Comparative Mitogenome Analysis of Gerbils and the Mitogenome Phylogeny of Gerbillinae (Rodentia: Muridae).
Brachiones przewalskii
Gerbillinae
Meriones tamariscinus
Mitochondrial genome
Phylogenetic analysis
Rhombomys opimus
Journal
Biochemical genetics
ISSN: 1573-4927
Titre abrégé: Biochem Genet
Pays: United States
ID NLM: 0126611
Informations de publication
Date de publication:
Dec 2022
Dec 2022
Historique:
received:
12
06
2019
accepted:
24
02
2022
pubmed:
23
3
2022
medline:
2
11
2022
entrez:
22
3
2022
Statut:
ppublish
Résumé
To enrich the mitogenomic database of Gerbillinae (Rodentia: Muridae), mitogenomes of three gerbils from different genera, Meriones tamariscinus (16,393 bp), Brachiones przewalskii (16,357 bp), and Rhombomys opimus (16,352 bp), were elaborated and compared with those of other gerbils in the present study. The three gerbil mitogenomes consisted of 2 ribosomal RNA genes, 13 protein-coding genes (PCGs), 22 transfer RNA genes, and one control region. Here, gerbil mitogenomes have shown unique characteristics in terms of base composition, codon usage, non-coding region, and the replication origin of the light strand. There was no significant correlation between the nucleotide percentage of G + C and the phylogenetic status in gerbils, and between the GC content of PCGs and the leucine count. Phylogenetic relationships of the subfamily Gerbillinae were reconstructed by 7 gerbils that represented four genera based on concatenated mitochondrial DNA data using both Bayesian Inference and Maximum Likelihood. The phylogenetic analysis indicated that M. tamariscinus was phylogenetically distant from the genus Meriones, but has a close relationship with R. opimus. B. przewalskii was closely related to the genus Meriones rather than that of R. opimus.
Identifiants
pubmed: 35314913
doi: 10.1007/s10528-022-10213-8
pii: 10.1007/s10528-022-10213-8
doi:
Substances chimiques
RNA, Transfer
9014-25-9
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2226-2249Subventions
Organisme : National Natural Science Foundation of China
ID : 30870294
Organisme : National Natural Science Foundation of China
ID : 31372179
Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Akaike H (1974) A new look at the statistical model identification. IEEE Trans Autom Control 19:716–723
Alhajeri BH, Hunt OJ, Steppan SJ (2015) Molecular systematics of gerbils and deomyines (Rodentia: Gerbillinae, Deomyinae) and a test of desert adaptation in the tympanic bulla. J Zool Syst Evol Res 53:312–330
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
pubmed: 2231712
Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580
pubmed: 9862982
pmcid: 148217
Bibb MJ, Van Etten RA, Wright CT, Walberg MW, Clayton DA (1981) Sequence and gene organization of mouse mitochondrial DNA. Cell 26:167–180
pubmed: 7332926
Boore JL (1999) Animal mitochondrial genomes. Nucleic Acids Res 27:1767–1780
pubmed: 10101183
pmcid: 148383
Campbell V, Lapointe FJ (2011) Retrieving a mitogenomic mammal tree using composite taxa. Mol Phylogenet Evol 58:149–156
pubmed: 21134474
Charneski CA, Honti F, Bryant JM, Hurst LD, Feil EJ (2011) Atypical at skew in Firmicute genomes results from selection and not from mutation. PLoS Genet 7:e1002283
pubmed: 21935355
pmcid: 3174206
Chevret P, Dobigny G (2005) Systematics and evolution of the subfamily Gerbillinae (Mammalia, Rodentia, Muridae). Mol Phylogenet Evol 35:674–688
pubmed: 15878135
Clayton DA (1991) Replication and transcription of vertebrate mitochondrial DNA. Annu Rev Cell Biol 7:453–478
pubmed: 1809353
Ding L, Li WJ, Liao JC (2016a) Characterization of the complete mitochondrial genome of Phodopus roborovskii (Rodentia: Cricetidae) and systematic implications for Cricetinae phylogenetics. Biochem Syst Ecol 69:226–235
