Protein-coding Gene Sequences Research Articles

Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data.

All living organisms fall into discrete clusters of closely related individuals on the basis of gene sequence similarity. Evolutionary genetic theory predicts that in the bacterial world, each sequence similarity cluster should correspond to an ecologically distinct population. Indeed, surveys of sequence diversity in protein-coding genes show that sequence clusters correspond to ecological populations. Future population surveys of protein-coding gene sequences can be expected to disclose many previously unknown ecological populations of bacteria. Sequence similarity clustering in protein-coding genes is recommended as a primary criterion for demarcating taxa.

Heterozygosity, heteromorphy, and phylogenetic trees in asexual eukaryotes.

Little attention has been paid to the consequences of long-term asexual reproduction for sequence evolution in diploid or polyploid eukaryotic organisms. Some elementary theory shows that the amount of neutral sequence divergence between two alleles of a protein-coding gene in an asexual individual will be greater than that in a sexual species by a factor of 2tu, where t is the number of generations since sexual reproduction was lost and u is the mutation rate per generation in the asexual lineage. Phylogenetic trees based on only one allele from each of two or more species will show incorrect divergence times and, more often than not, incorrect topologies. This allele sequence divergence can be stopped temporarily by mitotic gene conversion, mitotic crossing-over, or ploidy reduction. If these convergence events are rare, ancient asexual lineages can be recognized by their high allele sequence divergence. At intermediate frequencies of convergence events, it will be impossible to reconstruct the correct phylogeny of an asexual clade from the sequences of protein coding genes. Convergence may be limited by allele sequence divergence and heterozygous chromosomal rearrangements which reduce the homology needed for recombination and result in aneuploidy after crossing-over or ploidy cycles.

Characteristics of major structural protein coding gene and leader-body sequence in subgenomic mRNA of porcine reproductive and respiratory syndrome virus isolated in Japan.

Nucleotide sequence, 1713nt in length, of porcine reproductive and respiratory syndrome virus (PRRSV) isolated in Japan was determined. The sequence encompassed 3 overlapping open reading frames (ORFs), ORF5 to ORF7. These ORFs encodes major structural proteins of PRRSV. The deduced amino acid sequence of each ORF showed higher than 87.5% identity with an American isolate, and lower (54.6 to 80.5%) identity with an European isolate. This result supported a previous report about antigenic characteristics of the EDRD-1 strain. Leader-body junction sequence in subgenomic mRNA of the EDRD-1 strain was determined by sequencing cDNA clones of subgenomic RNAs. A common sequence motif of 5 nucleotide, represented by UA(A/G)CC, was identified as the junction sequence.

Mitochondrial control region and protein coding genes sequence variation among phenotypic forms of brown trout Salmo trutta from northern Italy.

The Pô River basin of northern Italy is the home of distinctive and endemic morphological forms of brown trout Salmo trutta. We used PCR-direct sequencing and RFLP techniques to study variation in the mitochondrial control region of 225 trout in order to assess genetic relatedness among 18 populations from that region. The distribution analysis of these genotypes among north Italian populations confirmed the phylogenetic differentiation of marbled trout Salmo trutta marmoratus populations and the postglacial origin of S. t. carpio. Extensive genetic heterogeneity was observed among morphologically identical S. t. fario populations. Introgression with domestic strains of Atlantic basin origin was detected in all forms. In order to assess the phylogenetic congruence detected in coding and noncoding regions of the mitochondrial genome, we also analysed sequence variation in segments of the cytochrome b and ATPase subunit VI genes among representatives of all variants detected in the analysis of the control region. Variation in protein coding genes was only slightly less than that observed in the control region of the same individuals, both in terms of number of variants detected and of pairwise sequence divergence estimates among variants. Phylogenetic analysis based on protein coding genes sequences identified the same phylogenetic groupings defined by the control region analysis and also allowed a partial resolution of their phyletic relationships that was previously unresolved. However, coding and noncoding segments differed substantially in the transition-transversion ratio (17:0 in coding segments vs. 17:6 in control region segments).

FISH: a guide to protein-coding DNA sequences in the GenBank database.

FISH (Fast Index Search for Homologous coding sequences) consists of a database and associated software and is intended to function as a directory of protein-coding gene sequences. The FISH index contains descriptions of 22,361 DNA sequences from release 69.0 of the GenBank genetic sequence database. Complete coding sequences are represented numerically with counts of nucleotides and synonymous codons, and with GenBank LOCUS names and short descriptions. The software permits the database to be queried by GenBank LOCUS name, sequence length (expressed as total number of codons), or by comparison with a DNA sequence. In the latter case, the numerical descriptions are compared with simple distance measures in place of actual DNA sequences. The FISH package can be used to rapidly assemble lists of similar coding sequences, without regard to functional annotation or sequence alignments. Typical search times are well under a minute on widely available IBM-compatible microcomputers.

Compilation of sequences of protein-coding genes in chloroplast DNA including cyanelle and cyanobacterial homologues

Compilation of sequences of protein-coding genes in chloroplast DNA including cyanelle and cyanobacterial homologues

Evolution of late H2A, H2B, and H4 histone genes of the sea urchin, Strongylocentrotus purpuratus.

Sea urchins possess several distinct sets of histone genes, including "early" genes, maximally active in cleavage and blastula stages, and "late" genes, active from the late blastula stage onwards. We determined the nucleotide sequences of six sea urchin (Strongylocentrotus purpuratus) late histone genes located on four genomic segments. Comparative analysis of these sequences identified several conserved elements in 5' flanking regions, including the sequences ATGPyATANTATA shared by all late genes and GGCGGGAAATTGAAAA shared by two late H4s. Comparisons of protein-coding sequences of late H4 and H2B genes with their early counterparts showed that silent sites have diverged to the theoretical maximum, indicating that early and late histone gene classes diverged at least 200 million years ago. Since extant echinoderms evolved from a common ancestor at about that time, it is likely that early and late histone gene sets are characteristic of all echinoderm groups. Amino acid sequences derived from nucleotide sequences of late H2A and H2B gistone genes differ substantially from amino acid sequences of their late counterparts. Most such differences are in highly mutable positions. A few, however, occur in positions that do not mutate frequently and thus may reflect functional differences between the early and late forms of the H2A and H2B proteins.