Isolation and identification of TL-DNA/plant junctions in Convolvulus arvensis transformed by Agrobacterium rhizogenes strain A4

We have constructed a Charon 4A phage library containing insert DNA isolated from a morning glory (Convolvulus arvensis) plant (clone 7) regenerated from a root organ culture incited by Agrobacterium rhizogenes, strain A4. Using a subcloned region of the Ri plasmid as (32)P-labeled probe, two lambda clones containing most of the 'left' T-DNA (TL) region were isolated. One of these lambda clones contains the left TL-DNA/plant junction, which was located by comparing nucleotide sequences from the appropriate regions of the Ri plasmid and this lambda clone. A 25-bp sequence found near this left TL-DNA/plant junction matches the 25-bp terminal sequence found at or near T-DNA/plant junctions of both nopaline- and octopine-type A. tumefaciens Ti plasmids. A possible location for the right Ri TL-DNA/plant junction in C. arvensis clone 7 was found by obtaining the nucleotide sequence surrounding its mapped location. Hybridization of plant DNA found adjacent to the left TL-DNA/plant junction against total C. arvensis DNA shows that this T-DNA integration occurred in a plant DNA region that does not contain highly repetitive DNA sequences. Nucleotide sequence analysis of 1004 bp of this plant DNA revealed no complete or partial open reading frames, but this plant DNA does have the potential to form various secondary structures which might play a role in the T-DNA integration event

Nucleotide Sequence Analysis of 77.7 kb of the Human V[beta] T-Cell Receptor Gene Locus: Direct Primer-Walking Using Cosmid Template DNAs

The nucleotide sequence of 77.7 kb from the human T-cell receptor [beta]-chain locus was determined directly from three overlapping cosmid clones using the primer-walking approach. Computer-aided analyses of this sequence reveal the presence of at least 11 genic regions that are closely related to the human T-cell receptor [beta] variable region (TCRBV) gene family. These include five germline sequences that have previously been determined, V[beta]21.2, V[beta]8.1, V[beta]8.2, V[beta]8.3, and V[beta]16, and four whose sequences have partially been determined at the mRNA level, V[beta]6, V[beta]23, V[beta]12.2, V[beta]24. The two remaining V[beta] Tcr-related sequences have eluded discovery by cDNA and RT-PCR cloning and genomic blot hybridization methods. These two V[beta] Tcr-related genes lack >75% nucleotide sequence identity with any other V[beta] Tcr gene member and therefore, by convention, are referred to as new subfamily members V[beta]25 and V[beta]26. This lack of shared identity with other subfamily members explains why they were not detected by hybridization. The promoter regions of these V[beta] Tcr genes contain the conserved Tcr decamer element located between 80 and 110 bp 5' of the translation start site, generally near a putative TATAA promoter element. Our sequence analysis also reveals that a 3.3-kb duplication unit was involved in the recombination event that produced the closely related V[beta]8.1 and 8.2 gene subfamily members. This sequenced region of the V[beta] locus contains an average number of repetitive DNA elements (21 Alu, three L1, three MER, and three retrovirus-related elements).Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/31701/1/0000637.pd

The nucleotide sequences of the 3’ terminal regions of papaya ringspot virus strains W and P

The sequences of cDNA clones encoding most of the NI b protein, the coat protein and the 3 ' untranslated region of papaya ringspot virus (PRV) strains W and P have been determined. The open reading frame of P strain PRV was confirmed by amino acid analysis. Nucleotide sequence comparisons of these strains show that they share a 98-2 % identity in their NI b gene regions and a 97-7 % identity in their coat protein genes. The sequences of these two strains are distinct from other potyvirus types, confirming their classification as two strains of the same virus. The NI b amino acid sequence possesses conserved amino acids characteristic of RNA-dependent RNA polymerases. Comparison of the coat protein amino acid sequence with those of other potyviruses shows perfectly conserved amino acids which may have functional significance

The sequence of the gorilla fetal globin genes: evidence for multiple gene conversions in human evolution. Mol Biol Evol

Two fetal globin genes (“r and 9) from one chromosome of a lowland gorilla (Gorilla gorilla gorilla) have been sequenced and compared to three human loci (a Gy-gene and two?-alleles). A comparison of regions of local homology among these five sequences indicates that long after the duplication that produced the two nonallelic y-globin loci of catarrhine primates, about 35 million years (Myr) ago, at least one gene conversion event occurred between these loci. This conversion occurred not long before the ancestral divergence (about 6 Myr ago) of Homo and Gorilla. After this ancestral divergence, a minimum of three more gene conversion events occurred in the human lineage. Each human?-allele shares specific sequence features with the gorilla?-gene; one such distinctive allelic feature involves the simple repeated sequence in IVS 2. This suggests that early in the human lineage the y-genes may have undergone a crossing-over event mediated by this simple repeated sequence. The DNA sequences from coding regions of both Gr- and y-loci, a comparison of 292 codons in the corresponding gorilla and human genes, show an unusually low evolutionary rate, with only two nonsilent differences and