Molecular characterization of DNA encoding 16S–23S rRNA intergenic spacer regions and 16S rRNA of pectolyticErwiniaspecies

2002 ◽  
Vol 48 (5) ◽  
pp. 387-398 ◽  
Author(s):  
A Fessehaie ◽  
S H De Boer ◽  
C A Lévesque
Keyword(s):  
16S Rdna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
23S Rrna ◽  
Species Structure ◽  
Trna Genes ◽  
Sequence Information ◽  
Dna Encoding

Sequences of 16S rDNAs and the intergenic spacer (IGS) regions between the 16S and 23S rDNA of bacterial strains from genus Erwinia were determined. Comparison of 16S rDNA sequences from different species and subspecies clearly revealed intraspecies–subspecies homology and interspecies heterogeneity. Phylogenetic analyses of 16S rDNA sequence data revealed that Erwinia spp. formed a discrete monophyletic clade with moderate to high bootstrap values. PCR amplification of the 16S–23S rDNA regions using primers complementary to the 3' end of 16S and 5' end of 23S rRNA genes generated two DNA fragments. The small 16S–23S rDNA IGS regions of Erwinia spp. examined in this study varied considerably in size and nucleotide sequence. Multiple sequence alignment and phylogenetic analysis of small IGS sequence data showed a consistent relationship among the test strains that was roughly in agreement with the 16S rDNA data that reflected the accepted species and subspecies structure of the taxon. Sequence data derived from the large IGS resolved the strains into coherent groups; however, the sequence information would not allow any phylogenetic conclusion, because it failed to reflect the accepted species structure of the test strains.Key words: Erwinia spp., 16S rDNA, intergenic spacer region, tRNA genes, phylogeny.

scholarly journals Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: Comparative analyses, identification of mutational hotspots and phylogenetic implications

2020 ◽  
Author(s):  
Gurusamy Raman ◽  
KyuTae Park ◽  
Joo Hwan Kim ◽  
SeonJoo Park
Keyword(s):  
Genome Sequence ◽  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
Trna Genes ◽  
Comparative Analyses ◽  
Sister Clade ◽  
Mutational Hotspots ◽  
Phylogenetic Implications ◽  
Cp Genome

Abstract Background: The invasive species Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, no extensive molecular studies of this plant have been conducted. Results: Here, the complete chloroplast (cp) genome sequence of X. spinosum was assembled and analyzed. The cp genome of X. spinosum was 152,422 base pairs (bp) in length, with a quadripartite circular structure. The cp genome contained 115 unique genes, including 80 PCGs, 31 tRNA genes, and 4 rRNA genes. Comparative analyses revealed that X. spinosum contains a large number of repeats (999 repeats) and 701 SSRs in its cp genome. Fourteen divergences (Π > 0.03) were found in the intergenic spacer regions. Phylogenetic analyses revealed that Parthenium is a sister clade to both Xanthium and Ambrosia and an early-diverging lineage of subtribe Ambrosiinae, although this finding was supported with a very weak bootstrap value. Conclusion: The identified hotspot regions could be used as molecular markers for resolving phylogenetic relationships and species identification in the genus Xanthium.

A novel mitogenomic rearrangement for Odorrana schmackeri (Anura: Ranidae) and phylogeny of Ranidae inferred from thirteen mitochondrial protein-coding genes

2014 ◽  
Vol 35 (3) ◽  
pp. 331-343 ◽  
Author(s):  
Yongmin Li ◽  
Huabin Zhang ◽  
Xiaoyou Wu ◽  
Hui Xue ◽  
Peng Yan ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Mitochondrial Protein ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes

