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Xuan R, Gao J, Lin Q, Yue W, Liu T, Hu S, Song G. Mitochondrial DNA Diversity of Mesocricetus auratus and Other Cricetinae Species among Cricetidae Family. Biochem Genet 2022; 60:1881-1894. [PMID: 35122557 PMCID: PMC8817650 DOI: 10.1007/s10528-022-10195-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 01/25/2022] [Indexed: 11/29/2022]
Abstract
Unique anatomical and physiological features have made hamster species desirable research models. Comparative genomics and phylogenetic analysis of the hamster family members to clarify their evolution and genetic relationship, can provide a genetic basis for the comprehension of the variable research results obtained using different hamster models. The Syrian golden hamster (Mesocricetus auratus) is the most widely used species. In this study, we sequenced the complete mitochondrial genome (mitogenome) of M. auratus, compared it with the mitogenome of other Cricetinae subfamily species, and defined its phylogenetic position in the Cricetidae family. Our results show that the mitogenome organization, gene arrangement, base composition, and genetic analysis of the protein coding genes (PCGs) of M. auratus are similar to those observed in previous reports on Cricetinae species. Nonetheless, our analysis clarifies some striking differences of M. auratus relative to other subfamily members, namely distinct codon usage frequency of TAT (Tyr), AAT (Asn), and GAA (Glu) and the presence of the conserved sequence block 3 (CSB-3) in the control region of M. auratus mitogenome and other hamsters (not found in Arvicolinae). These results suggest the particularity of amino acid codon usage bias of M. auratus and special regulatory signals for the heavy strand replication in Cricetinae. Additionally, Bayesian inference/maximum likelihood (BI/ML) tree shows that Cricetinae and Arvicolinae are sister taxa sharing a common ancestor, and Neotominae split prior to the split between Cricetinae and Arvicolinae. Our results support taxonomy revisions in Cricetulus kamensis and Cricetulus migratorius, and further revision is needed within the other two subfamilies. Among the hamster research models, Cricetulus griseus is the species with highest sequence similarity and closer genetic relationship with M. auratus. Our results show mitochondrial DNA diversity of M. auratus and other Cricetinae species and provide genetic basis for judgement of different hamster models, promoting the development and usage of hamsters with regional characteristics.
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Affiliation(s)
- Ruijing Xuan
- Laboratory Animal Center, Shanxi Medical University, Taiyuan, 030001, China
| | - Jiping Gao
- Laboratory Animal Center, Shanxi Medical University, Taiyuan, 030001, China
| | - Qiang Lin
- Key Laboratory of Genome Information and Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Wenbin Yue
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu, 030801, China
| | - Tianfu Liu
- Laboratory Animal Center, Shanxi Medical University, Taiyuan, 030001, China
| | - Songnian Hu
- Key Laboratory of Genome Information and Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Guohua Song
- Laboratory Animal Center, Shanxi Medical University, Taiyuan, 030001, China.
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İbiş O, Koepfli KP, Özcan S, Tez C. Whole mitogenomes of Turkish white-toothed shrews, genus Crocidura (Eulipotyphla: Soricidae), with new insights into the phylogenetic positions of Crocidura leucodon and the Crocidura suaveolens group. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00579-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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İbiş O, Yesari Selçuk A, Teber S, Baran M, Kaya A, Özcan S, Kefelioğlu H, Tez C. Complete mitogenomes of Turkish tree squirrels, Sciurus anomalus and S. vulgaris, (Sciuridae: Rodentia: Mammalia) and their phylogenetic status within the tribe Sciurini. Gene 2022; 841:146773. [PMID: 35905846 DOI: 10.1016/j.gene.2022.146773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/03/2022] [Accepted: 07/24/2022] [Indexed: 11/04/2022]
Abstract
The genus Sciurus, a member of the family Sciuridae, is widely distributed in the Holarctic region. To better understand mitogenomic characteristics and to reveal internal phylogenetic relationships of the genus, 20 complete mitogenomes of Turkish tree squirrels were successfully sequenced for the first time, including 19 for S. anomalus (from 16,505 bp to 16,510 bp) and one for S. vulgaris (16,511 bp). The mitogenomes of two species were AT-biased. All tRNAs for two species displayed a typical clover-leaf structure, except for tRNASer(AGY). The tRNA Serine1 (S1)-GCT structure lacked the dihydrouridine (DHU) loop and stem. Based on mitogenomic dataset for phylogeny of Sciurinae, phylogenetic analyses (Bayesian Inference and Maximum Likelihood) did not support monophyly of Sciurus and proposed that S. anomalus, the most basal taxa in the Sciurini tribe, had at least five mitogenome lineages, which were also supported by network analysis. The dissimilarities among the five linegaes of S. anomalus ranged from 0.0042 (0.42%) to 0.0062 (0.62%) using K2P sequence pairwise distances. In addition to this mitogenomic analysis result, phylogenetic analyses using the CYTB + D-loop dataset proposed the existence of at least nine lineages for S. anomalus, which was different than those of the previous studies. The current study proposed that the use of mitogenomic data for reconstructing the phylogeny of Turkey' Sciurus holds an important value for revealing evolutionary relationships.
