Nucleotide Sequence Comparison (nucleotide + sequence_comparison)

Distribution by Scientific Domains

Selected Abstracts

Partial genomic organization of ribosomal protein S7 gene from malaria vector Anopheles stephensi

INSECT SCIENCE, Issue 2 2007
Abstract In this study, we describe the partial genomic organization of ribosomal protein S7 gene isolated from the mosquito Anopheles stephensi. Initially a 558 bp partial cDNA sequence was amplified as precursor mRNA sequence containing 223 bp long intron. 5, and 3, end sequences were recovered using end specific rapid amplification of cDNA ends (RACE) polymerase chain reaction. The full-length cDNA sequence was 914 nucleotide long with an open reading frame capable of encoding 192 amino acid long protein with calculated molecular mass of 22 174 Da and a pI point of 9.94. Protein homology search revealed > 75% identity to other insect's S7 ribosomal proteins. Analysis of sequence alignment revealed several highly conserved domains, one of which is related to nuclear localization signal (NLS) region of human rpS7. Interestingly, intron nucleotide sequence comparison with A. gambiae showed a lesser degree of conservation as compared to coding and untranslated regions. Like this, early studies on the genomic organization and cDNA/ Expressed sequence tag analysis (EST) could help in genome annotation of A. stephensi, and would be likely to be sequenced in the future. [source]

Development and characterization of SCAR markers associated with a dominant genic male sterility in rapeseed

PLANT BREEDING, Issue 1 2008
D. F. Hong
Abstract Rs1046AB is a dominant genic male sterility (DGMS) line in rapeseed, in which the sterility has always been thought to be conditioned by the interaction of a male sterility gene (Ms) and its non-allelic restorer gene (Rf). This system provides not only a tool for assisting in recurrent selection but also a promising system for hybrid production. Based on previous studies, two amplified fragment length polymorphism markers linked with the Ms gene were converted into a dominant and a co-dominant sequence characterized amplified region (SCAR) marker, respectively. The putative linear order relationship of three dominant SCAR markers with the same genetic distance from the Rf gene, was also determined by an examination of whether the homologues of these markers are present or not in different lines carrying Rf. A bigger fragment generated by the closest marker linked to the Rf gene was observed in all lines carrying the recessive allele rf, suggesting that this marker is a co-dominant marker, which was further confirmed by nucleotide sequence comparison of these fragments. SCAR markers specific for Ms and Rf will be especially valuable in marker-assisted DGMS three-line breeding. [source]

Genome Organization of an Infectious Clone of Tomato Leaf Curl Virus (Philippines), a New Monopartite Begomovirus*

Tatsuya Kon
Abstract Complete nucleotide sequence of infectious cloned DNA of Tomato leaf curl virus from Philippines (ToLCV-Ph) was determined. The single circular DNA molecule comprises 2755 nucleotides. ToLCV-Ph DNA contains six open reading frames (ORFs) each capable of encoding proteins with a molecular weight greater than 10 kDa. A partial dimeric ToLCV-Ph DNA clone was constructed in a binary vector and used to agroinoculate tomato plants (Lycopersicon esculentum Mill. cv. Zuikou 102). Typical leaf curl symptoms were observed, showing that the single DNA component is sufficient for infectivity. In total nucleotide sequence comparisons with other geminiviruses, ToLCV-Ph was most closely related to Ageratum yellow vein virus (AYVV) (79% identity), ToLCV-Laos (78%), Soyabean crinkle leaf virus -Thailand (78%) and ToLCV-Taiwan (77%). The significant but relatively low sequence identity in the genomic DNA between ToLCV-Ph and other geminiviruses suggests that it is a distinct geminivirus in the genus Begomovirus. [source]

Novel archaeal plasmid pAH1 and its interactions with the lipothrixvirus AFV1

Tamara Basta
Summary At present very little is known about interactions between extrachromosomal genetic elements in Archaea. Here we describe an Acidianus strain which carries naturally a novel 28 kb conjugative plasmid-like element, pAH1, and also serves as a laboratory host for lipothrixvirus AFV1. In an attempt to establish a system for studying plasmid,virus interactions we characterized the genome of pAH1 which closely resembles those of the Sulfolobus conjugative plasmids pARN3 and pARN4. pAH1 integrates site specifically into, and excises from, the host chromosome indicating a dynamic interaction with the latter. Although nucleotide sequence comparisons revealed extensive intergenomic exchange during the evolution of archaeal conjugative plasmids, pAH1 was shown to be stably maintained suggesting that the host system is suitable for studying plasmid,virus interactions. AFV1 infection and propagation leads to a loss of the circular form of pAH1 and this effect correlates positively with the increase in the intracellular quantity of AFV1 DNA. We infer that the virus inhibits plasmid replication since no pAH1 degradation was observed. This mechanism of archaeal viral inhibition of plasmid propagation is not observed in bacteria where relevant bacteriophages either are dependent on a conjugative plasmid for successful infection or are excluded by a resident plasmid. [source]