Coding of insertion-deletion events of the chloroplastic intergene atp beta-rbcL for the phylogeny of the Valerianeae tribe (Valerianaceae).
A preliminary analysis of the sequence alignment of the chloroplast intergene atp beta-rbcL in tribe Valerianeae reveals that insertion-deletion evolutionary events ('indels'), combined with nucleotide substitutions, have occurred in large zones in some of the studied taxa. Due to the frequent occurrence and large size of indels within this tribe, intergene length varies from 531 to 788 base pairs within the studied species. This situation poses gap coding problems that we had to tackle before phylogenetic analysis. Four methods of gap coding were used: elimination of gapped sites ('complete omission'), 'missing data', 'fifth base' and Barriel's coding method, which translates indels into new multistate characters in the data matrix. After application of these four methods of data treatment, phylogenetic analyses (maximum parsimony) did not lead to very different results. Three robust clades emerged in each case, corresponding to the Centranthinae subtribe (genus Centranthus), the Fediinae subtribe (genera Fedia and Valerianella), and the American species of Valeriana. The theoretical basis and biological significance of these four methods are discussed in order to apply the best ones in future studies.
Raymúndez
María B
MB
Facultad de Ciencias, Instituto de Biología Experimental, Universidad Central de Venezuela, Apartado 47114, Los Chaguaramos, Caracas 1041, Venezuela.
Mathez
Joël
J
Xena de Enrech
Nereida
N
Dubuisson
Jean-Yves
JY
D020029:Base Pairing; D001483:Base Sequence; D025222:Chloroplast Proton-Translocating ATPases / Q000235:genetics; D002736:Chloroplasts / Q000235:genetics*; D016384:Consensus Sequence; D021901:DNA, Intergenic / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics*; D019143:Evolution, Molecular; D017343:Genes, Plant; D005819:Genetic Markers; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D012273:Ribulose-Bisphosphate Carboxylase / Q000235:genetics; D016415:Sequence Alignment; D017384:Sequence Deletion; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D028161:Valerianaceae / Q000145:classification / Q000235:genetics*
D021901:DNA, Intergenic; D018744:DNA, Plant; D005819:Genetic Markers; D010940:Plant Proteins; D025222:Chloroplast Proton-Translocating ATPases; C101625:RbcL protein, plastid; D012273:Ribulose-Bisphosphate Carboxylase