Analisis Filogenetik Gen gyrA dan gyrB dari Genus Mesorhizobium, Rhizobium dan Ensifer

Edwin Thomas Apituley; Efraim Samson; Amos Killay

doi:10.30598/biofaal.v4i2pp118-127

Edwin Thomas Apituley Jurusan Biologi FMIPA Unpatti
Efraim Samson Program Studi Biologi, Fakultas MIPA Universitas Pattimura, Ambon – Indonesia
Amos Killay Program Studi Sains Biomedis, Fakultas MIPA Universitas Pattimura, Ambon - Indonesia

DOI: https://doi.org/10.30598/biofaal.v4i2pp118-127

Keywords: DNA gyrase; filogeni; rhizobium; ensifer; mesorhizobium

Abstract

Nucleotide sequence of gyrA and gyrB genes encoding subunit A and B of gyrase enzyme from genus of Rhizobium, Ensifer and Mesorhizobium were analyzed to determine evolutionary relationship among them. Maximum Likelihood and Kimura 2 parameter methods were used to construct phylogenetic tree and measure genetic distance. Phylogenetic tree based on nucleotide sequence of gyrA gene was compared to phylogenetic tree based on nucleotide sequence of gyrB gene. Comparison of identity percentage among nucleotide sequence of gyrA gene from genus Rhizobium, Ensifer and Mesorhizobium show similarity, where each of them have narrow range of identity percentage, however nucleotide sequence of gyrB gene from genus Rhizobium and Ensifer show wider identity percentage range than genus Mesorhizobium. Several member of genus Rhizobium and Ensifer have double copy of gyrB gene with identity percentage less than 50 percent between them. Topology of phylogenetic tree based on nucleotide sequence of gyrA gene have similar topology to topology of phylogenetic tree based on nucleotide sequence of gyrB gene, except for additional branch formed by one of additional copy of gyrB sequences.

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Author Biographies

Efraim Samson, Program Studi Biologi, Fakultas MIPA Universitas Pattimura, Ambon – Indonesia

GyrA and gyrB genes encoding subunit A and B of gyrase enzyme have often been used as
molecular chronometer in phylogenetics analysis including nitrogen fixing microorganisms
such as genus of Rhizobium, Ensifer dan Mesorhizobium. Nucleotide variation and gene
copy number usually limit interpretation of phylogenetics analysis using gen sequence as
molecular chronometer. In this study, gyrA and gyrB sequences from genus of Rhizobium,
Ensifer and Mesorhizobium were analyzed to determine evolutionary relationship among
them. Maximum Likelihood and Kimura 2 parameter methods were used to construct
phylogenetic tree and measure genetic distance. Phylogenetic tree based on nucleotide
sequence of gyrA gene was compared to phylogenetic tree based on nucleotide sequence of
gyrB gene. Comparison of identity percentage among nucleotide sequence of gyrA gene
from genus Rhizobium, Ensifer and Mesorhizobium show similarity, where each of them
have narrow range of identity percentage, however nucleotide sequence of gyrB gene from
genus Rhizobium and Ensifer show wider identity percentage range than genus
Mesorhizobium. Several member of genus Rhizobium and Ensifer have double copy of gyrB
gene with identity percentage less than 50 percent between them. Topology of phylogenetic
tree based on nucleotide sequence of gyrA gene have similar topology to topology of
phylogenetic tree based on nucleotide sequence of gyrB gene, except for additional branch
formed by one of additional copy of gyrB sequences.

Amos Killay, Program Studi Sains Biomedis, Fakultas MIPA Universitas Pattimura, Ambon - Indonesia

GyrA and gyrB genes encoding subunit A and B of gyrase enzyme have often been used as
molecular chronometer in phylogenetics analysis including nitrogen fixing microorganisms
such as genus of Rhizobium, Ensifer dan Mesorhizobium. Nucleotide variation and gene
copy number usually limit interpretation of phylogenetics analysis using gen sequence as
molecular chronometer. In this study, gyrA and gyrB sequences from genus of Rhizobium,
Ensifer and Mesorhizobium were analyzed to determine evolutionary relationship among
them. Maximum Likelihood and Kimura 2 parameter methods were used to construct
phylogenetic tree and measure genetic distance. Phylogenetic tree based on nucleotide
sequence of gyrA gene was compared to phylogenetic tree based on nucleotide sequence of
gyrB gene. Comparison of identity percentage among nucleotide sequence of gyrA gene
from genus Rhizobium, Ensifer and Mesorhizobium show similarity, where each of them
have narrow range of identity percentage, however nucleotide sequence of gyrB gene from
genus Rhizobium and Ensifer show wider identity percentage range than genus
Mesorhizobium. Several member of genus Rhizobium and Ensifer have double copy of gyrB
gene with identity percentage less than 50 percent between them. Topology of phylogenetic
tree based on nucleotide sequence of gyrA gene have similar topology to topology of
phylogenetic tree based on nucleotide sequence of gyrB gene, except for additional branch
formed by one of additional copy of gyrB sequences.