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. 2024 Nov 23;9(11):1611–1614. doi: 10.1080/23802359.2024.2432349

The complete mitochondrial genome of Sicista caudata Thomas, 1907 (Rodentia: Sicistidae) and its phylogenetic analyses

Zhu Liu 1,✉, Fu-Ying Zhang 1, Zhi-Hui Zhang 1, Qiu-Ying Guo 1
PMCID: PMC11587713  PMID: 39588494

Abstract

This study aimed to examine the complete mitogenome sequence of Sicista caudata Thomas, 1907. A circular double-stranded structure made up the mitochondrial genome of S. caudata. The complete length of the mitochondrial genome was 16,629 bp. The mitochondrial genome of S. caudata included 13 protein-coding genes, one control region, 22 tRNA genes, two rRNA genes, and one origin of L-strand replication. S. caudata was supported by bootstrap values of 100%. This study verified the evolutionary status of S. caudata in the Superfamily Dipodoidea at the molecular level.

Keywords: Sicista caudata, mitogenome, phylogenetic trees

Introduction

Sicista caudata Thomas, 1907 belongs to the order Rodentia, Superfamily Dipodoidea, family Sicistidae, subfamily Sicistinae, genus Sicista (Wilson and Reeder 2005). External morphological characteristics: Small body size (60–71 mm), with an extremely long tail (the ratio of tail length to body length is 152–178%). The dorsal fur is tan-yellow, with the mid-dorsal fur being darker and without longitudinal stripes. The ventral side is grayish-yellow, with the base of the fur being gray (Gao et al. 2024). It has a propensity for social living, uses tree cavities as a concealed habitat, is skilled at climbing, and is primarily nocturnal (Piao 2019). The population density of Sicistidae in the wild is low. Specimens of Sicistidae are difficult to obtain. This is especially true of S. caudata. Since S. caudata was discovered on the Russian island of Sakhalin in 1907, no more than 10 specimens have been reported so far. International Union for Conservation of Nature (IUCN) lists it as ‘data deficient’. Due to the rarity of Sicistidae animals, no mitochondrial genome of S. caudata has been reported. In this study, the complete mitochondrial genome of S. caudata was sequenced, and the phylogenetic relationships within the Superfamily Dipodoidea were analyzed. The mitochondrial genome of S. caudata is the first reported in Sicistidae.

Materials and methods

A male S. caudata sample was collected from Hengdaohezi City (44°48′44″N, 129°02′04″E), Heilongjiang Province, China, in August 2023 (Figure 1). The Cyt b gene sequence of the specimen was blasted against the GenBank database. The sequence OR672123 was the most similar to the specimen from S. caudata (MK259965), and the percent identity was 96.32%. The sample was stored at −75 °C before use and deposited at the Animal and Plant Herbarium of Mudanjiang Normal University (Liu Zhu, swxlz0@126.com) under the voucher number CWJS202304. Material in the CWJS202304 collection includes: skull, flayed specimen, muscle tissue, and internal organs (heart, liver, spleen, lungs, and kidneys). Genomic DNA was extracted from leg muscle using the EasyPure genomic DNA kit (TransGen Biotech Co., Beijing, China). We designed 15 pairs of primers for polymerase chain reaction (PCR) based on the reported mitochondrial genome of Dipodoidea (Figure S1, Table S1). PCR reaction conditions: initial denaturation at 94 °C for 4 min, denaturation at 94 °C for 45 s, annealing at 52–56 °C for 1 min, extension at 72 °C for 90 s, and final extension at 72 °C for 7 min, with 35 cycles. The first-generation sequencing technology was used for sequencing in this study (ABI 3730 sequencer; Boshi Biotechnology Co. Ltd., Harbin, China). The sequences were assembled using DNAstar, analyzed, and adjusted manually. The annotation of the S. caudata mitochondrial genome was performed using web-based services MITOS (Bernt et al. 2013) and software PhyloSuite v 1.2.2 (Zhang et al. 2020). The circular mitochondrial genome map of S. caudata was drawn using SnapGene 6.0.2 (Tello et al. 2022). In this study, the molecular phylogeny of S. caudata was investigated using the complete mitochondrial genomes of 11 species from nine genera (Sicista, Allactaga, Dipus, Euchoreutes, Jaculus, Scarturus, Stylodipus, Eozapus, and Orientallactaga) in Superfamily Dipodoidea deposited in the GenBank. The phylogenetic tree was constructed using 13 protein-coding genes of the complete mitochondrial genome through MEGA 11.0 software (Tamura et al. 2021). The phylogenetic tree was constructed using the General Time Reversible model of maximum-likelihood method with 1000 bootstrap replications.

Figure 1.

Figure 1.

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Pictures of external and skull morphologies. Pictures courtesy of Zhu Liu.

