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An additional record of Fejervarya manoharani Garg and Biju from the Western Ghats with a description of its complete mitochondrial genome

S. KUMAR KIRAN, V. S. ANOOP, K. C. SIVAKUMAR, RAGHUNATHAN DINESH, J. P. MANO, DEUTI KAUSHIK, GEORGE SANIL

Abstract


An additional sighting of newly described frog species, Fejervarya manoharani Garg and Biju, outside of the type locality along with their morphological data is reported herewith. We are also providing the whole DNA sequence of the mitochondrial genome with its gene organization as additional data to distinguish this species from its congeners. The mitogenome of F. manoharani was 17,654 bp in length. It contains 38 genes including two rRNAs, 23 tRNAs, 13 protein-coding genes and a control region. Similar to other dicroglossid frogs, a tandem duplication of tRNAMet was found. The ND5 gene was located at the 3' end of the control region like in three other Fejervarya species for which mitogenomic data are available. A rearrangement of four tRNA genes, namely Leucine, Threonine, Proline, and Phenylalanine, between ND5 and 12S rRNA, differing from other Fejervarya species, was also observed.

 


Keywords


Amphibia, Distribution, Fejervarya, taxonomy, Western Ghats, whole mitogenome

References


Alam, M.S., Kurabayashi, A., Hayashi, Y., Sano, N., Khan, M.M.R., Fujii, T. & Sumida, M. (2010) Complete mitochondrial genomes and novel gene rearrangements in two dicroglossid frogs, Hoplobatrachus tigerinus, and Euphlyctis hexadactylus, from Bangladesh. Genes & Genetic Systems, 85, 219‒232.
https://doi.org/10.1266/ggs.85.219

Anoop, V.S., Kumar, K.S., Sivakumar, K.C., Reghunathan, D., Manoj, P., Deuti, K. & George, S. (2017) The complete mitochondrial genome of Euphlyctis karaavali (Amphibia: Anura) with a note on its range expansion. Conservation Genetics Resources, 1–4. [published online]
https://doi.org/10.1007/s12686-017-0703-7

Altschul, S., Gish, W., Miller, W., Myers, E.W. & Lipman, D. (1990) Basic local alignment tool. Journal of Molecular Biology, 215, 403‒410.
https://doi.org/10.1016/S0022-2836(05)80360-2

Bernt, M., Donath, A., Jühling, F., Externbrink, F., Florentz, C., Fritzsch, G., Pütz, J., Middendorf, M. & Stadler, P.F. (2013) MITOS: Improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution, 69, 313‒319.
https://doi.org/10.1016/j.ympev.2012.08.023

Boore, J.L. (1999) Animal mitochondrial genomes. Nucleic Acids Research, 27, 1767‒1780.
https://doi.org/10.1093/nar/27.8.1767

Boulenger, G.A. (1920) A monograph of the South Asian, Papuan, Melanesian and Australian frogs of the genus Rana. Records of the Indian Museum, 20, 1–223.
https://doi.org/10.5962/bhl.title.12471

Chevreux, B., Pfisterer, T., Drescher, B., Driesel, A.J., Müller, W.E., Wetter, T. & Suhai, S. (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Research, 14, 1147‒1159.
https://doi.org/10.1101/gr.1917404

Darriba, D., Taboada, G.L., Doallo, R. & Posada, D. (2012) jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9, 772.
https://doi.org/10.1038/nmeth.2109

Dinesh, K., Vijayakumar, S., Channakeshavamurthy, B., Toreskar, V., Kulkarni, N.U. & Shanker, K. (2015) Systematic status of Fejervarya (Amphibia, Anura, Dicroglossidae) from South and SE Asia with the description of a new species from the Western Ghats of Peninsular India. Zootaxa, 3999 (1), 79‒94.
https://doi.org/10.11646/zootaxa.3999.1.5

Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 783‒791.
https://doi.org/10.2307/2408678

Feng, L., Zhang, X. & Zhao, G.-F. (2016) The complete mitochondrial genome of the scaleshell Leptodea leptodon (Bivalvia: Unionidae). Conservation Genetics Resources, 8, 443‒445.
https://doi.org/10.1007/s12686-016-0592-1

Garg, S. & Biju, S.D. (2017) Description of four new species of Burrowing Frogs in the Fejervarya rufescens complex (Dicroglossidae) with a notes on morphological affinities of Fejervarya species in Western Ghats. Zootaxa, 4277 (4), 451–490.
https://doi.org/10.11646/zootaxa.4277.4.1

Hall, T.A. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95‒98.

