Collection of Mitochondrial tRNA Sequences and Anticodon Identification for Acheta domesticus

Abstract:

The mitochondria are organelles found within eukaryotic cell, possess own small circular DNA (mtDNA) apart from the most of DNA found in cell nucleus. The transcription and translation of mtDNA requires tRNA that often encoded by mtDNA itself. The mtDNA evolves faster than genomic DNA primary due to mitochondrial dysfunction and pathogenesis. The genes of mitochondria tRNA (mt tRNA) are prone to mutate that links to mitochondrial activity and protein synthesis machinery. It is important to understand the codon use by mt tRNA for Acheta domesticus to understand evolutionary relationship within closely related species and mitochondrial protein synthesis machinery. The present study uses the High throughput RNA sequencing data to identify mt tRNA genes using to examine the codon use for mitochondrial protein synthesis process. The conservative property of tRNA secondary structure assisted identified and confirmed anchored tRNA sequences with respective amino acid anticodon according to genetic code for tRNA in mtDNA. This study provides mt tRNA sequences to understand evolution of mitochondrial tRNA of Acheta domesticus with other related species to establish phylogeny. Moreover, mt tRNAs are the exons that provides partial sequences for mitochondria DNA. The novel approach for tRNA identification will guide other studies for PCR free in silico analysis.

• Periodical: Materials Science Forum (Volume 967)
• Pages: 65-70
• DOI: https://doi.org/10.4028/www.scientific.net/MSF.967.65
• Online since: August 2019
• Authors: Yash Munnalal Gupta, Kittisak Buddhachat, Surin Peyachoknagul, Somjit Homchan*
• Keywords: Acheta domesticus, Anticodon, Mitochondrial DNA, Mitochondrial tRNA, Phylogeny, RNA Sequencing

References

[1] T. J. Walker. House cricket, Acheta domesticus. 2007 October 2017; Information on http://entomology.ifas.ufl.edu/creatures/misc/crickets/adomest.html.

[2] C. Kipkoech, J. N. Kinyuru, S. Imathiu, and N. Roos, Use of house cricket to address food security in Kenya: Nutrient and chitin composition of farmed crickets as influenced by age, African J. Agricultural Research. 12(44) (2017) 3189-3197.

DOI: 10.5897/ajar2017.12687

[3] R. G. Harrison and S. M. Bogdanowicz, Mitochondrial DNA phylogeny of North American field crickets: perspectives on the evolution of life cycles, songs, and habitat associations, J. Evolutionary Biology. 8(2) (1995) 209-232.

DOI: 10.1046/j.1420-9101.1995.8020209.x

[4] T. Suzuki, A. Nagao, and T. Suzuki, Human mitochondrial tRNAs: biogenesis, function, structural aspects, and diseases, Annual Review of Genetics. 45 (2011) 299-329.

DOI: 10.1146/annurev-genet-110410-132531

[5] G. S. Shadel, Expression and maintenance of mitochondrial DNA: new insights into human disease pathology, The American J. Pathology. 172(6) (2008) 1445-1456.

DOI: 10.2353/ajpath.2008.071163

[6] R. DeSalle, B. Schierwater, and H. Hadrys, MtDNA: The small workhorse of evolutionary studies, Front Biosci (Landmark Ed). 22 (2017) 873-87.

DOI: 10.2741/4522

[7] A. Linderholm, Ancient DNA: the next generation–chapter and verse, Biological J. Linnean Soc. 117(1) (2015) 150-160.

DOI: 10.1111/bij.12616

[8] L.-S. Dai, B.-J. Zhu, Y. Zhao, C.-F. Zhang, and C.-L. Liu, Comparative mitochondrial genome analysis of Eligma narcissus and other lepidopteran insects reveals conserved mitochondrial genome organization and phylogenetic relationships, Scientific Reports. 6 (2016) 26387.

DOI: 10.1038/srep26387

[9] S. L. Cameron, C. L. Lambkin, S. C. Barker, and M. F. Whiting, A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision, Systematic Entomology. 32(1) (2007) 40-59.

