Contrasting modes of evolution acting on the complex N locus for rust resistance in flax
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Summary Three rust resistance specificities, N , N1 and N2 , map to the complex N locus of flax. We used a degenerate PCR approach, with primers directed to the nucleotide binding site (NBS) domain characteristic of many plant resistance genes, to isolate resistance gene analogs (RGAs) from flax. One RGA clone detected RFLPs co‐segregating with alleles of the N locus. With this probe we isolated four related genes that occur within a 30kbp region and encode proteins with NBS and leucine‐rich repeat (LRR) domains and N‐terminal Toll/Interleukin‐1 Receptor homology (TIR) domains. One of these four genes was identified as the N resistance gene by sequence analysis of three mutant alleles and by transgenic expression. We isolated homologous genes from two flax lines containing the N1 or N2 specificities and from flax lines carrying no N locus resistance specificities. Analysis of shared polymorphisms among this set of 18 N locus sequences revealed three groups of genes with independent lineages. Sequence exchanges have only occurred between genes within each group, but not between groups. Two of the groups contain only one sequence from each haplotype and probably represent orthologous genes. However, the third group contains two genes from each haplotype. We suggest that the re‐assortment of variation by recombination/gene conversion at this locus is limited by the degree of sequence identity between genes.Keywords:
Homology
Ri plasmid was developed and a 585bp fragment of rolC gene was amplified by PCR via primer of rolC gene,and the fragment was cloned into vector pUCm-T.Comparison with previously published nucleotide sequence showed that the homology was 100%.But another clone gene nucleotide sequence showed that the homology was 99% with it.
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Cloning (programming)
Primer (cosmetics)
clone (Java method)
Sequence homology
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The nucleotide sequence of Bacillus phage Ø29 genes 14 (g14) and 15 (g15) have been determined and shown to encode proteins with molecular weights of 15, 014 and 28, 022, respectively. The g14 open reading frame(ORF) was confirmed by sequencing a sus14(1241) mutant. Gene product 15 (gp15) has considerable homology with Salmonella phage P22 lysozyme and lesser homology with Escherichia coli phage 14 lysozyne. Putative translation signals are identified. In addition, the role of a previously described promoter, B2, is discussed.
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TUB of Sedirea japonica was cloned and sequence analyzed,and the result would provide an important basis for selecting a reference gene and studying the function of TUB. The total RNA of Sedirea japonica scapes was extracted by CTAB method and the partial sequence of Sedirea japonica TUB was cloned by RT-PCR,which was1 055 bp long and encoded 351 amino acids residues. Its amino acid sequence contained a conservative region GGGTGSG. The sequencing result revealed that the TUB gene fragment from Sedirea japonica homology comparison with other plants TUB gene sequences in the Gen Bank shows that they share 75%- 96% nucleotide sequence homology,96% nucleotide sequence homology with Doritaenopsis hybrid TUB,the amino acid sequence homology is above 96% and amino acid sequence homology high similarity with the monocotyledon. The cloned genes were TUB gene fragment,which were registered them into Gen Bank( respective accession number: KP686397).
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A hemolysin gene from six streptcoccus suis type 2 strains isolated in Jiangsu was amplified by PCR using a pair of specific primers.The PCR product from strain HA9801 was sequenced and nucleotide sequence analysis revealed the hemolysin gene from strain HA9801 had a high homology to strains 1933(99%).
Homology
Hemolysin
Sequence homology
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Cloning (programming)
Conserved sequence
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The fliC gene of the E. coli B38 flagellin has been cloned and its nucleotide sequence determined using the terminator method. According to the sequencing data, the flagellin contains 565 amino acid residues which exceeds by 65 residues the number of amino acid residues in the earlier decoded E. coli K12 flagellin. Strong homology was observed in the two flagellins among the 160 initial and 89 tail-ended residues, whereas the central, variable parts showed no homology. Similar to the K12 flagellin, the B38 flagellin has no serines, cysteines or tryptophans. The variable part of the fliC E. coli B38 gene contains a Chi-site which initiates the genetic recombination in E. coli and related species.
