Sequence and phylogenetic analysis of the complete mitochondrial genome of Lasiopodomys mandarinus mandarinus (Arvicolinae, Rodentia)

Li, Yangwei; Shi, Yuhua; Lu, Jiqi; Ji, Weihong; Wang, Zhenlong

doi:10.1016/j.gene.2016.08.035

Cited by 11 publications

(10 citation statements)

References 36 publications

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“…All tRNAs varied in size from 62 bp (trnC) to 74 bp (trnL1 (UUR) and trnK) in C. kumu and ranged from 65 bp (trnC) to 74 bp (trnL1 (UUR) and trnK) in L. microptera . This tRNA genomic architecture is identical to all Scorpaeniformes species examined to date 39, 40 . All of the 22 tRNA genes could be folded into typical cloverleaf secondary structures with the exception of trnS2 (AUN).…”

Section: Resultsmentioning

confidence: 61%

“…All of the 22 tRNA genes could be folded into typical cloverleaf secondary structures with the exception of trnS2 (AUN). The secondary structure of trnS2 (AUN) lacks a DHU stem, and this phenomenon has been observed in many animals of metazoan mitogenomes including Scorpaeniformes species 39, 40 . A 7 bp amino acid acceptor stem is conserved in all tRNAs, except for trnaV and trnaL1 (UUR) in L. microptera , which has a 9 bp amino acid acceptor stem.…”

Section: Resultsmentioning

confidence: 94%

“…They are separated by the trnV. The location was the case in most vertebrates 34, 35, 39, 40 .

Figure 4Predicted secondary structures for the tRNA genes in the C. kumu and L. microptera mitogenome. …”

Section: Resultsmentioning

confidence: 98%

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The first two complete mitochondrial genomes for the family Triglidae and implications for the higher phylogeny of Scorpaeniformes

Cui

Dong

et al. 2017

Sci Rep

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The mitochondrial genome (mitogenome) can provide useful information for analyzing phylogeny and molecular evolution. Scorpaeniformes is one of the most diverse teleostean orders and has great commercial importance. To develop mitogenome data for this important group, we determined the complete mitogenomes of two gurnards Chelidonichthys kumu and Lepidotrigla microptera of Triglidae within Scorpaeniformes for the first time. The mitogenomes are 16,495 bp long in C. kumu and 16,610 bp long in L. microptera. Both the mitogenomes contain 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and two non-coding regions. All PCGs are initiated by ATG codons, except for the cytochrome coxidase subunit 1 (cox1) gene. All of the tRNA genes could be folded into typical cloverleaf secondary structures, with the exception of tRNASer(AGN) lacks a dihydrouracil (DHU) stem. The control regions are both 838 bp and contain several features common to Scorpaeniformes. The phylogenetic relationships of 33 fish mitogenomes using Bayesian Inference (BI) and Maximum Likelihood (ML) based on nucleotide and amino acid sequences of 13 PCGs indicated that the mitogenome sequences could be useful in resolving higher-level relationship of Scorpaeniformes. The results may provide more insight into the mitogenome evolution of teleostean species.

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Section: Resultsmentioning

confidence: 61%

Section: Resultsmentioning

confidence: 94%

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The first two complete mitochondrial genomes for the family Triglidae and implications for the higher phylogeny of Scorpaeniformes

Cui

Dong

et al. 2017

Sci Rep

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“…The length of the 12S rRNA and 16S rRNA were 944 bp and 1,687 bp and A+T contents were 53.28% and 56.97%, respectively. The location of the 12 rRNAs was between trnF and trnV, and the location of the 16 rRNAs was between trnV and trnL1 (UUR), which were similar for most vertebrates [ 31 , 34 , 35 ].…”

