Detection of heteroplasmy and nuclear mitochondrial pseudogenes in the Japanese spiny lobster Panulirus japonicus

AbstractPartial mtDNA cytochrome oxidase subunit I (COI) fragments and near entire stretch of 12S rDNA (12S) and control region (Dloop) of the Japanese spiny lobster (Panulirus japonicus) (n = 3) were amplified by PCR and used for direct nucleotide sequencing and for clone library-based nucleotide sequence analysis. Nucleotide sequences of a total of 75 clones in COI, 77 in 12S and 92 in Dloop were determined. Haplotypes of the clones matched with those obtained by direct sequencing were determined to be genuine mtDNA sequence of the individual. Phylogenetic analysis revealed several distinct groups of haplotypes in all three regions. Genuine mtDNA sequences were observed to form a group with their closely related variables, and most of these variables may be due to amplification error but a few to be heteroplasmy. Haplotypes determined as nuclear mitochondrial pseudogenes (NUMTs) formed distinct groups. Nucleotide sequence divergence (K2P distance) between genuine haplotypes and NUMTs were substantial (7.169–23.880% for COI, 1.336–23.434% for 12S, and 7.897–71.862% for Dloop). These values were comparable to or smaller than those between species of the genus Panulirus, indicating that integration of mtDNA into the nuclear genome is a continuous and dynamic process throughout pre- and post-speciation events. Double peaks in electropherograms obtained by direct nucleotide sequencing were attributed to common nucleotides shared by multiple NUMTs. Information on the heteroplasmy and NUMTs would be very important for addressing their impact on direct nucleotide sequencing and for quality control of nucleotide sequences obtained.

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Population structure of Japanese spiny lobster Panulirus japonicus inferred by nucleotide sequence analysis of mitochondrial COI gene

Fisheries Science ◽

10.1111/j.1444-2906.2007.01367.x ◽

2007 ◽

Vol 73 (3) ◽

pp. 550-556 ◽

Cited By ~ 24

Author(s):

Nariaki INOUE ◽

Hiromi WATANABE ◽

Shigeaki KOJIMA ◽

Hideo SEKIGUCHI

Keyword(s):

Population Structure ◽

Sequence Analysis ◽

Nucleotide Sequence ◽

Spiny Lobster ◽

Coi Gene ◽

Nucleotide Sequence Analysis ◽

Mitochondrial Coi ◽

Mitochondrial Coi Gene ◽

Panulirus Japonicus

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Nucleotide sequence analysis of a matrix and small hydrophobic protein dicistronic mRNA of bovine respiratory syncytial virus demonstrates extensive sequence divergence of the small hydrophobic protein from that of human respiratory syncytial virus

Journal of General Virology ◽

10.1099/0022-1317-72-7-1715 ◽

1991 ◽

Vol 72 (7) ◽

pp. 1715-1720 ◽

Cited By ~ 19

Author(s):

S. K. Samal ◽

M. Zamora

Keyword(s):

Respiratory Syncytial Virus ◽

Sequence Analysis ◽

Nucleotide Sequence ◽

Sequence Divergence ◽

Nucleotide Sequence Analysis ◽

Hydrophobic Protein ◽

Extensive Sequence ◽

Small Hydrophobic Protein ◽

Syncytial Virus ◽

Small Hydrophobic

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Phylogenetic Relationships among Members of the Coregoninae Inferred from Direct Sequencing of PCR-Amplified Mitochondrial DNA

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f93-236 ◽

1993 ◽

Vol 50 (10) ◽

pp. 2112-2118 ◽

Cited By ~ 14

Author(s):

S. Fournier Lockwood ◽

Robert E. Dillinger Jr. ◽

Tim P. Birt ◽

John M. Green ◽

Thomas P. Snyder

Keyword(s):

Mitochondrial Dna ◽

Phylogenetic Relationships ◽

Sequence Data ◽

Direct Sequencing ◽

Cladistic Analysis ◽

Sequence Divergence ◽

Amino Acid Replacement ◽

Mitochondrial Cytochrome B ◽

Mtdna Sequence ◽

Polymerase Chain

We determined the DNA sequence of a portion of the mitochondrial cytochrome b gene for eight members of the Coregoninae (Salmonidae) from North America in an effort to elucidate phylogenetic relationships in the subfamily. DNA was prepared for sequencing by the polymerase chain reaction (PCR). Direct estimates of mitochondrial DNA (mtDNA) sequence divergence among taxa ranged from 0.0% between Arctic cisco (Coregonus autumnalis) from the Mackenzie River, Canada, and cisco (C. artedi) from the Laurentian Great Lakes to 5.8% between the inconnu (Stenodus leucichthys) and the round whitefish (Prosopium cylindraceum). As has been noted in other fish species and vertebrates in general, third position silent substitutions predominated over any other type of nucleotide change. No amino acid replacement substitutions were found among any of the eight taxa examined. Comparison of mtDNA sequence divergence estimates from this and other studies suggests that the radiation of the genera within the Coregoninae occurred relatively recently (2–6 million yr B.P.). Cladistic analysis of the mtDNA sequence data yields a hypothesis of relationships that supports previous genetic and morphological classifications of coregonines.