Flagellin
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Terminator (solar)
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In this study,an avian influenza viruses(AIV)was isolated from Hunan province,and it was identified to be H5N1.According to the published sequence of H5N1 HA and NA genes,two pairs of specific primers were synthesized.The whole genetic encoding of the isolated strain of HA and NA genes were about 1.7 kb and 1.4 kb nucleotide with a single opening frame.The homology analysis showed that the homology of HA genes between the isolate and twelve reference viruses was 95.9%-98.0%,the homology of NA genes was 87.0%-98.4%.The deduced analysis of HA genes splitting site suggested that the nucleotides contain characteristic sequence of splitting site of high pathogenic AIV strain.
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Sequence homology
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The nucleotide sequences of two different rat lens gamma-crystallin cDNA clones, pRL gamma 2 and pRL gamma 3, have been determined. pRL gamma 3 contains the complete coding information for a gamma-crystallin of 173 amino acids whereas pRL gamma 2 is incomplete in that it lacks the codons for the first three amino acids of a separate but very homologous gamma-crystallin of identical length. Both rat gamma-crystallins are homologous to the known amino acid sequence of bovine gamma-crystallin II which is only a single amino acid longer. The length of the region downstream the coding sequence to the A-A-T-A-A-A polyadenylylation signal sequence is 40 nucleotides in each clone. In pRL gamma 3 the poly(A) signal sequence is followed at 14 nucleotides by a remnant of the poly(A) tail which indicates that this clone contains a complete 3' noncoding region. pRL gamma 2 has only seven nucleotides following this signal sequence and no poly(A) tail, suggesting an incomplete 3' end. The cDNA clones show an overall nucleotide sequence homology of 85%. The mutual homology at the amino acid level is 73% whereas their amino acid homology with bovine gamma-crystallin II is about 70%. The nucleotide sequence of each clone also reveals a high intragenic homology and seems to be duplicated in itself. We suggest that the gamma-crystallin genes have arisen by multiple duplications of a primordial gene which consisted of about 120 nucleotides.
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Coding region
Crystallin
Protein primary structure
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Five swine fever viruses were isolated from 17 samples,which were collected from 13 large farms in 10 districts of Yunnan province.The nucleotide sequence analysis showed 99.99% homology among 3 isolates from KunMing,YuXi and QuJing and between 2 isolates from DaLi and BaoShan.All of these 5 isolates belonged to Genegroup 2.The titers of 5 isolates were about 2×106 TCID50/mL in PK-15 cells and the viruses could be detected by using fluorescent antibody technique.The full-length sequences of E0 and E2 genes about 700 bp and 1200 bp were amplified by RT-PCR,and then cloned into pMD18-T vectors.Sequence analysis showed that the E0 and E2 nucleotide fragments were 697 bp and 1173 bp in length,respectively.The nucleotide and amino acid sequences revealed 95.4% and 96.6% homology in E0 gene and 82.5% and 84.3% homology in E2 gene with CSFV Shimen strain.Animal experimentation showed that two isolates did not cause typical clinical signs of CSF but induced persistent infection in the challenged pigs.
Classical swine fever
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Sequence homology
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Isolates of HTLV-I have been characterized from a number of different regions of the world; however, there has not been a nucleotide sequence analysis of an HTLV-I isolate from a South American country. Reported here is an individual from Chile identified with the HTLV-I-associated neurological disease HAM/TSP. The sera and the nucleic acid sequence of the HTLV-I present in peripheral blood lymphocytes from this Chilean HAM/TSP patient over a two year period are characterized. During this time, the patient's condition grew progressively worse. While the serological profile of this patient was unremarkable in comparison with other HAM/TSP patients previously described, nucleic acid sequence analysis identified two nucleotide positions which contained nucleotides unique to this Chilean isolate. The nucleotide sequence analysis also indicates that the Chilean HTLV-I isolate is more closely related to Caribbean and Japanese isolates of HTLV-I than to the African and U.S. isolates described so far.
Sequence (biology)
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