A Comparative Genomic and Transcriptional Survey Providing Novel Insights into Bone Morphogenetic Protein 2 (bmp2) in Fishes
Abstract
:1. Introduction
2. Results
2.1. Variation of bmp2 Copy Number in Different Fish Species for a Phylogenetic Analysis
2.2. Synteny Data
2.3. Sequence Alignment and Three-Dimensional (3D) Structure Prediction of Zebrafish bmp2a Gene and bmp2b Gene
2.4. Structural Analysis of bmp2a and bmp2b
2.5. Transcriptional Level Studies of Various Tissues of Nile Tilapia and Bluntnose Black Bream
3. Discussion
3.1. Possible Reasons for Copy Number Variations among Vertebrates
3.2. Adaptive Evolution of bmp2s in Vertebrates
3.3. The Relationship between the Structure and Function of bmp2
4. Methods and Materials
4.1. Acquisition of bmp2a and bmp2b for Nucleotide and Protein Sequences
4.2. Phylogenetic Analysis and Sequence Alignment
4.3. Analyses of Conserved Synteny and Gene Structures
4.4. qRT-PCR Analysis of bmp2a and bmp2b for Nile Tilapia and Bluntnose Black Bream
4.5. Tertiary Structure and Function Prediction of Zebrafish bmp2 Protein
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
TGF-β | Transforming growth factor beta |
LAP | Latency associated peptide |
MAFFT | Multiple sequence alignment based on fast Fourier transform |
hao1 | Hydroxyacid oxidase 1 |
tmx4 | Thioredoxin related transmembrane protein 4 |
Napba | N-ethylmaleimide-sensitive factor attachment |
crls1 | Cardiolipin synthase 1 |
mcm8 | Minichromosome maintenance 8 |
Gpcpd1 | Glycerophosphocholine phosphodiesterase 1 |
trmt6 | tRNA methyltransferase 6 |
fermt1 | Fermitin family member 1 |
TAAR12j | Trace amine associated receptor 12j |
TAAR12e | Trace amine associated receptor 12e |
TAAR12g | Trace amine associated receptor 12g |
TAAR12f | Trace amine associated receptor 12f |
TAAR12a | Trace amine associated receptor 12a |
TAAR12b | Trace amine associated receptor 12b |
TAAR12c | Trace amine associated receptor 12c |
TAAR10 | Trace amine-associated receptor 10 |
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Class | Common Name | Species Name | bmp2a | bmp2b |
---|---|---|---|---|
Actinopterygii | Snakehead fish | Channa argus | 0 | 1 |
Large yellow croaker | Larimichthys crocea | 0 | 1 | |
Giant-fin mudskipper | Periophthalmus magnuspinnatus | 0 | 1 | |
Black porgy | Acanthopagrus schlegelii | 0 | 1 | |
Cave-restricted golden-line fish (Sa) | Sinocyclocheilus anshuiensis | 2 | 2 | |
Semi-cave-dwelling golden-line fish (Sr) | Sinocyclocheilus rhinocerous | 2 | 2 | |
Surface-dwelling golden-line fish (Sg) | Sinocyclocheilus grahami | 2 | 1 | |
Kanglang fish | Anabarilius sgrahami | 1 | 1 | |
Catfish | Silurus asotus | 1 | 1 | |
Channel catfish | ictalurus punctatus | 1 | 1 | |
Lined_seahorse | Hippocampus erectus | 0 | 1 | |
Longjaw grenadier anchovy | Coilia macrognathos | 1 | 0 | |
Spotted gar | Lepisosteus oculatus | 0 | 1 | |
Golden arowana | Scleropages formosus | 0 | 1 | |
Bluntnose black bream | Megalobrama amblycephala | 1 | 1 | |
Atlantic herring | Clupea harengus | 1 | 1 | |
Hilsa shad | Tenualosa ilisha | 2 | 1 | |
Mexican tetra | mexicanus | 1 | 1 | |
Zebrafish | Danio rerio | 1 | 1 | |
Japanese medaka | Oryzias latipes | 1 | 1 | |
Nile tilapia | Oreochromis niloticus | 1 | 1 | |
Gilthead seabream | Sparus aurata | 1 | 1 | |
Tongue sole | Cynoglossus semilaevis | 1 | 1 | |
Japanese flounder | Paralichthys olivaceus | 1 | 1 | |
Atlantic salmo | Salmo salar | 2 | 2 | |
Fugu rubripes | Takifugu rubripes | 1 | 1 | |
Sarcopterygii | Coelacanth | Latimeria chalumnae | 0 | 1 |
Holocephali | Australian ghostshark | Callorhinchus milii | 1 | 1 |
Mammalis | Platypus | Ornithorhynchus anatinus | 1 | 1 |
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Yang, G.; Qin, Z.; Kou, H.; Liang, R.; Zhao, L.; Jiang, S.; Lin, L.; Zhang, K. A Comparative Genomic and Transcriptional Survey Providing Novel Insights into Bone Morphogenetic Protein 2 (bmp2) in Fishes. Int. J. Mol. Sci. 2019, 20, 6137. https://doi.org/10.3390/ijms20246137
Yang G, Qin Z, Kou H, Liang R, Zhao L, Jiang S, Lin L, Zhang K. A Comparative Genomic and Transcriptional Survey Providing Novel Insights into Bone Morphogenetic Protein 2 (bmp2) in Fishes. International Journal of Molecular Sciences. 2019; 20(24):6137. https://doi.org/10.3390/ijms20246137
Chicago/Turabian StyleYang, Guang, Zhendong Qin, Hongyan Kou, Rishen Liang, Lijuan Zhao, Shoujia Jiang, Li Lin, and Kai Zhang. 2019. "A Comparative Genomic and Transcriptional Survey Providing Novel Insights into Bone Morphogenetic Protein 2 (bmp2) in Fishes" International Journal of Molecular Sciences 20, no. 24: 6137. https://doi.org/10.3390/ijms20246137