scholarly journals Banana contains a diverse array of endogenous badnaviruses

2005 ◽  
Vol 86 (2) ◽  
pp. 511-520 ◽  
Author(s):  
Andrew D. W. Geering ◽  
Neil E. Olszewski ◽  
Glyn Harper ◽  
Benham E. L. Lockhart ◽  
Roger Hull ◽  
...  
Keyword(s):  
Nuclear Genome ◽  
Synonymous Substitution ◽  
Selective Constraint ◽  
Musa Balbisiana ◽  
Reading Frame ◽  
B Genome ◽  
Species Analysis ◽  
Breeding Programmes ◽  
Distinct Sequence ◽  
High Degree

Banana streak disease is caused by several distinct badnavirus species, one of which is Banana streak Obino l'Ewai virus. Banana streak Obino l'Ewai virus has severely hindered international banana (Musa spp.) breeding programmes, as new hybrids are frequently infected with this virus, curtailing any further exploitation. This infection is thought to arise from viral DNA integrated in the nuclear genome of Musa balbisiana (B genome), one of the wild species contributing to many of the banana cultivars currently grown. In order to determine whether the DNA of other badnavirus species is integrated in the Musa genome, PCR-amplified DNA fragments from Musa acuminata, M. balbisiana and Musa schizocarpa, as well as cultivars ‘Obino l'Ewai’ and ‘Klue Tiparot’, were cloned. In total, 103 clones were sequenced and all had similarity to open reading frame III in the badnavirus genome, although there was remarkable variation, with 36 distinct sequences being recognized with less than 85 % nucleotide identity to each other. There was no commonality in the sequences amplified from M. acuminata and M. balbisiana, suggesting that integration occurred following the separation of these species. Analysis of rates of non-synonymous and synonymous substitution suggested that the integrated sequences evolved under a high degree of selective constraint as might be expected for a living badnavirus, and that each distinct sequence resulted from an independent integration event.

scholarly journals Rates of synonymous substitution and base composition of nuclear genes in Drosophila.

Genetics ◽  
1992 ◽  
Vol 130 (4) ◽  
pp. 855-864
Author(s):  
E N Moriyama ◽  
T Gojobori
Keyword(s):  
Nuclear Genome ◽  
Nuclear Gene ◽  
Synonymous Substitution ◽  
Selective Constraint ◽  
Nuclear Genes ◽  
Functional Genes ◽  
Silent Substitution ◽  
Codon Positions ◽  
Synonymous Substitution Rates ◽  
Mutation Pattern

Abstract We compared the rates of synonymous (silent) substitution among various genes in a number of species of Drosophila. First, we found that even for a particular gene, the rate of synonymous substitution varied considerably with Drosophila lineages. Second, we showed a large variation in synonymous substitution rates among nuclear genes in Drosophila. These rates of synonymous substitution were correlated negatively with C content and positively with A content at the third codon positions. Nucleotide sequences were also compared between pseudogenes and their functional homologs. The C content of the pseudogenes was lower than that of the functional genes and the A content of the former was higher than that of the latter. Because the synonymous substitution for functional genes and the nucleotide substitution for pseudogenes are exempted from any selective constraint at the protein level, these observations could be explained by a biased pattern of mutation in the Drosophila nuclear genome. Such a bias in the mutation pattern may affect the molecular clock (local clock) of each nuclear gene of each species. Finally, we obtained the average rates of synonymous substitution for three gene groups in Drosophila; 11.0 x 10(-9), 17.5 x 10(-9) and 27.1 x 10(-9)/site/year.