Ding L, Li WJ, Liao JC (2016b) Mitochondrial genome of Cricetulus migratorius (Rodentia: Cricetidae): Insights into the characteristics of the mitochondrial genome and the phylogenetic relationships of Cricetulus species. Gene 595:121–129
pubmed: 27717890
Doda JN, Wright CT, Clayton DA (1981) Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences. Proc Natl Acad Sci USA 78:6116–6120
pubmed: 6273850
pmcid: 348988
Fabre PH, Hautier L, Dimitrov D, Douzery EJ (2012) A glimpse on the pattern of rodent diversification: a phylogenetic approach. BMC Evol Biol 12:88
pubmed: 22697210
pmcid: 3532383
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376
pubmed: 7288891
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
pubmed: 28561359
Gibson A, Gowri-Shankar V, Higgs PG, Rattray M (2005) A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods. Mol Biol Evol 22:251–264
pubmed: 15483324
Gissi C, Iannelli F, Pesole G (2008) Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species. Heredity 101:301–320
pubmed: 18612321
Grant JR, Stothard P (2008) The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res 36:181–184
Grantham R, Gautier C, Gouy M (1980) Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res 8:1893–1912
pubmed: 6159596
pmcid: 324046
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98
Havird JC, Santos SR (2014) Performance of single and concatenated sets of mitochondrial genes at inferring metazoan relationships relative to full mitogenome data. PLoS ONE 9:e84080
pubmed: 24454717
pmcid: 3891902
Hillis DM, Bull JJ (1993) An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol 42:182–192
Hixson J, Wong T, Clayton DA (1986) Both the conserved stem-loop and divergent 5’-flanking sequences are required for initiation at the human mitochondrial origin of light-strand DNA replication. J Biol Chem 261:2384–2390
pubmed: 3944140
Hutchison CA, Newbold JE, Potter SS, Edgell MH (1974) Maternal inheritance of mammalian mitochondrial DNA. Nature 251:536–538
pubmed: 4423884
Ito M, Jiang W, Sato JJ, Zhen Q, Jiao W, Goto K, Sato H, Ishiwata K, Oku Y, Chai JJ (2010) Molecular phylogeny of the subfamily Gerbillinae (Muridae, Rodentia) with emphasis on species living in the Xinjiang-Uygur Autonomous Region of China and based on the mitochondrial cytochrome b and cytochrome c oxidase subunit II genes. Zool Sci 27:269–278
Jiang X, Gao J, Ni L, Hu J, Li K, Sun F, Xie J, Bo X, Gao C, Xiao J (2012) The complete mitochondrial genome of Microtus fortis calamorum (Arvicolinae, Rodentia) and its phylogenetic analysis. Gene 498:288–295
pubmed: 22387301
Kim JS, Kim MJ, Jeong JS, Kim I (2018) Complete mitochondrial genome of Saturnia jonasii (Lepidoptera: Saturniidae): Genomic comparisons and phylogenetic inference among Bombycoidea. Genomics 110:274–282
pubmed: 29191682
Lan Y, Liu M, Cao Y (2018) The complete mitochondrial genome of Psammomys obesus (Rodentia: Muridae). Mitochondrial DNA Part B 3:97–98
pubmed: 33474080
pmcid: 7800552
Lanfear R, Calcott B, Ho SY, Guindon S (2012) Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol 29:1695–1701
pubmed: 22319168
Lavrov DV, Brown WM, Boore JL (2000) A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus. Proc Natl Acad Sci USA 97:13738–13742
pubmed: 11095730
pmcid: 17645
Leaché AD, Reeder TW (2002) Molecular systematics of the eastern fence lizard (Sceloporus undulatus): a comparison of Parsimony, Likelihood, and Bayesian approaches. Syst Biol 51:44–68
pubmed: 11943092
Li CL, Du XY, Gao J, Wang C, Guo HG, Dai FW, Sa XY, An W, Chen ZW (2016) Phylogenetic analysis of the Mongolian gerbil (Meriones unguiculatus) from China based on mitochondrial genome. Genet Mol Res. https://doi.org/10.4238/gmr.15037703
doi: 10.4238/gmr.15037703
pubmed: 28081284