We determined the complete nucleotide sequence of the mitochondrial genome of Odorrana schmackeri (family Ranidae). The O. schmackeri mitogenome (18 302 bp) contained 13 protein-coding genes, 2 rRNA genes, 21 tRNA genes and a single control region (CR). In the new mitogenome, the distinctive feature is the loss of tRNA-His, which could be explained by a hypothesis of gene substitution. The new sequence data was used to assess the phylogenetic relationships among 23 ranid species mostly from China using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic analyses support two families (Ranidae, Dicroglossidae) for Chinese ranids. In Ranidae, we support the genus Amolops should be retained in the subfamily Raninae rather than in a distinct subfamily Amolopinae of its own. Meanwhile, the monophyly of the genus Odorrana was supported. Within Dicroglossidae, four tribes were well supported including Occidozygini, Dicroglossini, Limnonectini and Paini. More mitochondrial genomes and nuclear genes are required to decisively evaluate phylogenetic relationships of ranids.

scholarly journals Analysis of 16S-23S rRNA Intergenic Spacer Regions of Vibrio cholerae and Vibrio mimicus

1999 ◽  
Vol 65 (5) ◽  
pp. 2202-2208 ◽  
Author(s):  
Jongsik Chun ◽  
Anwarul Huq ◽  
Rita R. Colwell
Keyword(s):  
Vibrio Cholerae ◽  
Sequence Data ◽  
Intergenic Spacer ◽  
23S Rrna ◽  
Trna Genes ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Rdna Sequences ◽  
Vibrio Mimicus ◽  
El Tor

ABSTRACT Vibrio cholerae identification based on molecular sequence data has been hampered by a lack of sequence variation from the closely related Vibrio mimicus. The two species share many genes coding for proteins, such as ctxAB, and show almost identical 16S DNA coding for rRNA (rDNA) sequences. Primers targeting conserved sequences flanking the 3′ end of the 16S and the 5′ end of the 23S rDNAs were used to amplify the 16S-23S rRNA intergenic spacer regions of V. cholerae and V. mimicus. Two major (ca. 580 and 500 bp) and one minor (ca. 750 bp) amplicons were consistently generated for both species, and their sequences were determined. The largest fragment contains three tRNA genes (tDNAs) coding for tRNAGlu, tRNALys, and tRNAVal, which has not previously been found in bacteria examined to date. The 580-bp amplicon contained tDNAIle and tDNAAla, whereas the 500-bp fragment had single tDNA coding either tRNAGlu or tRNAAla. Little variation, i.e., 0 to 0.4%, was found among V. cholerae O1 classical, O1 El Tor, and O139 epidemic strains. Slightly more variation was found against the non-O1/non-O139 serotypes (ca. 1% difference) and V. mimicus (2 to 3% difference). A pair of oligonucleotide primers were designed, based on the region differentiating all of V. cholerae strains from V. mimicus. The PCR system developed was subsequently evaluated by using representatives of V. cholerae from environmental and clinical sources, and of other taxa, including V. mimicus. This study provides the first molecular tool for identifying the species V. cholerae.

Molecular Differentiation of Renibacterium salmoninarum Isolates from Worldwide Locations

1999 ◽  
Vol 65 (3) ◽  
pp. 961-968 ◽  
Author(s):  
Thomas H. Grayson ◽  
Lynne F. Cooper ◽  
Franck A. Atienzar ◽  
Mark R. Knowles ◽  
Martyn L. Gilpin
Keyword(s):  
Rapd Analysis ◽  
Intergenic Spacer ◽  
Its Region ◽  
Single Copy ◽  
Rrna Genes ◽  
23S Rrna ◽  
Trna Genes ◽  
Renibacterium Salmoninarum ◽  
Pathogen Dna ◽  
Obligate Pathogen