Howlader, M.S.A., Nair, A. & Meril, J. (2016) A new species of frog (Anura: Dicroglossidae) discovered from the mega city of Dhaka. PloS ONE, 11, e0149597.
https://doi.org/10.1371/journal.pone.0149597

Islam, M.M., Kurose, N., Khan, M.R., Nishizawa, T., Kuramoto, M., Alam, M.S., Hasan, M., Kurniawan, N., Nishioka, M. & Sumida, M. (2008) Genetic divergence and reproductive isolation in the genus Fejervarya (Amphibia: Anura) from Bangladesh inferred from morphological observations, crossing experiments, and molecular analyses. Zoological Science, 25, 1084‒1105.
https://doi.org/10.2108/zsj.25.1084

Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C. & Thierer, T. (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28, 1647‒1649.
https://doi.org/10.1093/bioinformatics/bts199

Kumar, K.S., Sivakumar, K.C., Reghunathan, D., Manoj, P. & George, S. (2017) The complete mitochondrial genome of Indirana semipalmata (Amphibia: Anura). Conservation Genetics Resources, 9, 83‒86.
https://doi.org/10.1007/s12686-016-0625-9

Kumar, S., Stecher, G. & Tamura, K. (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870‒1874.
https://doi.org/10.1093/molbev/msw054

Kurabayashi, A., Usuki, C., Mikami, N., Fujii, T., Yonekawa, H., Sumida, M. & Hasegawa, M. (2006) Complete nucleotide sequence of the mitochondrial genome of a Malagasy poison frog Mantella madagascariensis: evolutionary implications on mitochondrial genomes of higher anuran groups. Molecular Phylogenetics and Evolution, 39, 223‒236.
https://doi.org/10.1016/j.ympev.2005.11.021

Laslett, D. & Canbäck, B. (2008) ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics, 24, 172‒175.
https://doi.org/10.1093/bioinformatics/btm573

Liu, Z.-Q., Wang, Y.-Q. & Su, B. (2005) The mitochondrial genome organization of the rice frog, Fejervarya limnocharis (Amphibia: Anura): a new gene order in the vertebrate mtDNA. Gene, 346, 145‒151.
https://doi.org/10.1016/j.gene.2004.10.013

Lohse, M., Drechsel, O., Kahlau, S. & Bock, R. (2013) OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Research, 41(Web Server Issue), 575–581. [W575‒W581]
https://doi.org/10.1093/nar/gkt289

Lowe, T.M. & Eddy, S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research, 25, 955‒964.

Myers, C.W. & Duellman, W.E. (1982) A new species of Hyla from Cerro Colorado and other tree frog records and geographical notes from western Panama. American Museum Novitates, 2752, 1‒32.

Ren, Z., Zhu, B., Ma, E., Wen, J., Tu, T., Cao, Y., Hasegawa, M. & Zhong, Y. (2009) Complete nucleotide sequence and gene arrangement of the mitochondrial genome of the crab-eating frog Fejervarya cancrivora and evolutionary implications. Gene, 441, 148‒155.
https://doi.org/10.1016/j.gene.2008.09.010

Rusk, N. (2011) Torrents of sequence. Nature Methods, 8, 44‒45.
https://doi.org/10.1038/nmeth.f.330

San Mauro, D., García-París, M. & Zardoya, R. (2004) Phylogenetic relationships of discoglossid frogs (Amphibia: Anura: Discoglossidae) based on complete mitochondrial genomes and nuclear genes. Gene, 343, 357‒366.
https://doi.org/10.1016/j.gene.2004.10.001

Savage, J. & Heyer, W. (1997) Digital webbing formulae for anurans: a refinement. Herpetological Review, 28, 131.

Savage, J.M. & Heyer, W.R. (1967) Variation and distribution in the tree‐frog genus Phyllomedusa in Costa Rica, Central America: With 6 figures. Studies on Neotropical Fauna and Environment, 5, 111‒131.

Simossis, V.A. & Heringa, J. (2005) PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Research, 33, 289–294. [W289‒W294]
https://doi.org/10.1093/nar/gki390

Sumida, M., Kanamori, Y., Kaneda, H., Kato, Y., Nishioka, M., Hasegawa, M. & Yonekawa, H. (2001) Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of the Japanese pond frog Rana nigromaculata. Genes & Genetic Systems, 76, 311‒325.
https://doi.org/10.1266/ggs.76.311

Sumida, M., Kondo, Y., Kanamori, Y. & Nishioka, M. (2002) Inter-and intraspecific evolutionary relationships of the rice frog Rana limnocharis and the allied species R. cancrivora inferred from crossing experiments and mitochondrial DNA sequences of the 12S and 16S rRNA genes. Molecular Phylogenetics and Evolution, 25, 293‒305.
https://doi.org/10.1016/S1055-7903(02)00243-9

Thompson, J.D., Higgins, D.G. & Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 4673‒4680.
https://doi.org/10.1093/nar/22.22.4673

Zhang, P., Zhou, H., Chen, Y.-Q., Liu, Y.-F. & Qu, L.-H. (2005) Mitogenomic perspectives on the origin and phylogeny of living amphibians. Systematic Biology, 54, 391‒400.
https://doi.org/10.1080/10635150590945278




DOI: http://dx.doi.org/10.11646/zootaxa.4277.4.2

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