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1.
Article in English | MEDLINE | ID: mdl-24892490

ABSTRACT

In this study, the complete mitochondrial genome sequence of Amphilophus citrinellus was firstly sequenced and determined. The total genome is 16,522 bp in length with an A + T content of 54.19%, and contained 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and two main non-coding regions. The gene composition and order is similar to that of most other vertebrates, as is base composition and codon usage. These data will provide useful molecular information for phylogenetic relationships within the family Cichlidae species.


Subject(s)
Cichlids/genetics , Genome, Mitochondrial/physiology , Phylogeny , Animals , Base Sequence , Fish Proteins/genetics , Mitochondrial Proteins/genetics , Molecular Sequence Data , RNA/genetics , RNA, Mitochondrial , RNA, Ribosomal/genetics , RNA, Transfer/genetics
2.
Article in English | MEDLINE | ID: mdl-24438265

ABSTRACT

We determined the complete mitochondrial genome of Tilapia buttikoferi, which was 16,577 bp in length with an A + T content of 53.0%, containing 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a complete control region. The gene arrangement was similar to that of typical fishes. The total base composition of the mitogenome was 25.6% T, 30.8% C, 27.4% A and 16.2% G. Of the 13 protein-coding genes, 12 genes start with an ATG codon, except for COX1 with GTG. Seven (ND1, ND2, COX1, ATPase8, ATPase6, ND4L and ND6) used TAA or AGA as the termination codon, whereas six (COX2, COX3, ND3, ND4, ND5 and cyt b) had incomplete stop codon T. Its control region was atypical in being short at 861 bp, and contained TACAT motif and one microsatellite-like region (TA)7. This mitogenome sequence data may be useful for phylogenetic and systematic analyses within the family Cichlaidae.


Subject(s)
Genome, Mitochondrial , Tilapia/genetics , Animals , Base Composition/genetics , Base Pairing/genetics , Base Sequence , DNA, Circular/genetics , DNA, Mitochondrial/genetics , Open Reading Frames/genetics , RNA, Transfer/genetics
3.
Ying Yong Sheng Tai Xue Bao ; 27(4): 1277-1284, 2016 Apr 22.
Article in Chinese | MEDLINE | ID: mdl-29732786

ABSTRACT

The high-risk invasive apple snail Pomacea canaliculata has greatly threatened the agriculture, ecosystem integrity and public health. In order to provide scientific evidence for effective prevention and control of P. canaliculata, a most suitable ecological niche model was selected to predict the potential suitable distribution areas of P. canaliculata in China. Based on 377 reported occurrence points and 19 bioclimatic variables, four ecological niche models, MaxEnt, GARP, BIOCLIM, and DOMAIN, the potential geographic suitable distribution areas were predicted for the invasive snail. Then, the results of different models were analyzed and compared with two statistical criteria, the area under the Receiver Operating Characteristic curve (AUC) and Kappa value. The results showed that all of the four ecological niche models could simulate the snail's distributions very well. More specifically, the MaxEnt model outperformed the others in all aspects of predicting the snail's potential distribution (AUC=0.955±0.004, Kappa=0.845±0.017), followed by GARP and DOMAIN. Although BIOCLIM offered the lowest prediction accuracy, its AUC was 0.898±0.017 and its Kappa value was 0.771±0.025. Based on the MaxEnt model, the prediction results showed that the potential suitable distribution areas of P. canaliculata were mainly located in the south of 30° N in China, but there was some regions spreading over the north of 30° N. The potential areas accounted for 13.2% of the national land in area. Notably, Guangdong, Guangxi, Hunan, Chongqing, Zhejiang and the coastal areas of Fujian were potentially high-risk areas. In conclusion, this study would be an important reference for the prevention and control of the invasive apple snail P. canaliculata and it also would be an example of predicting the potential distribution of aquatic alien species on large scale.


Subject(s)
Animal Distribution , Ecosystem , Malus , Snails , Agriculture , Animals , China , Climate , Introduced Species , Models, Theoretical
4.
Mitochondrial DNA ; 26(5): 698-9, 2015.
Article in English | MEDLINE | ID: mdl-24325672

ABSTRACT

We sequenced the complete mitogenome of northern spotted barramundi Scleropages jardinii, an ancestral bonytongue with economic and conservation value. The mitogenome is 16,670 bp in length with an A + T content of 52.9%, and contains 13 protein-coding genes, 2rRNAs, 22 tRNAs and a control region. The gene order and arrangement is similar to that of other Osteoglossidae species, as is base composition and codon usage. These data will provide useful molecular information for phylogenetic relationships within the family Osteoglossidae species.


Subject(s)
Fishes/genetics , Genome, Mitochondrial , Mitochondria/genetics , Animals , Base Composition , Gene Order , Genome Size , Phylogeny , Sequence Analysis, DNA
5.
Mitochondrial DNA ; 26(6): 857-8, 2015.
Article in English | MEDLINE | ID: mdl-24409899

ABSTRACT

We determined the first complete mitochondrial genome sequence of Potamotrygon motoro from South American freshwater stingrays. The total length of P. motoro mitogenome is 17,448 bp, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region, with the genome organization and gene order being identical to that of the typical vertebrate. The overall nucleotide composition is 32.3% A, 24.4% T, 30.5% C and 12.8% G. These data will provide useful molecular information for phylogenetic relationships within the family Potamotrygonidae species.