Molecular cloning and sequence analysis of putative chicken prolactin cDNA

1989 ◽  
Vol 2 (1) ◽  
pp. 21-30 ◽  
Author(s):  
M.C. Hanks ◽  
J.A. Alonzi ◽  
P.J. Sharp ◽  
H.M. Sang
Keyword(s):  
Amino Acids ◽  
Genomic Dna ◽  
Signal Sequence ◽  
Peptide Sequence ◽  
Mrna Levels ◽  
Reading Frame ◽  
Ring Dove ◽  
Prolactin Gene ◽  
Pituitary Glands ◽  
High Degree

ABSTRACT A cDNA library was prepared from mRNA isolated from anterior pituitary glands of incubating bantam hens, in which prolactin mRNA levels were predicted to be very high. Nine clones, representing abundant mRNA species, were identified and shown to contain homologous sequences. Two clones, of 871 bp and 580 bp, were analysed by DNA sequencing. The shorter clone was found to be a truncated cDNA product but otherwise identical to the longer clone. The 871 bp cDNA, PRL101, contains an open reading frame capable of encoding a polypeptide of 229 amino acids. This putative polypeptide has a high degree of homology to mammalian prolactins (approximately 70%), strongly suggesting that PRL101 encodes chicken preprolactin. The protein was predicted to have a 30 amino acid signal sequence which would be cleaved off to give a mature protein of 199 amino acids. The peptide sequence also had a 26% homology to chicken growth hormone, which is related to prolactin. This similarity confirms the conclusion that PRL101 is a chicken prolactin cDNA clone. An abundant mRNA of approximately 880 b was detected in poly(A)+ RNA from pituitary glands probed with PRL101. Analysis of chicken genomic DNA showed that there is one copy of the prolactin gene in the genome. PRL101 hybridized strongly to genomic DNA from closely related galliforms (quail and turkey) and less strongly to DNA from more distantly related species (duck and ring dove).

scholarly journals Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A- and B-genome diploid species of peanut

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 608 ◽  
Author(s):  
Yufang Guo ◽  
Sameer Khanal ◽  
Shunxue Tang ◽  
John E Bowers ◽  
Adam F Heesacker ◽  
...  
Keyword(s):  
Comparative Mapping ◽  
Diploid Species ◽  
B Genome ◽  
High Degree

scholarly journals Sequence Heterogeneity of TT Virus and Closely Related Viruses

2000 ◽  
Vol 74 (7) ◽  
pp. 2990-3000 ◽  
Author(s):  
Yury E. Khudyakov ◽  
Mian-er Cong ◽  
Barbara Nichols ◽  
Deoine Reed ◽  
Xiao-Guang Dou ◽  
...  
Keyword(s):  
Infectious Agent ◽  
The United States ◽  
Unknown Etiology ◽  
Reading Frame ◽  
Genome Region ◽  
Tt Virus ◽  
Genetic Groups ◽  
New Genotype ◽  
Genotype 2 ◽  
High Degree

ABSTRACT TT virus (TTV) is a recently discovered infectious agent originally obtained from transfusion-related hepatitis. However, the causative link between the TTV infection and liver disease remains uncertain. Recent studies demonstrated that genome sequences of different TTV strains are significantly divergent. To assess genetic heterogeneity of the TTV genome in more detail, a sequence analysis of PCR fragments (271 bp) amplified from open reading frame 1 (ORF1) was performed. PCR fragments were amplified from 5 to 40% of serum specimens obtained from patients with different forms of hepatitis who reside in different countries (e.g., China, Egypt, Vietnam, and the United States) and from normal human specimens obtained from U.S. residents. A total of 170 PCR fragments were sequenced and compared to sequences derived from the corresponding TTV genome region deposited in GenBank. Genotypes 2 and 3 were found to be significantly more genetically related than any other TTV genotype. Moreover, three sequences were shown to be almost equally related to both genotypes 2 and 3. These observations suggest a merger of genotypes 2 and 3 into one genotype, 2/3. Additionally, five new groups of TTV sequences were identified. One group represents a new genotype, whereas the other four groups were shown to be more evolutionary distant from all known TTV sequences. The evolutionary distances between these four groups were also shown to be greater than between TTV genotypes. The phylogenetic analysis suggested that these four new genetic groups represent closely related yet different viral species. Thus, TTV exists as a “swarm” of at least five closely related but different viruses. These observations suggest a high degree of genetic complexity within the TTV population. The finding of the additional TTV-related species should be taken into consideration when the association between TTV infections and human diseases of unknown etiology is studied.