DOI: 10.1111/j.1365-3113.2006.00355.x

[10] A. Carapelli, P. Liò, F. Nardi, E. Van der Wath, and F. Frati, Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea, BMC Evolutionary Biology. 7(2) (2007) S8.

DOI: 10.1186/1471-2148-7-s2-s8

[11] J. B. Stewart and A. T. Beckenbach, Phylogenetic and genomic analysis of the complete mitochondrial DNA sequence of the spotted asparagus beetle Crioceris duodecimpunctata, Molecular Phylogenetics & Evolution. 26(3) (2003) 513-526.

DOI: 10.1016/s1055-7903(02)00421-9

[12] S. Zheng, Y. Li, X. Yang, J. Chen, J. Hua, and Y. Gao, DNA barcoding identification of Pseudococcidae (Hemiptera: Coccoidea) using the mitochondrial COI gene, Mitochondrial DNA Part B. 3(1) (2018) 419-423.

DOI: 10.1080/23802359.2018.1457988

[13] Y. Kumazawa and M. Nishida, Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics, J. Molecular Evolution. 37(4) (1993) 380-398.

DOI: 10.1007/bf00178868

[14] C. M. Bosworth, S. Grandhi, M. P. Gould, and T. LaFramboise, Detection and quantification of mitochondrial DNA deletions from next-generation sequence data, BMC Bioinformatics. 18(12) (2017) 407.

DOI: 10.1186/s12859-017-1821-7

[15] R. Leinonen, H. Sugawara, M. Shumway, and I. N. S. D. Collaboration, The sequence read archive, Nucleic Acids Research. 39(suppl_1) (2010) D19-D21.

DOI: 10.1093/nar/gkq1019

[16] E. Afgan, D. Baker, B. Batut, M. van den Beek, D. Bouvier, M. Čech, J. Chilton, D. Clements, N. Coraor, and B. A. Grüning, The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update, Nucleic Acids Research. 46(W1) (2018) W537-W544.

DOI: 10.1093/nar/gky379

[17] P. J. Cock, J. M. Chilton, B. Grüning, J. E. Johnson, and N. Soranzo, NCBI BLAST+ integrated into Galaxy, Gigascience. 4(1) (2015) 39.

DOI: 10.1186/s13742-015-0080-7

[18] W. YE, J.-p. DANG, L.-d. XIE, and Y. HUANG, Complete mitochondrial genome of Teleogryllus emma (Orthoptera: Gryllidae) with a new gene order in Orthoptera, Zoological Research. 29(3) (2008) 236-244.

DOI: 10.3724/sp.j.1141.2008.00236

[19] W. Lee, J. Park, J. Choi, K. Jung, B. Park, D. Kim, J. Lee, K. Ahn, W. Song, and S. Kang, IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes, BMC Genomics. 10(1) (2009) 148.

DOI: 10.1186/1471-2164-10-148

[20] C. Camacho, G. Coulouris, V. Avagyan, N. Ma, J. Papadopoulos, K. Bealer, and T. L. Madden, BLAST+: architecture and applications, BMC Bioinformatics. 10(1) (2009) 421.

DOI: 10.1186/1471-2105-10-421

[21] T. M. Lowe and P. P. Chan, tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes, Nucleic Acids Research. 44(W1) (2016) W54-W57.

DOI: 10.1093/nar/gkw413

[22] A. R. Gruber, R. Lorenz, S. H. Bernhart, R. Neuböck, and I. L. Hofacker, The vienna RNA websuite, Nucleic Acids Research. 36(suppl_2) (2008) W70-W74.

DOI: 10.1093/nar/gkn188

[23] M. Sprinzl, C. Steegborn, F. Hübel, and S. Steinberg, Compilation of tRNA sequences and sequences of tRNA genes, Nucleic Acids Research. 24(1) (1996) 68-72.

DOI: 10.1093/nar/24.1.68

[24] R. D. Dowell and S. R. Eddy, Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints, BMC Bioinformatics. 7(1) (2006) 400.

DOI: 10.1186/1471-2105-7-400