performs strict reproductive division of labor. We sequenced the M. triviale mitogenome using next-generation sequencing methods. The circular mitogenome of M. triviale was 16,290 bp in length, consisting of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single non-coding region of 568 bp. The base composition was AT-biased (82%). Gene order rearrangements were detected and likely to be unique to genus Monomorium. We announce the M. triviale mitogenome as additional genomic resources for phylogenetic characterization of Monomorium and comparative genomics of parthenogenetic ant species.

scholarly journals Characterization of the complete mitochondrial genome sequence of Tracheophilus cymbius (Digenea), the first representative from the family Cyclocoelidae

2019 ◽  
Vol 94 ◽  
Author(s):  
Y. Li ◽  
X.X. Ma ◽  
Q.B. Lv ◽  
Y. Hu ◽  
H.Y. Qiu ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Trna Genes ◽  
Coding Region ◽  
Closely Related Species ◽  
Protein Coding ◽  
The Family ◽  
Mt Genome ◽  
High Statistical Support

Abstract Tracheophilus cymbius (Trematoda: Cyclocoelidae) is a common tracheal fluke of waterfowl, causing serious loss in the poultry industry. However, taxonomic identification of T. cymbius remains controversial and confused. Mitochondrial (mt) genomes can provide genetic markers for the identification of closely related species. We determined the mt genome of T. cymbius and reconstructed phylogenies with other trematodes. The T. cymbius mt genome is 13,760 bp in size, and contains 12 protein-coding genes (cox 1–3, nad 1–6, nad 4L, cyt b and atp 6), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes and one non-coding region. All are transcribed in the same direction. The A + T content is 62.82%. ATG and TAG are the most common initiation and termination codons, respectively. Phylogenetic analyses of concatenated nucleotide sequences show T. cymbius grouping in suborder Echinostomata, and clustering together, with high statistical support, as a sister taxon with Echinochasmus japonicus (Echinochasmidae), the two forming a distinct branch rooted to the ancestor of all Echinostomatidae and Fasciolidae species. This is the first report of the T. cymbius mt genome, and the first reported mt genome within the family Cyclocoelidae. These data will provide a significant resource of molecular markers for studying the taxonomy, population genetics and systematics of trematodes.

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