ABSTRACT Renibacterium salmoninarum is a genospecies that is an obligate pathogen of salmonid fish and is capable of intracellular survival. Conventional typing systems have failed to differentiate isolates of R. salmoninarum. We used two methods to assess the extent of molecular variation which was present in isolates from different geographic locations. In one analysis we investigated possible polymorphisms in a specific region of the genome, the intergenic spacer (ITS) region between the 16S and 23S rRNA genes. In the other analysis we analyzed differences throughout the genome by using randomly amplified polymorphic DNA (RAPD). We amplified the spacer region of 74 isolates by using PCR and performed a DNA sequence analysis with 14 geographically distinct samples. The results showed that the 16S-23S ribosomal DNA spacer region of R. salmoninarum is highly conserved and suggested that only a single copy of the rRNA operon is present in this slowly growing pathogen. DNA sequencing of the spacer region showed that it was the same length in all 14 isolates examined, and the same nucleotide sequence, sequevar 1, was obtained for 11 of these isolates. Two other sequevars were found. No tRNA genes were found. We found that RAPD analysis allows reproducible differentiation between isolates of R. salmoninarum obtained from different hosts and different geographic regions. By using RAPD analysis it was possible to differentiate between isolates with identical ITS sequences.

scholarly journals Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 386
Author(s):  
Hengwu Ding ◽  
Ran Zhu ◽  
Jinxiu Dong ◽  
De Bi ◽  
Lan Jiang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Higher Plants ◽  
Phylogenetic Analyses ◽  
Structural Evolution ◽  
Taxonomic Revision ◽  
Rrna Operon ◽  
Rrna Genes ◽  
23S Rrna ◽  
Trna Genes ◽  
Phylogenetic Implications

The genus Sedum, with about 470 recognized species, is classified in the family Crassulaceae of the order Saxifragales. Phylogenetic relationships within the Saxifragales are still unresolved and controversial. In this study, the plastome of S. plumbizincicola was firstly presented, with a focus on the structural analysis of rrn operon and phylogenetic implications within the order Saxifragaceae. The assembled complete plastome of S. plumbizincicola is 149,397 bp in size, with a typical circular, double-stranded, and quadripartite structure of angiosperms. It contains 133 genes, including 85 protein-coding genes (PCGs), 36 tRNA genes, 8 rRNA genes, and four pseudogenes (one ycf1, one rps19, and two ycf15). The predicted secondary structure of S. plumbizincicola 16S rRNA includes three main domains organized in 74 helices. Further, our results confirm that 4.5S rRNA of higher plants is associated with fragmentation of 23S rRNA progenitor. Notably, we also found the sequence of putative rrn5 promoter has some evolutionary implications within the order Saxifragales. Moreover, our phylogenetic analyses suggested that S. plumbizincicola had a closer relationship with S. sarmentosum than S. oryzifolium, and supported the taxonomic revision of Phedimus. Our findings of the present study will be useful for further investigation of the evolution of plastid rRNA operon and phylogenetic relationships within Saxifragales.

scholarly journals Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: Comparative analyses, identification of mutational hotspots and phylogenetic implications

2020 ◽  
Author(s):  
Gurusamy Raman ◽  
KyuTae Park ◽  
Joo Hwan Kim ◽  
SeonJoo Park
Keyword(s):  
Genome Sequence ◽  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
Trna Genes ◽  
Comparative Analyses ◽  
Sister Clade ◽  
Mutational Hotspots ◽  
Phylogenetic Implications ◽  
Cp Genome

Abstract Background: The invasive species Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, no extensive molecular studies of this plant have been conducted. Results: Here, the complete chloroplast (cp) genome sequence of X. spinosum was assembled and analyzed. The cp genome of X. spinosum was 152,422 base pairs (bp) in length, with a quadripartite circular structure. The cp genome contained 115 unique genes, including 80 PCGs, 31 tRNA genes, and 4 rRNA genes. Comparative analyses revealed that X. spinosum contains a large number of repeats (999 repeats) and 701 SSRs in its cp genome. Fourteen divergences (Π > 0.03) were found in the intergenic spacer regions. Phylogenetic analyses revealed that Parthenium is a sister clade to both Xanthium and Ambrosia and an early-diverging lineage of subtribe Ambrosiinae, although this finding was supported with a very weak bootstrap value. Conclusion: The identified hotspot regions could be used as molecular markers for resolving phylogenetic relationships and species identification in the genus Xanthium.