Li R, Shu X, Li X, Meng L, Li B (2018) Comparative mitogenome analysis of three species and monophyletic inference of Catantopinae (Orthoptera: Acridoidea). Genomics 111:1728–1735
pubmed: 30503746
Lobry JR (1996) Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 13:660–665
pubmed: 8676740
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964
pubmed: 9023104
pmcid: 146525
Luo GJ, Liao JC (2016a) The complete mitochondrial genome of Meriones libycus (Rodentia: Cricetidae) and its phylogenetic analysis. Mitochondrial DNA Part A 27:2545–2546
Luo GJ, Liao JC (2016b) The complete mitochondrial genome of Meriones meridianus (Rodentia: Cricetidae) and its phylogenetic analysis. Mitochondrial DNA Part A 27:2547–2548
Luo ZX, Chen W, Gao W (2000) Fauna Sinica: Mammalia vol. 6, Rodentia Part III: Cricetidae. Science Press, Beijing (Chinese)
Malyarchuk B, Derenko M, Denisova G (2014) A mitogenomic phylogeny and genetic history of sable (Martes zibellina). Gene 550:56–67
pubmed: 25110108
Marková S, Filipi K, Searle JB, Kotlík P (2015) Mapping 3′ transcript ends in the bank vole (Clethrionomys glareolus) mitochondrial genome with RNA-Seq. BMC Genomics 16:1–9
Nowak RM (1999) Walker’s Mammals of the world. John Hopkins University Press, Baltimore
Ojala D, Montoya J, Attardi G (1981) tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–474
pubmed: 7219536
Pavlinov IY (1986) Taxonomic significance of the male genital morphology in the subfamily Gerbillinae (Mammalia: Rodentia). Bull Mosc Soc Natur 91:8–16 (English abstract)
Pavlinov IY (2008) A review of phylogeny and classification of Gerbillinae (Mammalia: Rodentia). Moscow University Publishing, Moscow
Pereira SL (2000) Mitochondrial genome organization and vertebrate phylogenetics. Genet Mol Res 23:745–752
Perna NT, Kocher TD (1995) Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol 41:353–358
pubmed: 7563121
Piganeau G, Gardner M, Eyre-Walker A (2004) A broad survey of recombination in animal mitochondria. Mol Biol Evol 21:2319–2325
pubmed: 15342796
Povolotskaya IS, Kondrashov FA, Ledda A, Vlasov PK (2012) Stop codons in bacteria are not selectively equivalent. Biol Direct 7:30
pubmed: 22974057
pmcid: 3549826
Ren L, Shang Y, Yang L, Shen X, Chen W, Wang Y, Cai J, Guo Y (2019) Comparative analysis of mitochondrial genomes among four species of muscid flies (Diptera: Muscidae) and its phylogenetic implications. Int J Biol Macromol 127:357–364
pubmed: 30658142
Renaud S, Chevret P, Michaux J (2007) Morphological vs. molecular evolution: ecology and phylogeny both shape the mandible of rodents. Zool Scr 36:525–535
Revell LJ (2012) phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol Evol 3:217–223
Reyes A, Gissi C, Pesole G, Saccone C (1998) Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Mol Biol Evol 15:957–966
pubmed: 9718723
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542
pubmed: 22357727
pmcid: 3329765
Sahyoun AH, Bernt M, Stadler PF, Tout K (2014) GC skew and mitochondrial origins of replication. Mitochondrion 17:56
pubmed: 24911382
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
pubmed: 3447015
Sarvani RK, Parmar DR, Tabasum W, Thota N, Sreenivas A, Gaur A (2018) Characterization of the complete mitogenome of Indian Mouse Deer, Moschiola indica (Artiodactyla: Tragulidae) and its evolutionary significance. Sci Rep 8:2697
pubmed: 29426945
pmcid: 5807545
Sbisà E, Nardelli M, Tanzariello F, Tullo A, Saccone C (1990) The complete and symmetric transcription of the main non coding region of rat mitochondrial genome: in vivo mapping of heavy and light transcripts. Curr Genet 17:247–253
pubmed: 1692771
Sbisà E, Tanzariello F, Reyes A, Pesole G, Saccone C (1997) Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene 205:125–140
pubmed: 9461386