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Cloning and nucleotide sequence analysis of transfer RNA genes from Mycoplasma mycoides

Biochemical Journal ◽

10.1042/bj2320223 ◽

1985 ◽

Vol 232 (1) ◽

pp. 223-228 ◽

Cited By ~ 14

Author(s):

T Samuelsson ◽

P Elias ◽

F Lustig ◽

Y S Guindy

Keyword(s):

Sequence Analysis ◽

Nucleotide Sequence ◽

Trna Gene ◽

Transfer Rna ◽

Nucleotide Sequences ◽

Transcriptional Unit ◽

Nucleotide Sequence Analysis ◽

Trna Genes ◽

Mycoplasma Mycoides ◽

Rna Genes

As part of an investigation of the tRNA genes of Mycoplasma mycoides, two HindIII fragments of mycoplasma DNA comprising 0.4 and 2.5 kilobases (kb), respectively, were cloned in pBR322 and their nucleotide sequences determined. Only one tRNA gene was found in the 0.4 kb fragment, the gene for tRNAArg with the anticodon TCT, while the 2.5 kb fragment contained nine different tRNA genes arranged in a cluster which presumably constitutes a transcriptional unit. The clustered tRNA genes, with their respective anticodons, were as follows: Arg (ACG), Pro (TGG), Ala (TGC), Met (CAT), Ile (CAT), Ser (TGA), fMet (CAT), Asp (GTC), and Phe (GAA).

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THE OCCURRENCE AND SEQUENCE ANALYSIS OF MILKY HEMOLYMPH DISEASE IN LOBSTER PANULIRUS HOMARUS FROM DIFFERENT LOCATIONS IN INDONESIA

Journal of Aquaculture and Fish Health ◽

10.20473/jafh.v9i1.15913 ◽

2020 ◽

Vol 9 (1) ◽

pp. 48

Author(s):

Sudewi Sudewi ◽

Zeny Widiastuti ◽

Ida Komang Wardana ◽

Ketut Mahardika

Keyword(s):

Phylogenetic Analysis ◽

Sequence Analysis ◽

Nucleotide Sequence ◽

Spiny Lobster ◽

Pcr Analysis ◽

Nucleotide Sequence Analysis ◽

Disease Occurrence ◽

Geographical Regions ◽

Disease Agent ◽

Relationship Of

Among the high significance diseases in spiny lobster farming, Milky Hemolymph Disease of Spiny Lobster (MHD-SL) is considered as the most devastating disease which caused in mortality up to 80 % and morbidity to 100%. Investigations of this disease were mostly performed for farmed lobster and no observation was conducted for wild lobster. This study was carried out first, to investigate milky hemolymph disease occurrence both in wild and farmed spiny lobster Panulirus homarus from different locations by PCR analysis. Second, to perform nucleotide sequence analysis in order to identify, and to describe relationship of the milky disease agent obtained in this study with the disease agent from several geographical regions by phylogenetic analysis. Adult farmed lobsters were collected from Lombok, Pangandaran and Pegametan, while wild lobsters were obtained from Jembrana, Lombok, and Banyuwangi coastal areas. One farmed lobster from Pegametan and two farmed lobsters from Lombok were infected with the milky disease. Nucleotide sequence analysis demonstrated that the causative agent of milky disease obtained in this study (MHD-1, 2, and 3) exhibited 99% homologous nucleotide sequence with milky disease agent from Vietnam that was uncultured Rickettsia-like Bacteria (RLB). As a consequence, further work is needed most importantly on how to cultivate milky disease agent in order to find proper methods to alleviate milky disease problems. This paper is the first report on phylogenetic analysis of milky disease from Indonesia that pointed out a closed relationship between milky disease in the present study and from Vietnam, Madagascar, Mozambique and Tanzania.

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Genetic diversity and nucleotide sequence analysis of powdery mildew marker and Vf2RAD resistant gene in apple (Malus domestica) land races

Innovaciencia Facultad de Ciencias Exactas Físicas y Naturales ◽

10.15649/2346075x.460 ◽

2018 ◽

Vol 6 (1) ◽

pp. 1-10

Author(s):

Shaymaa H. Ali ◽

Jaladet M. S. Jubrael ◽

Caroline Bowsher

Keyword(s):

