Cytochrome b Gene Sequence of the Sugarcane Borer,Diatraea saccharalis(Lepidoptera:Pyraloidea:Crambidae)
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The mitochondrial cytochrome b gene of Diatraea saccharalis was amplified and sequenced and was found to be 1146 bp in length.The cyt b gene sequences from four orders including Diptera,Coleoptera,Thysanura,and Lepidoptera,were analyzed with molecular biology software.Nucleotide composition,transitions and transversions,amino acid composition,genetic distance,and the phylogenetic relationship among these insects were examined.The results indicated that Lepidopteran insects possessed a higher A+T content,and was 75.1% in D.saccharalis.There was no conspicuous relationship between A+T content and A/T-skewness.Nucleotide substitution occurred mostly at the third position,and transitions were greater than transversions.Codon usage could reflect base compositional bias of AT.The amino acid sequences were believed to be more accurate than nucleotide sequences in genetic distance.The phylogenetic analysis was performed using cyt b gene sequences,and the results supported a monophyletic Endopterygota(Diptera+ Lepidoptera + Coleoptera),a monophyletic Mecopterida(Diptera + Lepidoptera),a monophyletic Diptera,a monophyletic Lepidoptera,and a monophyletic Coeloptera.Keywords:
Crambidae
Diatraea saccharalis
Monophyly
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Paraphyly
Monophyly
Maximum parsimony
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In the present study, a partial sequence of 440 bp of Cyt b gene were subjected to phylogenetic analysis to understand the intrageneric, interspecific and intraspecific variations in nine species of stink bugs of family Pentatomidae. The final aligned data pertained to 18 Cyt b sequences of 440 bp representing 10 species and 5 genera. Sequence of Aeschyntelus notatus, belonging to family Rhopalidae, was included in the analysis as the out-group taxon. The intraspecific divergence ranged from 0.2 to 7.2% whilst interspecific divergence ranged from 3.8 to 10.3% and intergeneric distance ranged from 12.1 to 20.2%The pairwise genetic distances were calculated and phylograms were constructed using Maximum Likelihood, Maximum Parsimony, and Neighbour-Joining methods. The database analysis showed hierarchical increase in percentage divergence across different taxonomic levels and revealed a clear pattern of increased nucleotide diversity from conspecific to congeneric to intra subfamily level using Cyt b gene fragment.
Subfamily
Maximum parsimony
Molecular Phylogenetics
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Megachilidae
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Partial DNA sequences of the mitochondrial 16S ribosomal RNA and NADH 1 dehydrogenase genes (831 bp) were determined for 7 species of the parasitic wasp genus Cotesia, including all three members of the Cotesia flavipes species complex. Cladistic analy sis was used to infer a phylogenetic tree and examine the relationships among members of the C. flavipes complex. The DNA sequences were also used to determine the extent of se quence variation among members of the complex in order to evaluate the specific status of each of the three species. Unweighted parsimony analysis indicated that the C. flavipes com plex is monophyletic and that C. chilonis and C. sesamiae are more closely related to each other with respect to C. flavipes. However, we were unable to confirm that C. chilonis and C. sesamiae are in fact separate species as only ~1% sequence divergence was observed in a pairwise comparison of the DNA sequences for these two species. A list of potentially use ful diagnostic characters is presented.
Monophyly
Maximum parsimony
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Crambidae
Ostrinia
Subfamily
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Intraspecific differentiation of the Japanese brown frog Rana japonica was investigated by analyzing nucleotide sequences of the mitochondrial cytochrome b (cyt b) gene in order to clarify phylogenetic relationships among three population groups known to exist in this species. The nucleotide sequences of 447 base pair (bp) segments were determined by the PCR-direct sequencing method on 31 individuals from 14 populations of R. japonica from Honshu, and phylogenetic trees were constructed by the UPGMA and NJ methods using Rana catesbeiana as an outgroup. A sequence alignment provided 92 variable sites (15 corresponded to the first codon position, three to the second, and 74 to the third), and 19 haplotypes were identified from 31 frogs. The sequence divergences were 0.22∼2.50% (x̄ = 0.65%) within populations, 0.22∼12.02% (x̄ = 7.34%) between populations, and 23.59∼27.89% (x̄ = 26.19%) between R. japonica and R. catesbeiana. Although many nucleotide substitutions were silent mutations, 12 amino acid replacements were found to occur within R. japonica. A high frequency of transitions relative to transversions was observed within R. japonica. The present nucleotide sequence data showed that the eastern and western groups of R. japonica was considerably differentiated to each other, and that the Akita population of the northwestern group was evidently derived from the eastern group, but the Nakajo and Izumozaki populations of the northwestern group diverged considerably from each of the eastern and the western groups.
UPGMA
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【Aim】To explore the phylogenetic relationships within and between three major subfamilies( Polyommatinae,Theclinae and Lycaeninae) of the Chinese lycaenids based on the mitochondrial gene sequence data. 【Methods】The partial mitochondrial COI and Cytb genes of 53 species were amplified and determined with PCR method,the sequence variation of these species were also analyzed,and the phylogenetic trees of these lycaenid species were reconstructed with maximum-likelihood( ML) and Bayesian-inference( BI) methods. 【Results】The results of the sequence analysis showed that the two combined genes are 1 431 bp in length,including 855 conserved sites,576 variable sites and 488parsimonious-informative sites,and the average percentage of A + T is 74. 5%,which is much higher than that of G + C( 25. 5%). The results of phylogenetic analyses indicated that the Polyommatinae and Lycaeninae were monophyletic groups,whereas the Theclinae was a paraphyletic group. All the taxa in this study contained three main clades: the first was the subfamily Lycaeninae,the second was the subfamily Polyommatinae plus the tribes Hypolycaenini and Aphnaeini of the subfamily Theclinae,and the third was the other four tribes of the subfamily Theclinae,with their relationship as((( Theclini +Arhopalini) + Deudorigini) + Eumaeini). 【Conclusion 】The subfamily Lycaeninae is a monophyletic group,while the Polyommatinae and Theclinae are more closely to each other,with the relationship of their main groups awaiting further investigation.
Paraphyly
Subfamily
Monophyly
Lycaenidae
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Anomala
Subgenus
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The cytochrome oxidase gene (COI) was employed to assess the genetic variation in different populations of Cotesia flavipes . Partial sequences of the COI gene for the populations from Bangalore, Hyderabad, New Delhi and Shimla were analyzed to assess the homology and the usefulness of this genetic region for phylogenetic studies. PCR using COI-F and COI-R primers amplified a product of approximately 550 bp which was similar for all the four populations. Populations were by and large similar in the COI gene sequenced and there was no variation with our sequences and those of sequences worldwide. The multiple alignments were performed for four populations which revealed similarity of the partial COI gene sequences. Comparative analysis of partial sequences of COI gene produced a phylogenetic tree. Phylogenetic analysis revealed that all our populations were in a single clade with high boot strap value, suggesting highest similarity.
Genetic distance
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