Section: Resultsmentioning

confidence: 99%

Mitochondrial genome of the garfish Hyporhamphus quoyi (Beloniformes: Hemiramphidae) and phylogenetic relationships within Beloniformes based on whole mitogenomes

et al. 2018

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Mitochondrial DNA (mtDNA) can provide genome-level information (e.g. mitochondrial genome structure, phylogenetic relationships and codon usage) for analyzing molecular phylogeny and evolution of teleostean species. The species in the order Beloniformes have commercial importance in recreational fisheries. In order to further clarify the phylogenetic relationship of these important species, we determined the complete mitochondrial genome (mitogenome) of garfish Hyporhamphus quoyi of Hemiramphidae within Beloniformes. The mitogenome was 16,524 bp long and was typical of other teleosts mitogenomes in size and content. Thirteen PCGs started with the typical ATG codon (with exception of the cytochrome coxidase subunit 1 (cox1) gene with GTG). All tRNA sequences could be folded into expected cloverleaf secondary structures except for tRNASer (AGN) which lost a dihydrouracil (DHU) stem. The control region was 866 bp in length, which contained some conserved sequence blocks (CSBs) common to Beloniformes. The phylogenetic relationship between 26 fish Beloniformes species was analyzed based on the complete nucleotide and amino acid sequences of 13 PCGs by two different inference methods (Maximum Likelihood and Bayesian Inference). Phylogenetic analyses revealed Hemiramphidae as the sister group to Exocoetidae and it is a paraphyletic grouping. Our results may provide useful information on mitogenome evolution of teleostean species.

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“…It spends most of its life above the ground. Because L. mandarinus and L. brandtii have a close evolutionary relationship and distinct life histories [23], they are ideal animal models for comparative studies on the mechanisms underlying adaptation to hypoxia in subterranean mammals [24].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis of the response provided by Lasiopodomys mandarinus to severe hypoxia includes enhancing DNA repair and damage prevention

et al. 2020

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Background: Severe hypoxia induces a series of stress responses in mammals; however, subterranean rodents have evolved several adaptation mechanisms of energy metabolisms and O 2 utilization for hypoxia. Mammalian brains show extreme aerobic metabolism. Following hypoxia exposure, mammals usually experience irreversible brain damage and can even develop serious diseases, such as hypoxic ischemic encephalopathy and brain edema. To investigate mechanisms underlying the responses of subterranean rodents to severe hypoxia, we performed a cross-species brain transcriptomic analysis using RNA sequencing and identified differentially expressed genes (DEGs) between the subterranean rodent Lasiopodomys mandarinus and its closely related aboveground species L. brandtii under severe hypoxia (5.0% O 2 , 6 h) and normoxia (20.9% O 2 , 6 h). Results: We obtained 361 million clean reads, including 69,611 unigenes in L. mandarinus and 69,360 in L. brandtii. We identified 359 and 515 DEGs by comparing the hypoxic and normoxia groups of L. mandarinus and L. brandtii, respectively. Gene Ontology (GO) analysis showed that upregulated DEGs in both species displayed similar terms in response to severe hypoxia; the main difference is that GO terms of L. brandtii were enriched in the immune system. However, in the downregulated DEGs, GO terms of L. mandarinus were enriched in cell proliferation and protein transport and those of L. brandtii were enriched in nuclease and hydrolase activities, particularly in terms of developmental functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that upregulated DEGs in L. mandarinus were associated with DNA repair and damage prevention as well as angiogenesis and metastasis inhibition, whereas downregulated DEGs were associated with neuronal synaptic transmission and tumor-associated metabolic pathways. In L. brandtii, upregulated KEGG pathways were enriched in the immune, endocrine, and cardiovascular systems and particularly in cancer-related pathways, whereas downregulated DEGs were associated with environmental information processing and misregulation in cancers.

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Sequence and phylogenetic analysis of the complete mitochondrial genome of Lasiopodomys mandarinus mandarinus (Arvicolinae, Rodentia)

Cited by 11 publications

References 36 publications

The first two complete mitochondrial genomes for the family Triglidae and implications for the higher phylogeny of Scorpaeniformes

The first two complete mitochondrial genomes for the family Triglidae and implications for the higher phylogeny of Scorpaeniformes

Mitochondrial genome of the garfish Hyporhamphus quoyi (Beloniformes: Hemiramphidae) and phylogenetic relationships within Beloniformes based on whole mitogenomes

Transcriptome analysis of the response provided by Lasiopodomys mandarinus to severe hypoxia includes enhancing DNA repair and damage prevention

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