Subject(s)
Genome, Mitochondrial , Skates, Fish/genetics , Animals , Base Composition , Gene Order , Phylogeny , Sequence Analysis, DNA/methods
6.
Cell Stress Chaperones ; 19(4): 579-89, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24368711

ABSTRACT

Heat-shock protein 70 (HSP70) is one of the most important heat-shock proteins that helps organisms to modulate stress response via over-expression. The HSP70 gene from Pomacea canaliculata was cloned using the RACE approach; the gene is 2,767 bp in length and contains an open reading frame of 1,932 bp, which is encoded by a polypeptide of 643 amino acids. BLAST analysis showed that the predicted amino acid sequence of the P. canaliculata HSP70 gene shared a relatively high similarity with that of other known eukaryotic species that display conserved HSP characteristics. The phylogeny demonstrated a separate clustering of the apple snail HSP70 with other constitutive members from other mollusk species. Quantitative real-time RT-PCR was used to detect the differential expression of HSP70 in both sexes of P. canaliculata at different temperature conditions. These results showed that HSP70 transcript levels decreased slightly under cold shock and increased significantly under heat-shock conditions in both sexes compared to normal temperatures (26 °C). Under cold-shock treatment, the sex effect was not significant. With heat treatment, HSP70 expression could be induced at 36 °C in both females and males, and it peaked at 42 and 39 °C in females and males, respectively. In addition, a clear time-dependent HSP70 expression pattern of the apple snail exposed to the same high temperature (36 °C) was observed at different time points. The maximal induction of HSP70 expression appeared at 12 and 48 h in males and females after heat shock, respectively. The maximal induction in females was significantly higher compared to males under heat stimulus. Taken together, these results strongly suggested that males were more susceptible to heat than females and provided useful molecular information for the ecological adaptability of P. canaliculata against extreme environmental stress.


Subject(s)
Gene Expression Regulation , HSP70 Heat-Shock Proteins/genetics , Snails/physiology , Stress, Physiological , Amino Acid Sequence , Animals , Base Sequence , Female , HSP70 Heat-Shock Proteins/chemistry , Male , Malus/parasitology , Molecular Sequence Data , Phylogeny , Sequence Alignment , Snails/chemistry , Snails/genetics , Temperature
7.
Gene ; 511(2): 320-5, 2012 Dec 15.
Article in English | MEDLINE | ID: mdl-23036711

ABSTRACT

The present study examined the genetic variation of the family Osteoglossidae from different geographical locations based on the mitochondrial NADH dehydrogenase subunit 2 (ND2) and ATPase subunit 6 (ATPase6) genes; we then re-constructed the phylogenetic relationships using the two sequences in combination. The results showed that the partial sequences of mitochondrial ND2 and ATPase6 of the family Osteoglossidae were 813 bp and 669 bp, respectively. A total of 42 species-specific nucleotide positions of the family Osteoglossidae were found to be useful for molecular identification. The sequence variation showed greater differences (8.3%~28.1% for the combined sequences, 8.3%~26.7% for the ND2 gene, and 9.3%~28.7% for the ATPase6 gene) among the different species of Osteoglossidae, and there was a significant association between the genetic difference and geographical location. Phylogenetic analyses using neighbor-joining, Bayesian inference, and maximum parsimony (MP) methods based on the combined sequences of the two genes were able to distinguish the different species and were in agreement with the existing taxonomy based on morphological characters and in association with the geographical distribution among seven species of the family Osteoglossidae.


Subject(s)
DNA, Mitochondrial/genetics , Fishes/genetics , Genetic Variation , Phylogeny , Adenosine Triphosphatases/genetics , Animals , Base Sequence , DNA Primers , NADH Dehydrogenase/genetics , Polymerase Chain Reaction , Sequence Homology, Nucleic Acid
8.
Yi Chuan Xue Bao ; 32(1): 19-29, 2005 Jan.
Article in English | MEDLINE | ID: mdl-15715434

ABSTRACT

In this study,the full-length cDNAs of GH (Growth Hormone) gene was isolated from six important economic fishes, Siniperca kneri, Epinephelus coioides, Monopterus albus, Silurus asotus, Misgurnus anguillicaudatus and Carassius auratus gibelio Bloch. It is the first time to clone these GH sequences except E. coioides GH. The lengths of the above cDNAs are as follows: 953 bp, 1 023 bp, 825 bp, 1 082 bp, 1 154 bp and 1 180 bp. Each sequence includes an ORF of about 600 bp which encodes a protein of about 200 amino acid: S. kneri, E. coioides and M. albus GHs of 204 amino acid, S. asotus GH of 200 amino acid, M. anguillicaudatus and C. auratus gibelio GHs of 210 amino acid. Then detailed sequence analysis of the six GHs with many other fish sequences was performed. The six sequences all showed high homology to other sequences, especially to sequences within the same order, and many conserved residues were identified, most localized in five domains. The phylogenetic trees (MP and NJ) of many fish GH ORF sequences (including the new six) with Amia calva as outgroup were generally resolved and largely congruent with the morphology-based tree though some incongruities were observed, suggesting GH ORF should be paid more attention to in teleostean phylogeny.


Subject(s)
DNA, Complementary/analysis , Fishes/genetics , Growth Hormone/genetics , Sequence Homology, Amino Acid , Amino Acid Sequence , Animals , Base Sequence , Catfishes/genetics , Cloning, Molecular , Cypriniformes/genetics , Goldfish/genetics , Molecular Sequence Data , Open Reading Frames/genetics , Perciformes/genetics , Phylogeny , Sequence Alignment , Sequence Analysis, DNA
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