scholarly journals Genetic Diversity in the 3′ Terminal 4.7-kb Region of Grapevine leafroll-associated virus 3

2011 ◽  
Vol 101 (4) ◽  
pp. 445-450 ◽  
Author(s):  
Jinbo Wang ◽  
Abhineet M. Sharma ◽  
Siobain Duffy ◽  
Rodrigo P. P. Almeida
Keyword(s):  
Genetic Diversity ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Effective Population ◽  
Data Set ◽  
Reading Frame ◽  
Napa Valley ◽  
Synonymous Substitution Rates ◽  
Leafroll Disease

Grapevine leafroll-associated virus 3 (GLRaV-3; Ampelovirus, Closteroviridae), associated with grapevine leafroll disease, is an important pathogen found across all major grape-growing regions of the world. The genetic diversity of GLRaV-3 in Napa Valley, CA, was studied by sequencing 4.7 kb in the 3′ terminal region of 50 isolates obtained from Vitis vinifera ‘Merlot’. GLRaV-3 isolates were subdivided into four distinct phylogenetic clades. No evidence of positive selection was observed in the data set, although neutral selection (ratio of nonsynonymous to synonymous substitution rates = 1.1) was observed in one open reading frame (ORF 11, p4). Additionally, the four clades had variable degrees of overall nucleotide diversity. Moreover, no geographical structure among isolates was observed, and isolates belonging to different phylogenetic clades were found in distinct vineyards, with one exception. Considered with the evidence of purifying selection (i.e., against deleterious mutations), these data indicate that the population of GLRaV-3 in Napa Valley is not expanding and its effective population size is not increasing. Furthermore, research on the biological characterization of GLRaV-3 strains might provide valuable insights on the biology of this species that may have epidemiological relevance.

scholarly journals Structure and expression analysis of genes encoding ADP-glucose pyrophosphorylase large subunit in wheat and its relatives

Genome ◽  
2016 ◽  
Vol 59 (7) ◽  
pp. 501-507 ◽  
Author(s):  
Xiao-Wei Zhang ◽  
Si-Yu Li ◽  
Ling-Ling Zhang ◽  
Qiang Yang ◽  
Qian-Tao Jiang ◽  
...  
Keyword(s):  
Large Subunit ◽  
Full Length ◽  
Starch Accumulation ◽  
Coding Region ◽  
D Genome ◽  
Reading Frame ◽  
B Genome ◽  
Genome Donor ◽  
Adp Glucose Pyrophosphorylase ◽  
Donor Species

ADP-glucose pyrophosphorylase (AGP), which consists of two large subunits (AGP-L) and two small subunits (AGP-S), controls the rate-limiting step in the starch biosynthetic pathway. In this study, a full-length open reading frame (ORF) of AGP-L gene (named as Agp2) in wheat and a series of Agp2 gene sequences in wheat relatives were isolated. The coding region of Agp2 contained 15 exons and 14 introns including a full-length ORF of 1566 nucleotides, and the deduced protein contained 522 amino acids (57.8 kDa). Generally, the phylogenetic tree of Agp2 indicated that sequences from A- and D-genome donor species were most similar to each other and sequences from B-genome donor species contained more variation. Starch accumulation and Agp2 expression in wheat grains reached their peak at 21 and 15 days post anthesis (DPA), respectively.