Results

A circular double-stranded structure made up the mitochondrial genome of S. caudata (Figure 2). The length of the complete mitochondrial genome was 16,629 bp. The mitochondrial genome of S. caudata included 13 protein-coding genes, one control region, 22 tRNA genes, two rRNA genes, and one origin of L-strand replication. The total base composition of S. caudata mitochondrial genome was A (29.7%), T (28.1%), G (14.0%), and C (28.2%). We found significant A–T skew in base composition, especially in control regions and protein-coding genes. The ND6 gene and eight tRNA genes of S. caudata were encoded on the L strand. The other mitochondrial genes were encoded on the H strand. GenBank received the annotated mitochondrial genome sequences with accession number PP524730. The control region of the mitochondrial genome existed between the tRNA-Pro and tRNA-Phe. The control region had no structural genes but had only promoters and regulatory sequences for replication and transcription. The total length of 13 protein-coding gene sequences was 11,386 bp. The lengths of 22 tRNA genes were between 60 and 75 bp. The length of L-strand replication origin (OL) was 36 bp. The phylogenetic tree (Figure 3) illustrated the evolutionary relationships among various species. S. caudata (PP524730) was nested within the genus Sicista and exhibited a close phylogenetic affinity to S. strandi (MZ562682) and S. betulina (MZ570964). Additionally, the tree indicated that the genus Sicista was a member of the larger clade Dipodoidea. Our results indicated that S. caudata and other species from the Superfamily Dipodoidea had further phylogenetic relationships.

Figure 2.

Figure 2.

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Circular mitochondrial genome map of S. caudata. Clockwise represents its position in the H chain, counterclockwise means it is in the L chain. Green, rRNA; violet, protein-coding gene; gray, replication origin of L-strand and control region.

Figure 3.

Figure 3.

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Phylogenetic tree was constructed using 13 protein-coding genes of the complete mitochondrial genome through MEGA 11.0 software, and also constructed using the General Time Reversible model of maximum likelihood method with 1000 bootstrap replications. Sicista caudata (PP524730) is annotated and uploaded by this study. The following sequences were used: KP981422 (Luo and Liao 2016), KP981634 (Luo and Liao 2016), AJ416890 (unpublished), MT079957 (İbiş 2020), KR054628 (Luo et al. 2016), KJ648496 (Yue et al. 2015), MZ562682 (Andersen et al. 2022), MZ570964 (Andersen et al. 2022), KJ648495 (Yue et al. 2015), and KX058130 (Ding et al. 2016). The outgroup was ON041141 (Luo and Liao 2016).

Discussion and conclusions

The arrangement of genes in S. caudata mitochondrial genome was consistent with that in other Superfamily Dipodoidea species (Yue et al. 2015; Ding et al. 2016; Luo et al. 2016; Luo and Liao 2016; İbiş 2020; Andersen et al. 2022). S. caudata exhibited a close phylogenetic affinity to S. strandi and S. betulina. S. caudata and the other species from Superfamily Dipodoidea had a further phylogenetic relationship. This study verified the evolutionary status of S. caudata in the Superfamily Dipodoidea at the molecular level. The mitochondrial genome would be a significant supplement for the genetic background of S. caudata.

Supplementary Material

supplementary materials.docx
TMDN_A_2432349_SM8037.docx (153.8KB, docx)

Funding Statement

This study was supported by the Heilongjiang Provincial Department of Education Filing Project [1453QN028, 1452TD008, and 1451TD002] and the Heilongjiang Provincial Natural Funds [LH2021C095].

Author contributions

Zhu Liu, Fu-Ying Zhang, and Zhi-Hui Zhang collected the specimen and wrote the manuscript. Fu-Ying Zhang, Zhi-Hui Zhang, and Qiu-Ying Guo designed the experiment, identified the specimens, and analyzed the data; Zhu Liu, Fu-Ying Zhang, and Zhi-Hui Zhang were involved in the conception and design, funding acquisition, and interpretation of the data. All authors agreed to this final version of the manuscript.

Ethical approval

The specimen collection protocol was approved by Laboratory Animal Welfare Ethics Committee of Mudanjiang Normal University (IACUC-MNU-2022-014) and licensed by the local government. The specimen collected was neither non-protected animals nor endangered. Research procedures were carried out in accordance with applicable national guidelines. The specimen collected was dead.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The data supporting the findings of this study are publicly accessible on the GenBank website at https://www.ncbi.nlm.nih.gov/, under the reference number PP524730. The additional data can be accessed at BioSample: SAMN41038315, SRA: SRR29259733, and BioProject: PRJNA1102988. Raw data can be downloaded at https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR29259733&display=metadata.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

supplementary materials.docx
TMDN_A_2432349_SM8037.docx (153.8KB, docx)

Data Availability Statement

The data supporting the findings of this study are publicly accessible on the GenBank website at https://www.ncbi.nlm.nih.gov/, under the reference number PP524730. The additional data can be accessed at BioSample: SAMN41038315, SRA: SRR29259733, and BioProject: PRJNA1102988. Raw data can be downloaded at https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR29259733&display=metadata.

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