Sequence Analysis ◽

Nucleotide Sequence ◽

Powdery Mildew ◽

Genetic Distance ◽

Resistance Gene ◽

Phylogenetic Diversity ◽

Nucleotide Sequences ◽

Scab Resistance ◽

Nucleotide Sequence Analysis ◽

Nucleotide Substitutions

Introduction: DNA sequencing-based methods and nucleotide sequence analysis have become the most common molecular approaches currently used for molecular typing purposes and phylogenetic diversity analysis. Methods: In this study, the nucleotide sequence variations of Powdery mildew resistance gene marker (CH03c02) and the apple scab resistance gene (Vf2RAD) beside phylogenetic diversity of seven apple landraces have been investigated. The two-locus have been successfully cloned and their nucleotide sequences were determined across all studied landraces. Results: Results of sequence alignment of the Powdery mildew resistant locus (CH03c02), compared with that of the published sequence of the same locus of Discovery genotype (HiDRAS), revealed that the nucleotide variations of this locus ranged from 1 to 28 nucleotide substitutions across all seven apple landraces. Whilst, the nucleotide variations of VF2RAD ranged from 2-8 nucleotide substitutions across all the investigated landraces. The highest genetic distance (0.062) was between Amara and Barwari. Whereas, the lowest genetic distance (0.0015) was found between each of the Lubnani, Rechard, Ispartal, and the Ahmadagha. The nucleotide sequences of the two loci were concatenated and implemented to build a Neighbor-Joining tree. The seven apple landraces were successfully grouped into two main genetic clusters (C1 and C2) in the phylogenetic tree. Conclusions: It can be concluded that the cloning approach used in the current study was found to be very successful and helpful for obtaining the full nucleotide sequences of these two loci. The investigated loci were displayed nucleotide variations among the studied landraces. And, finding of these variations was allowed the distinguishing and discrimination of these landraces.

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Characterization of Mycobacterium avium clinical isolates in Japan using subspecies-specific insertion sequences, and identification of a new insertion sequence, ISMav6

Journal of Medical Microbiology ◽

10.1099/jmm.0.008623-0 ◽

2009 ◽

Vol 58 (7) ◽

pp. 945-950 ◽

Cited By ~ 25

Author(s):

Kazuya Ichikawa ◽

Tetsuya Yagi ◽

Makoto Moriyama ◽

Takayuki Inagaki ◽

Taku Nakagawa ◽

...

Keyword(s):

Sequence Analysis ◽

Nucleotide Sequence ◽

Mycobacterium Avium ◽

Insertion Sequence ◽

Point Mutations ◽

Clinical Isolates ◽

Nucleotide Sequence Analysis ◽

Nucleotide Sequencing ◽

Insertion Sequences ◽

Pcr Products

Clinical isolates of Mycobacterium avium (n=81) from patients with pulmonary infections who were HIV-negative and isolates (n=33) from HIV-positive patients were subjected to genetic analysis by PCR detection of three M. avium-specific insertion sequences (IS901, IS1245 and IS1311), and nucleotide sequencing of the heat-shock protein 65 (hsp65) gene. All clinical isolates were identified as ‘M. avium subspecies hominissuis’ by sequence analysis of hsp65. Compared with clinical isolates of M. avium reported elsewhere, IS1245 was found less frequently in Japanese isolates (96/114 isolates, 84 %) and IS901 was detected more frequently (76/114 isolates, 67 %). One isolate was found to lack IS1311, which has not been reported previously for ‘M. avium subsp. hominissuis’. Nucleotide sequence analysis of the PCR products for IS901 revealed that all clinical isolates had the same new insertion sequence, designated ISMav6, which had 60 point mutations compared with the nucleotide sequence of the original IS901. These results suggest that ‘M. avium subsp. hominissuis’ with ISMav6 is prevalent in Japan. ISMav6 may have implications for the virulence of M. avium and contribute to an increase of M. avium infections in this country.

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Sequencing Analysis and Phylogenetic Tree of HPV Isolated from Breast Cancer Patients at Thi-Qar Province/Iraq

10.32792/utq/utjsci/vol7/2/10 ◽

2020 ◽

pp. 37-40

Keyword(s):

Nucleotide Sequence ◽

Phylogenetic Tree ◽

Evolutionary Relationship ◽

Nucleotide Sequencing ◽

Sequencing Analysis ◽

Breast Cancer Patients ◽

The North ◽

Formalin Fixed Paraffin ◽

Formalin Fixed Paraffin Embedded ◽

History Of

Genetic variety examination has demonstrated fundamental to the understanding of the epidemiological and developmental history of Papillomavirus (HPV), for the development of accurate diagnostic tests and for efficient vaccine design. The HPV nucleotide diversity has been investigated widely among high-risk HPV types. To make the nucleotide sequence of HPV and do the virus database in Thi-Qar province, and compare sequences of our isolates with previously described isolates from around the world and then draw its phylogenetic tree, this study done. A total of 6 breast formalin-fixed paraffin-embedded (FFPE) of the female patients were included in the study, divided as 4 FFPE malignant tumor and 2 FFPE of benign tumor. The PCR technique was implemented to detect the presence of HPV in breast tissue, and the real-time PCR used to determinant HPV genotypes, then determined a complete nucleotide sequence of HPV of L1 capsid gene, and draw its phylogenetic tree. The nucleotide sequencing finding detects a number of substitution mutation (SNPs) in (L1) gene, which have not been designated before, were identified once in this study population, and revealed that the HPV16 strains have the evolutionary relationship with the South African race, while, the HPV33 and HPV6 showing the evolutionary association with the North American and East Asian race, respectively.

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