Stamatakis A (2014) RAxML Version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313
pubmed: 24451623
pmcid: 3998144
Steinberg S, Cedergren R (1994) Structural compensation in atypical mitochondrial tRNAs. Nat Struct Biol 1:507–510
pubmed: 7664076
Steppan SJ, Schenk JJ (2017) Muroid rodent phylogenetics: 900-species tree reveals increasing diversification rates. PLoS ONE 12:e0183070
pubmed: 28813483
pmcid: 5559066
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30:2725–2729
pubmed: 24132122
pmcid: 3840312
Team RC (2013) R: A language and environment for statistical computing. R foundation for statistical computing, Vienna. Computing 14:12–21
Thompson JD (1991) Phenotypic plasticity as a component of evolutionary change. Trends Ecol Evol 6:246–249
pubmed: 21232470
Triant DA, DeWoody JA (2006) Accelerated molecular evolution in Microtus (Rodentia) as assessed via complete mitochondrial genome sequences. Genetica 128:95–108
pubmed: 17028943
Uddin A, Choudhury MN, Chakraborty S (2017) Factors influencing codon usage of mitochondrial ND1 gene in Pisces, aves and mammals. Mitochondrion 37:17–26
pubmed: 28668667
Vaidya G, Lohman DJ, Meier R (2011) SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics 27:171–180
pubmed: 34875773
Wang J, Zhu S, Xu C (2008) Essential biochemistry. Higher Education Press, Beijing ((Chinese))
Weisrock DW (2012) Concordance analysis in mitogenomic phylogenetics. Mol Phylogenet Evol 65:194–202
pubmed: 22705824
Wilson DE, Reeder DM (2005) Mammal species of the world: a taxonomic and geographic reference, 3rd edn. Johns Hopkins University Press, Baltimore
Wolstenholme DR (1992) Animal mitochondrial DNA: structure and evolution. Int Rev Cytol 141:173–216
pubmed: 1452431
Yakovchuk P, Protozanova E, Frankkamenetskii MD (2006) Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res 34:564–574
pubmed: 16449200
pmcid: 1360284
Yang Z, Rannala B (1997) Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo method. Mol Biol Evol 14:717–724
pubmed: 9214744
Yom-Tov Y, Yom-Tov S, Moller H (1999) Competition, coexistence, and adaptation amongst rodent invaders to Pacific and New Zealand islands. J Biogeogr 26:947–958
Yu L, Wang X, Ting N, Zhang Y (2011) Mitogenomic analysis of Chinese snub-nosed monkeys: evidence of positive selection in NADH dehydrogenase genes in high-altitude adaptation. Mitochondrion 11:497–503
pubmed: 21292038
Yu P, Zhou L, Zhou XY, Yang WT, Zhang J, Zhang XJ, Wang Y, Gui JF (2019) Unusual AT-skew of Sinorhodeus microlepis mitogenome provides new insights into mitogenome features and phylogenetic implications of bitterling fishes. Int J Biol Macromol 129:339–350
pubmed: 30738158
Zardoya R, Garrido-Pertierra A, Bautista JM (1995) The complete nucleotide sequence of the mitochondrial DNA genome of the rainbow trout, Oncorhynchus mykiss. J Mol Evol 41:942–951
pubmed: 8587139
Zhang P, Chen YQ, Zhou H, Wang XL, Qu LH (2003) The complete mitochondrial genome of a relic salamander, Ranodon sibiricus (Amphibia: Caudata) and implications for amphibian phylogeny. Mol Phylogenet Evol 28:620–626
pubmed: 12927145
Zhang P, Liang D, Mao RL, Hillis DM, Cannatella DC, Wake DB (2013) Efficient sequencing of Anuran mtDNAs and a mitogenomic exploration of the phylogeny and evolution of frogs. Mol Biol Evol 30:1899–1915
pubmed: 23666244
Zhong HM, Zhang HH, Sha WL, Zhang CD, Chen YC (2010) Complete mitochondrial genome of the red fox (Vuples vuples) and phylogenetic analysis with other canid species. Zool Res 31:122–130
Zhou LZ, Ma Y, Li DQ (2001) Spatial distribution patterns of Chinese gerbils (gerbilline) in relation to environmental factors. Acta Zool Sin 47:616–624 ((English abstract))
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415
pubmed: 12824337
pmcid: 169194