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Demirtaş S, Budak M, Korkmaz EM, Searle JB, Bilton DT, Gündüz İ. The complete mitochondrial genome of Talpa martinorum (Mammalia: Talpidae), a mole species endemic to Thrace: genome content and phylogenetic considerations. Genetica 2022; 150:317-325. [PMID: 36029420 DOI: 10.1007/s10709-022-00162-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 08/04/2022] [Indexed: 11/04/2022]
Abstract
The complete mitogenome sequence of Talpa martinorum, a recently described Balkan endemic mole, was assembled from next generation sequence data. The mitogenome is similar to that of the three other Talpa species sequenced to date, being 16,835 bp in length, and containing 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, an origin of L-strand replication, and a control region or D-loop. Compared to other Talpa mitogenomes sequenced to date, that of T. martinorum differs in the length of D-loop and stop codon usage. TAG and T-- are the stop codons for the ND1 and ATP8 genes, respectively, in T. martinorum, whilst TAA acts as a stop codon for both ND1 and ATP8 in the other three Talpa species sequenced. Phylogeny reconstructions based on Maximum Likelihood and Bayesian inference analyses yielded phylogenies with similar topologies, demonstrating that T. martinorum nests within the western lineage of the genus, being closely related to T. aquitania and T. occidentalis.
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Affiliation(s)
- Sadık Demirtaş
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
| | - Mahir Budak
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Ertan M Korkmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853-2701, USA
| | - David T Bilton
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, Devon, PL4 8AA, UK.,Department of Zoology, University of Johannesburg, Auckland Park, PO Box 524, Johannesburg, 2006, South Africa
| | - İslam Gündüz
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey.
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Arbizu CI, Ferro-mauricio RD, Chávez-galarza JC, Vásquez HV, Maicelo JL, Poemape C, Gonzales J, Quilcate C, Corredor F. The Complete Mitochondrial Genome of a Neglected Breed, the Peruvian Creole Cattle (Bos taurus), and Its Phylogenetic Analysis. Data 2022; 7:76. [DOI: 10.3390/data7060076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
Abstract
Cattle spread throughout the American continent during the colonization years, originating creole breeds that adapted to a wide range of climate conditions. The population of creole cattle in Peru is decreasing mainly due to the introduction of more productive breeds in recent years. During the last 15 years, there has been significant progress in cattle genomics. However, little is known about the genetics of the Peruvian creole cattle (PCC) despite its importance to (i) improving productivity in the Andean region, (ii) agricultural labor, and (iii) cultural traditions. In addition, the origin and phylogenetic relationship of the PCC are still unclear. In order to promote the conservation of the PCC, we sequenced the mitochondrial genome of a creole bull, which also possessed exceptional fighting skills and was employed for agricultural tasks, from the highlands of Arequipa for the first time. The total mitochondrial genome sequence is 16,339 bp in length with the base composition of 31.43% A, 28.64% T, 26.81% C, and 13.12% G. It contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Among the 37 genes, 28 were positioned on the H-strand and 9 were positioned on the L-strand. The most frequently used codons were CUA (leucine), AUA (isoleucine), AUU (isoleucine), AUC (isoleucine), and ACA (threonine). Maximum likelihood reconstruction using complete mitochondrial genome sequences showed that the PCC is related to native African breeds. The annotated mitochondrial genome of PCC will serve as an important genetic data set for further breeding work and conservation strategies.
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Lamelas L, Aleix-Mata G, Rovatsos M, Marchal JA, Palomeque T, Lorite P, Sánchez A. Complete Mitochondrial Genome of Three Species of the Genus Microtus (Arvicolinae, Rodentia). Animals (Basel) 2020; 10:E2130. [PMID: 33207831 PMCID: PMC7696944 DOI: 10.3390/ani10112130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/09/2020] [Accepted: 11/14/2020] [Indexed: 11/17/2022] Open
Abstract
The 65 species of the genus Microtus have unusual sex-related genetic features and a high rate of karyotype variation. However, only nine complete mitogenomes for these species are currently available. We describe the complete mitogenome sequences of three Microtus, which vary in length from 16,295 bp to 16,331 bp, contain 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes and a control region. The length of the 13 PCGs and the coded proteins is the same in all three species, and the start and stop codons are conserved. The non-coding regions include the L-strand origin of replication, with the same sequence of 35 bp, and the control region, which varies between 896 bp and 930 bp in length. The control region includes three domains (Domains I, II and III) with extended termination-associated sequences (ETAS-1 and ETAS-2) in Domain I. Domain II and Domain III include five (CSB-B, C, D, E and F) and three (CSB-1, CSB-2, and CSB-3) conserved sequence blocks, respectively. Phylogenetic reconstructions using the mitochondrial genomes of all the available Microtus species and one representative species from another genus of the Arvicolinae subfamily reproduced the established phylogenetic relationships for all the Arvicolinae genera that were analyzed.
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Affiliation(s)
- Luz Lamelas
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain; (L.L.); (G.A.-M.); (J.A.M.); (T.P.); (P.L.)
| | - Gaël Aleix-Mata
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain; (L.L.); (G.A.-M.); (J.A.M.); (T.P.); (P.L.)
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic;
| | - Juan Alberto Marchal
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain; (L.L.); (G.A.-M.); (J.A.M.); (T.P.); (P.L.)
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain; (L.L.); (G.A.-M.); (J.A.M.); (T.P.); (P.L.)
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain; (L.L.); (G.A.-M.); (J.A.M.); (T.P.); (P.L.)
| | - Antonio Sánchez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain; (L.L.); (G.A.-M.); (J.A.M.); (T.P.); (P.L.)
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Gutiérrez J, Lamelas L, Aleix-Mata G, Arroyo M, Marchal JA, Palomeque T, Lorite P, Sánchez A. Complete mitochondrial genome of the Iberian Mole Talpa occidentalis (Talpidae, Insectivora) and comparison with Talpa europaea. Genetica 2018; 146:415-423. [PMID: 30145730 DOI: 10.1007/s10709-018-0033-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 08/01/2018] [Indexed: 12/23/2022]
Abstract
The complete mitogenome of Talpa occidentalis, the Iberian mole, was sequenced using a combination of the Illumina and Sanger methods. The 16,962 bp genome obtained contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region. Thirty-seven identical repetitions of a 10-nucleotide (CACACGTACG) repeat element were identified in the non-coding control region (D-loop). The number, order, and orientation of the mitochondrial genes are the same as in T. europaea, the only mitogenome published so far for this genus. These two mitogenomes differ only at the repeat element included in the control region. The phylogeny obtained for the Talpidae species using the protein-coding genes of these mitogenomes agrees with the current classification of this family.
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Affiliation(s)
- Juana Gutiérrez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Luz Lamelas
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Gaël Aleix-Mata
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - María Arroyo
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Juan Alberto Marchal
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Antonio Sánchez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain.
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