Incorporation Of DNA Sequences Research Articles

Phylogeny and circumscription of the near‐endemic Brazilian tribe Microlicieae (Melastomataceae)

The members of tribe Microlicieae in the flowering plant family Melastomataceae are nearly all endemic to the cerrado biome of Brazil. Traditional classifications of the Melastomataceae have attributed between 15 and 17 genera to the Microlicieae, but subsequent revisions have circumscribed the tribe more narrowly. The monophyly and intergeneric relationships of the Microlicieae were evaluated through phylogenetic analyses with molecular and morphological data sets. Incorporation of DNA sequences from the intron of the chloroplast gene rpl16 into a previously generated family-wide data set yielded a clade comprising Chaetostoma, Lavoisiera, Microlicia, Rhynchanthera, Stenodon, and Trembleya ("core Microlicieae"), with Rhynchanthera as the first-diverging lineage. The other four genera of Microlicieae sampled are placed in other clades: Eriocnema with Miconieae; Siphanthera with Aciotis, Nepsera, and Acisanthera of Melastomeae; Castratella as sister to Monochaetum of Melastomeae; and Cambessedesia as part of an unresolved polytomy in a large clade that includes most Melastomataceae. Analyses of the chloroplast genes rbcL and ndhF that included three core genera produced similar results, as did the combined analysis of all three data sets. Combined parsimony analyses of DNA sequences from rpl16 and the nuclear ribosomal intercistronic transcribed spacer (ITS) region of 22 species of core Microlicieae yielded generally low internal support values. Lavoisiera, recently redefined on the basis of several morphological characters, was strongly supported as monophyletic. A morphological phylogenetic analysis of the Microlicieae based on 10 parsimony-informative characters recovered a monophyletic core Microlicieae but provided no further resolution among genera. Penalized likelihood analysis with two calibration time windows produced an age estimate of 3.7 million years for the time of initial divergence of strictly Brazilian core Microlicieae. This date is in general agreement with the estimated age of the most active stage of development of cerrado vegetation and implies an adaptive shift from hydric to seasonally dry habitats during the early evolution of this group.

Relationship between nucleotide sequence and 3D protein structure of six genes in Escherichia coli, by analysis of DNA sequence using a Markov model

We speculate that structures of genes might have been produced not only by the origination of the gene by itself, but also by the combination of several parts of structures from other species, through events, such as gene transfer, fusion of DNA sequences, and rearrangement of DNA sequences, to create new functions in evolution. To study the relationship between the 3D structure and DNA sequence of proteins comprised of multi-domains, six genes in Escherichia coli, including those coding for Flavodoxin (ferredoxin) reductase, Flavin oxidoreductase, Integrase/recombinase xerD, Endonuclease III, Heat shock protein (grpE), and Elongation Factor Tu (tufB), were chosen, since the 3D structures of these proteins had been determined by X-ray crystallography. The DNA sequences were analyzed by probability as calculated by using a species-specific inhomogeneous Markov model and divided into regions. The probability was calculated by the GeneMark program from the third-order matrix of Class III genes (Escherichia coli horizontally transferred genes) produced with the Markov model by Borodovsky M. et al.. The probability indicates the degree of similarity to the DNA sequence of the genes that were used for producing the matrix with the Markov model. Moreover, the probability indicates whether the origin of the divided DNA sequence would be different from that of the Class III genes. The divided regions, except for those of Flavin oxidoreductase, corresponded to the structural domains classified by CATH. Namely, the divided regions, suggested to be of different origins by analysis with the Markov model, showed correspondence to the domains and the gross content of the 3D structure. We can ascertain which DNA sequences would have been incorporated into the structure of a gene as parts of the structure in evolution. We propose a hypothesis that in evolution, the structure of genes might have been arisen by the incorporation of DNA sequences from other species. Key Words: DNA sequence analysis, Markov model, evolution, structural evolution Area of Interest: Bioinformatics and Bio Computing

Modification of MR mutator activity in repair-deficient strains of Drosophila melanogaster

In Drosophila, MR (male recombination) second chromosomes are known to act as mutators and recombination-inducers in males. One explanation of MR-induced effects is that MR causes breakes at specific sites where, subsequently, insertion sequences become integrated. To examine the extent to which excision and incorporation of DNA sequences by MR is affected by enzymatic pathways involved in DNA repair, the following experiments were carried out. MR-chromosomes were introduced into males deficient for excision ( mei-9 a) or post-replication repair ( mei-41 D5) or into males carrying both repair-deficient mutations. MR activity was recorded by the occurrence of visible mutations at the sn ( singed) and ras ( raspberry) loci. The spontaneous mutation frequency for sn is 0.2 · 10 −5 (1/490 000) and for ras, 0.4 · 10 −5 (2/490 000). When MR is introduced into repair-proficient males the frequency of sn mutations is 51 · 10 −5 (16/30 795) and of ras mutations is 19 · 10 −5 (6/30 795). In MR males deficient for both excision and post-replication repair ( mei-9 a mei-41 D5) mutator activity is significantly enhanced; the frequency of sn mutations amounts to 225 · 10 −5 (174/77 219) and of ras mutations to 135 · 10 −5 (104/77 219). mei-9 a or mei-41 D5 alone also leads to an enhancement of the mutation frequencies, but this effect is of borderline significance.