Molecular Cloning and Characterization of cDNA Encoding Fibrinolytic Enzyme-3 from Earthworm Eisenia foetida

2004 ◽  
Vol 36 (4) ◽  
pp. 303-308 ◽  
Author(s):  
Guo-Qing Dong ◽  
Xiao-Ling Yuan ◽  
Ya-Jun Shan ◽  
Zhen-Hu Zhao ◽  
Jia-Pei Chen ◽  
...  
Keyword(s):  
Inclusion Bodies ◽  
Fibrinolytic Enzyme ◽  
Eisenia Foetida ◽  
Amino Acid Residues ◽  
Gene Encoding ◽  
Native Form ◽  
Reading Frame ◽  
Fibrin Plate ◽  
Earthworm Fibrinolytic Enzyme ◽  
High Degree

Abstract The earthworm fibrinolytic enzyme-3 (EFE-3, GenBank accession No: AY438622), from the earthworm Eisenia foetida, is a component of earthworm fibrinolytic enzymes. In this study, cDNA encoding the EFE-3 was cloned by RT-PCR. The cDNA contained an open reading frame of 741 nucleotides, which encoded a deduced protein of 247 amino acid residues, including signal sequences. EFE-3 showed a high degree of homology to earthworm (Lumbricus rebullus) proteases F-III-1, F-III-2, and bovine trypsin. The recombinant EFE-3 was expressed in E. coli as inclusion bodies, and the gene encoding the native form of EFE-3 was expressed in COS-7 cells in the medium. Both the refolding product of inclusion bodies and the secreted protease could dissolve the artificial fibrin plate.

scholarly journals Erratum: clinical and molecular characteristics of patients with 46,xy dsd due to nr5a1 gene mutations (Probl Endokrinol (Mosk). 2020 Sep 16;66(3):62-69. Russian. doi: 10.14341/probl12445)

2021 ◽  
Vol 67 (6) ◽  
pp. 124-126
Author(s):  
N. Yu. Kalinchenko ◽  
A. A. Kolodkina ◽  
N. Yu. Raygorodskaya ◽  
A. N. Tiulpakov
Keyword(s):  
Stop Codon ◽  
Premature Stop Codon ◽  
Gene Mutations ◽  
Synonymous Substitution ◽  
Molecular Characteristics ◽  
Missense Mutations ◽  
Reading Frame ◽  
Splicing Site

n the article some corrections were needed. Abstract: “Heterozygous SF1 variants were found in 36 out of 310 (11.6%) of cases, among them 15 were not previously described”. has been corrected to read “Heterozygous SF1 variants were found in 36 out of 310 (11.6%) of cases, among them 22 were not previously described”. Results: “Heterozygous SF1 variants were found in 36 out of 310 (11.6%) of cases, among them 15 were not previously described”, has been corrected to read “Heterozygous SF1 variants were found in 36 out of 310 (11.6%) of cases, among them 22 were not previously described”. Among the newly identified variants in the NR1A1 gene, two lead to the premature stop codon -p. Y197X and p. Y25X, two lead to a shift in the reading frame-p. N385fs and p. L245fs, which does not allow us to doubt their pathogenicityAmong the previously undescribed variant changes, 5 missense mutations (p. C283Y, p. C283B, p.H24Q, p.M126K, p.E81K) and 1  synonymous substitution affecting the splicing site (E330E) were evaluated as pathogenic, and 5 others as probably pathogenic.Has been corrected to read: Among the newly identified variants in the NR1A1 gene, two lead to the premature stop codon -p. Y197X and p. Y25X, two lead to a shift in the reading frame — p.N385SfsX10 and p.L245AfsX53, which does not allow us to doubt their pathogenicity Among the previously undescribed variants, 5 missense mutations (p.C283Y, p.С283F, p.H24Q, p.M126K, p.A82T) and 1 synonymous substitution affecting the splicing site (E330E) were predicted as pathogenic, and 5 others as probably pathogenic by calculating pathogenicity. The authors apologize for these errors. 

scholarly journals Genetic relationships among cultivated and wild bananas from East Kalimantan, Indonesia based on ISSR markers

2020 ◽  
Vol 21 (2) ◽  
Author(s):  
Widi Sunaryo ◽  
Wahida ◽  
Suria Darma Idris ◽  
Ananda Nuryadi Pratama ◽  
Kumrop Ratanasut ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Issr Marker ◽  
Similarity Coefficients ◽  
Musa Balbisiana ◽  
Economic Significance ◽  
East Kalimantan ◽  
B Genome ◽  
A Genome