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Affiliation(s)
- Osman İbiş
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey; Vectors and Vector-Born Diseases Research and Implementation Center, Erciyes University, Kayseri, Turkey.
| | - Ahmet Yesari Selçuk
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey; Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey.
| | - Saffet Teber
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey.
| | - Mehmet Baran
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey.
| | - Alaettin Kaya
- Department of Basic Sciences, Faculty of Veterinary Medicine, Dicle University, Diyarbakır, Turkey.
| | - Servet Özcan
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey; Department of Biology, Faculty of Sciences, Erciyes University, Kayseri, Turkey.
| | - Haluk Kefelioğlu
- Department of Biology, Faculty of Science and Letters, Ondokuz Mayıs University, Samsun, Turkey.
| | - Coşkun Tez
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey; Department of Biology, Faculty of Sciences, Erciyes University, Kayseri, Turkey.
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Ding L, Luo G, Zhou Q, Sun Y, Liao J. Comparative Mitogenome Analysis of Gerbils and the Mitogenome Phylogeny of Gerbillinae (Rodentia: Muridae). Biochem Genet 2022; 60:2226-2249. [PMID: 35314913 DOI: 10.1007/s10528-022-10213-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 02/24/2022] [Indexed: 11/02/2022]
Abstract
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.
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Affiliation(s)
- Li Ding
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China.,School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Guangjie Luo
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Quan Zhou
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yuanhai Sun
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jicheng Liao
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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Alhajeri BH. A morphometric comparison of the cranial shapes of Asian dwarf hamsters (Phodopus, Cricetinae, Rodentia). ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2021.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Ding L, Zhou Q, Sun Y, Feoktistova NY, Liao J. Two novel cricetine mitogenomes: Insight into the mitogenomic characteristics and phylogeny in Cricetinae (Rodentia: Cricetidae). Genomics 2019; 112:1716-1725. [PMID: 31669701 DOI: 10.1016/j.ygeno.2019.09.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/06/2019] [Accepted: 09/18/2019] [Indexed: 01/30/2023]
Abstract
Both Cricetus cricetus and Phodopus sungorus mitochondrial genomes (mitogenomes) were sequenced and elaborated for the first time in the present study. Their mitogenomes contained 37 genes and showed typical characteristics of the vertebrate mitogenome. Comparative analysis of 10 cricetine mitogenomes indicated that they shared similar characteristics with those of other cricetines in terms of genes arrangement, nucleotide composition, codon usage, tRNA structure, nucleotide skew and the origin of replication of light strand. Phylogenetic relationship of the subfamily Cricetinae was reconstructed using mitogenomes data with the methods of Bayesian Inference and Maximum Likelihood. Phylogenetic analysis indicated that Cricetulus kamensis was at basal position and phylogenetically distant from all other Cricetulus species but had a close relationship with the group of Phodopus, and supported that the genus Urocricetus deserved as a separate genus rank. The phylogenetic status of Tscherskia triton represented a separate clade corresponding to a diversified cricetine lineage (Cricetulus, Allocricetulus, and Cricetus).
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Affiliation(s)
- Li Ding
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China.
| | - Quan Zhou
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
| | - Yuanhai Sun
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
| | - Natalia Yu Feoktistova
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia
| | - Jicheng Liao
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China.
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