Comparative studies of Indian and Malaysian Thapaocleidus siamensis using molecular marker

Paper Details

Research Paper 01/01/2014
Views (804)
current_issue_feature_image
publication_file

Comparative studies of Indian and Malaysian Thapaocleidus siamensis using molecular marker

Saroj Rajvanshi, Nirupama Agrawal
J. Biodiv. & Environ. Sci. 4(1), 116-121, January 2014.
Copyright Statement: Copyright 2014; The Author(s).
License: CC BY-NC 4.0

Abstract

In the present communication the sequence of an exotic species of genus Thaparocleidus i.e T. siamensis (Lim, 1990) Lim, 1996 (collected in India) has been compared with that of Malaysian, on in silico basis using 28S rDNA. Since, both are morphologically more or less similar and effect of environment on T. siamensis cannot access structurally. Thus to evaluate the environmental effects on 28S rDNA region of T. siamensis, a comparative study has been done for Indian (obtained) and Malaysian (retrieved) T. siamensis using MEME Suite, MARNA and ExpaRNA (online softwares)). The results obtained showing a shift in genetic material because of climatic changes in India.

Billoud B, Guerrucci MA, Masselot M, Deutsch JS. 2000.  Cirripede  phylogeny  using  a novel approach: molecular morphometrics. Molecular Biology and Evolution 17, 1435–1445.

Grajales A, Aguilar C, Sanchez J. 2007. Phylogenetic reconstruction using secondary structures of internal transcribed spacer 2 (ITS2, rDNA): finding the molecular and morphological gap in Caribbean gorgonian corals. BMC Evolutionary Biology 7, 90.

Moritz C, Cicero C. 2005. DNA barcoding: promise and pitfalls. PLoS Biology 2, 1529–1531.

Schultz J, Maisel S, Gerlach D, Mueller T, Wolf M. 2005. A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA 11, 361–364.

Smith C, Heyne S, Richter AS, Will S, Backofen R. 2010. Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA. Nucleic Acid Research 38, W373-W377.

Rajvanshi S, Agrawal N. 2013. One known and unknown species of of the genus Thaparocleidus, Jain, 1952, infecting Sperata aor (Hamilton, 1822): Camparison with species from China, on molecular basis. Bioinformation 9 (11), 577-582.

Timothy L, Bailey, Charles E. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park, California. 28-36.

Thompson JD, Higgins DG, Gibson TJ. 2003. Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions- specific gap penalties and weight matrix choice. Nucleic Acid Research 22, 4673-80.

Tamura K, Nei M, Kumar S. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park, California. 101, 11030-11035.

Tandon V. 2007. Molecular taxonomy of trematodes parasites-protocols to follow. Manual of the workshop on fish-parasites-taxonomy capacity building. Andhra University, Visakhapatnam, India 79-86.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28, 2731-2739.

Will S, Reiche K, Hofacker IL, Peter FS, Backofen R. 2007. Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLoS Computational Biology 3(4), e65.

Will S, Joshi T, Hofacker IL, Stadler PF, Backofen R. 2012. LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs. RNA 18(5), 900-14.

Zwieb C, Glotz C, Brimacombe R. 1981 Secondary structure comparisons between small subunit ribosomal RNA molecules from six different species. Nucleic Acids Research 9, 3621– 3640. http://www.genomicsplace.com/gc_calc.html www.fishbase.org, version (04/2013).

Related Articles

In vitro assessment of Bambara groundnut M3 mutant genotypes for resistance to Macrophomina phaseolina (Tassi) Goid. in the seedling stage in Burkina Faso

Brahime Tingueri*, Souleymane Ouattara, Adjima Ouoba, Romain W. Soalla, Mahamadi Hamed Ouedraogo, J. Biodiv. & Environ. Sci. 28(6), 141-149, June 2026.

Impact of Beauveria bassiana and Metarhizium anisopliae on biochemical and antioxidant enzymes in Rhynchophorus ferrugineus (Olivier) infesting oil palm

M. Malarvizhi, N. Santhana Bharathi, K. Sujatha*, A. Vijaya Anand, R. Manikandan, J. P. Antony Prabhu, J. Biodiv. & Environ. Sci. 28(6), 129-140, June 2026.

Typhoon risk perception and preparedness after Sendong in Bayug Island

Dinah Millendez*, Lex Rei Brendon Hilario, Jay Rey Alovera, Elizabeth Edan Albiento, Melgie Alas, Peter Suson, J. Biodiv. & Environ. Sci. 28(6), 120-128, June 2026.

Floristic composition and woody species diversity in Campo-Ma’an National Park, South Cameroon

Achey Nkenfack Djike Baudelair*, Temgoua Lucie Félicité, Kuete Fogang Marcien, Nfondem Poumie Mohamed Mounir, Atoupka Abdel Malik, Djeuni Duplex Romuald, Kontchiachou Nkana Didier, J. Biodiv. & Environ. Sci. 28(6), 103-119, June 2026.

Comparative effects of bio-inoculant on nutrient dynamics of biodegradable waste

Anjelle-J G. Debosura*, Carlo Stephen O. Moneva, Corazon V. Ligaray, Elizabeth Edan M. Albiento, MA. Cecilia V. Almeda, Melgie A. Alas, Frandel Louis S. Dagoc, Peter D. Suson, J. Biodiv. & Environ. Sci. 28(6), 97-102, June 2026.

Impact of deforestation on the aquatic macroinvertebrate community and the ecological quality of Mé River (South-East, Côte d’Ivoire)

Gnago Dohou Affri*, Tapé Logboh David, Edia Oi Edia, J. Biodiv. & Environ. Sci. 28(6), 80-96, June 2026.

Vulnerability and regeneration potential of Bambusa vulgaris in Ebolowa, South Cameroon

Rodine Tchiofo Lontsi*, Duchesse Elvira Kepmou, Emilienne Laure Ngahane, Jacques Christophe Awoa Essam, Isaac Blaise Djoko, J. Biodiv. & Environ. Sci. 28(6), 68-79, June 2026.

Temporal availability of floral resources for the honey bee (Apis mellifera) in a forest ecosystem in the sudanian zone of Côte d’Ivoire: The case of Badenou classified forest

Dofoungo Koné*, Comlan Mawussi Koudegnan, Siendou Coulibaly, Fofana Séguéna, Bruno Marcel Iritié, Wandan Eboua Narcisse, J. Biodiv. & Environ. Sci. 28(6), 56-67, June 2026.