Abstract. Sunaryo W, Wahida, Idris SD, Pratama AN, Ratanasut K, Nurhasanah. 2020. Genetic relationships among cultivated and wild bananas from East Kalimantan, Indonesia based on ISSR markers. Biodiversitas 21: 824-832. East Kalimantan is one of biodiversity centers for banana in Indonesia including wild or cultivated bananas. This biodiversity is long-historical genetically contributed by the existence of wild cultivars, local/indigenous varieties or introduced accessions from other regions in Indonesia. The existence of cultivated bananas has played an important role in the socio-economic significance of the local people. The genetic contribution of wild and local banana from East Kalimantan to the cultivated bananas or vice versa is very interesting to study. This research reported the genetic relationships among wild and cultivated bananas using Inter Simple Sequence Repeat (ISSR) markers. Thirteen wild and cultivated banana samples collected from different districts of East Kalimantan Province were analyzed using 15 primers of ISSR marker. ISSR primers generated 133 loci, of which 132 were polymorphic (98.98 %) with an average of 9.43 loci per primer. The ISSR marker is very effective and powerful to detect and discriminate the polymorphisms among cultivated and wild bananas. This is supported by PIC value which ranged from 0.60 to 0.91 per primer with an average of 0.80 per primer. The marker index (MI) values were ranged from 1.62 to 11.48 per primer. Primer UBC 855 produced the highest MI value which was 11.48 per primer and UBC 848 resulted in the lowest (1.62 per primer). The similarity coefficients ranged from 0.43 to 0.81. The dendrogram constructed based on UPGMA divided the banana cultivars into 4 clusters, in which the first cluster comprised of the AA/AAA/AB genome bananas (Ambon, Kapas, Tembaga, Liar, and Tanduk). The second cluster composed of only Mauli Banana. The third cluster was comprised of six cultivated banana with AAB or ABB genome i.e., Raja, Rutai, Susu, Kepok, Awak, and Talas banana. The last cluster was only Klutuk Banana (BB genome). Wild bananas (Liar and Klutuk) was the ancestor of cultivated bananas since they contributed for A genome (Musa acuminate) and B genome (Musa balbisiana) to generate many triploid and cultivated bananas. Indigenous banana cultivars from Kalimantan, Rutai is closely related to Susu banana, while Talas banana is related to the AAB genome such as Raja, Rutai, Susu or ABB genome such as Awak and Kepok.

scholarly journals The carB Gene Encoding the Large Subunit of Carbamoylphosphate Synthetase from Lactococcus lactis Is Transcribed Monocistronically

1998 ◽  
Vol 180 (17) ◽  
pp. 4380-4386 ◽  
Author(s):  
Jan Martinussen ◽  
Karin Hammer
Keyword(s):  
Lactococcus Lactis ◽  
Large Subunit ◽  
Arginine Deiminase ◽  
Gene Encoding ◽  
Pyrimidine Nucleotides ◽  
Reading Frame ◽  
Glutathione Peroxidases ◽  
Carbamoylphosphate Synthetase ◽  
Genes Encoding ◽  
High Degree

ABSTRACT The biosynthesis of carbamoylphosphate is catalyzed by the heterodimeric enzyme carbamoylphosphate synthetase. The genes encoding the two subunits of this enzyme in procaryotes are normally transcribed as an operon, but the gene encoding the large subunit (carB) in Lactococcus lactis is shown to be transcribed as an isolated unit. Carbamoylphosphate is a precursor in the biosynthesis of both pyrimidine nucleotides and arginine. By mutant analysis,L. lactis is shown to possess only onecarB gene; the same gene product is thus required for both biosynthetic pathways. Furthermore, arginine may satisfy the requirement for carbamoylphosphate in pyrimidine biosynthesis through degradation by means of the arginine deiminase pathway. The expression of the carB gene is subject to regulation at the level of transcription by pyrimidines, most probably by an attenuator mechanism. Upstream of the carB gene, an open reading frame showing a high degree of similarity to those of glutathione peroxidases from other organisms was identified.

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