Sequence Length Variation of Internal Genic Space of 16S rDNA-23S rDNA in Bacterium with High Yield of Hydrogen Production

2011 ◽  
Vol 183-185 ◽  
pp. 1413-1416
Author(s):  
Yong Feng Li ◽  
Yi Xuan Wang ◽  
Lu Wang ◽  
Zhan Qing Wang
Keyword(s):  
16S Rdna ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
High Yield ◽  
23S Rrna ◽  
Sequence Length ◽  
Rrna Gene ◽  
Length Variation ◽  
Intergenic Spacer Region

To develop the identification of species for fermentative biohydrogen-producing bacterium, scholars have found a method which is based on PCR amplification of the 16S rRNA gene (rDNA)-23S rDNA intergenic regions. In the study, a large fragment of the rDNA operon, including the 16S rDNA, the intergenic spacer region (ISR) and approximately 2000 bases of the 23S rDNA, were polymerasechain reaction (PCR) amplified. The PCR amplification of the genomic DNA of Leptonema ilk strain 3055 using primers directed against conserved regions of the rRNA operon provided evidence that the 16S and 23S rRNA genes were linked via an intergenic spacer region. The sequencing of the intergenic spacer region indicated that it was 435 nucleotides in length and sequence similarity searches revealed that it bore no homology to any known sequences including tRNA available in databases.

scholarly journals Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: Comparative analyses, identification of mutational hotspots and phylogenetic implications

2020 ◽  
Author(s):  
Gurusamy Raman ◽  
KyuTae Park ◽  
Joo Hwan Kim ◽  
SeonJoo Park
Keyword(s):  
Genome Sequence ◽  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
Trna Genes ◽  
Comparative Analyses ◽  
Sister Clade ◽  
Mutational Hotspots ◽  
Phylogenetic Implications ◽  
Cp Genome

Abstract Background: The invasive species Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, no extensive molecular studies of this plant have been conducted. Results: Here, the complete chloroplast (cp) genome sequence of X. spinosum was assembled and analyzed. The cp genome of X. spinosum was 152,422 base pairs (bp) in length, with a quadripartite circular structure. The cp genome contained 115 unique genes, including 80 PCGs, 31 tRNA genes, and 4 rRNA genes. Comparative analyses revealed that X. spinosum contains a large number of repeats (999 repeats) and 701 SSRs in its cp genome. Fourteen divergences (Π > 0.03) were found in the intergenic spacer regions. Phylogenetic analyses revealed that Parthenium is a sister clade to both Xanthium and Ambrosia and an early-diverging lineage of subtribe Ambrosiinae, although this finding was supported with a very weak bootstrap value. Conclusion: The identified hotspot regions could be used as molecular markers for resolving phylogenetic relationships and species identification in the genus Xanthium.

scholarly journals Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Gurusamy Raman ◽  
Kyu Tae Park ◽  
JooHwan Kim ◽  
SeonJoo Park
Keyword(s):  
Genome Sequence ◽  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
Trna Genes ◽  
Comparative Analyses ◽  
Sister Clade ◽  
Mutational Hotspots ◽  
Phylogenetic Implications ◽  
Cp Genome

Abstract Background The invasive species Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, no extensive molecular studies of this plant have been conducted. Results Here, the complete chloroplast (cp) genome sequence of X. spinosum was assembled and analyzed. The cp genome of X. spinosum was 152,422 base pairs (bp) in length, with a quadripartite circular structure. The cp genome contained 115 unique genes, including 80 PCGs, 31 tRNA genes, and 4 rRNA genes. Comparative analyses revealed that X. spinosum contains a large number of repeats (999 repeats) and 701 SSRs in its cp genome. Fourteen divergences (Π > 0.03) were found in the intergenic spacer regions. Phylogenetic analyses revealed that Parthenium is a sister clade to both Xanthium and Ambrosia and an early-diverging lineage of subtribe Ambrosiinae, although this finding was supported with a very weak bootstrap value. Conclusion The identified hotspot regions could be used as molecular markers for resolving phylogenetic relationships and species identification in the genus Xanthium.

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