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Original Article

Complete mitogenome sequence of Caryophyllaeus brachycollis (Cestoda: Caryophyllidae) from China: Characterization and phylogenetic analyses of Caryophyllidea

Parasites, Hosts and Diseases 2025;63(4):317-326.
Published online: November 19, 2025

1Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China

2Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha 410078, China

3College of Animal Science and Technology, Tarim University, Alaer 843300, China

*Correspondence: hmw, 1592614474@qq.com, ypd, ghost978106510@163.com

These authors contributed equally to this work.

• Received: June 29, 2025   • Accepted: August 3, 2025

© 2025 The Korean Society for Parasitology and Tropical Medicine

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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  • Caryophyllaeus brachycollis mainly parasitizes the intestines of globally distributed freshwater fishes, and infection causes significant economic losses to the aquaculture industry. However, data on the molecular epidemiology, population genetics, and systematics of C. brachycollis are scarce. In this study, we sequenced the complete mitogenome of C. brachycollis isolated from Beijing, China. This circular mitogenome comprised 14,273 bp, which was 231 bp shorter than that of C. brachycollis isolated from Wuhan, China. The mitogenome contained 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 noncoding regions. Bayesian inference revealed that C. brachycollis belonged to the family Caryophyllaeidae. The taxonomic status of C. brachycollis is controversial when based solely on morphological features. A comparative analysis of the mitogenome sequence obtained in this study revealed novel molecular markers for the accurate ascertainment of the phylogenetic position of this parasite.
Caryophyllideans, the earliest diverging group of non-segmented tapeworms, are described by morphological and biological features and typically have a monozoic (non-proglottized) body plan [13]. They are globally distributed and host-specific, mainly parasitizing in the intestinal tracts of Cypriniformes and Siluriformes fishes. Infection leads to weight loss, reduced fecundity, and high mortality rates, severely impacting the aquaculture industry [49]. The evolution of Eucestoda is unclear. The results of studies analyzing nuclear DNA genes (large and small subunits of ribosomal DNA) suggest that Spathebothriidea is the most divergent eucestode [10,11], whereas those analyzing morphological features and large fragments of mitochondrial DNA suggest that Caryophyllidea is the earliest divergent taxon [3,12]. Therefore, a better understanding of the relationship between orders Spathebothriidea and Caryophyllidea is warranted.
Although the order Caryophyllidea is regarded as a key group in Eucestoda research, the systematic classification and phylogenetic relationships of its members remain controversial. The families Balanotaeniidae, Capingentidae, Caryophyllaeidae, and Lytocestidae [1,2] are generally considered to belong to this order. Caryophyllaeidae, which frequently parasitize cyprinid fish in the Palearctic region, is the biggest group within Caryophyllidea, comprising 20 genera [13]. However, a recent study suggested reclassification into 10 genera [2], including Caryophyllaeus (Gmelin, 1790). The number of species in this genus varies from the previously described 42 nominal taxa to the recently recognized 7 valid species [14,15], of which Caryophyllaeus brachycollis is an important member. C. brachycollis consists of 2 morphotypes based on morphological and molecular (large subunit of ribosomal DNA and cox1) characteristics [16,17]. Although the mitogenome is a useful marker for tapeworm identification, differentiation, and systematic analyses [1821], the complete mitogenome is only available for 1 morphotype, which was isolated from Wuhan, Hubei Province, China (CBCW). Because there is no data on the other morphotype, the molecular differentiation of C. brachycollis in China is unclear.
Thus, our study focused on obtaining the complete mitogenome of the other C. brachycollis morphotype, which was isolated from Beijing, China (CBCB). The aims were as follows: (i) sequence and annotate the complete CBCB mitogenome, (ii) determine differences between CBCB and CBCW, (iii) infer the phylogenetic relationship among members of the order Caryophyllidea, and (iv) identify the systematic and taxonomic status of the genus Caryophyllaeus. These findings would provide more molecular data for use in further Caryophyllidea analyses.
Ethics statement
The experimental protocol was established according to the ethical guidelines of the Institutional Animal Care and Use Committee and approved by the Ethics Committee of Hunan Agricultural University (No. 202282).
Sample collection and DNA extraction
Samples were collected from the intestines of Cyprinus carpio from Beijing Zoo, China. They were washed in physiological saline, and those morphologically identified as caryophyllidean were fixed in 70% (v/v) ethanol and stored at −40°C until use.
Total genomic DNA was extracted using sodium dodecyl sulfate/proteinase K treatment, followed by spin-column purification (Wizard SV Genomic DNA Purification System; Promega, Madison, WI, USA). The purified DNA was used as the template in PCR assays with the primer pair JB3/JB4.5 targeting a fragment of cox1 for amplification [22].
Sequencing, assembling, and verification
A genomic DNA library (with 350 bp inserts) was prepared and sequenced by Novogene (Tianjin, China) using a HiSeq 2500 sequencing platform (Illumina, San Diego, CA, USA) to obtain 250 bp paired-end reads. Geneious v11.1.5 software was used to filter and clean the raw data and assemble the complete CBCB mitogenome using the amplified cox1 sequences as initial references. The parameters were set as follows: minimum overlap identity, 99.0%; minimum overlap, 150 bp; and maximal gap size, 5 bp. The assembled mitogenome was further verified by long PCR experiments (Supplementary Fig. S1) using the primers listed in Supplementary Table S1.
Annotation, visualization, and sequence analysis
The boundaries of protein-coding genes (PCGs) were identified using the NCBI tool ORF Finder (https://www.ncbi.nlm.nih.gov/orffinder/). The initiation/termination codons for each PCG were identified following alignment with the CBCW mitogenome sequence using MAFFT v7.122 software. All PCG nucleotide sequences were translated to amino acid sequences using MEGA v11.0. Twenty-two transfer RNA (tRNA) genes were detected using ARWEN [23] and tRNAscan-SE [24]. Nucleotide composition and codon usage frequencies of the PCGs were analyzed using MEGA v11.0. The annotated CBCB mitogenome was visualized using the online server Proksee (https://proksee.ca/). The CBCW sequence was used as the reference genome for comparisons with CBCB.
Phylogenetic analyses
Phylogenetic analyses were performed using 6 mitogenome sequences of tapeworms within the order Caryophyllidea (Table 1) and Paruterina candelabraria (GenBank accession No. NC_039533) as the outgroup. Amino acid sequences were aligned using MAFFT v7.122 and concatenated into a single dataset. Ambiguous bases or gaps were excluded using Gblocks 0.91b software with the default parameters [25]. Phylogenetic analyses were performed using Bayesian inference (BI) and maximum likelihood (ML) methods. BI analysis was run in MrBayes 3.1.1 using an approach similar to that of Ronquist and Huelsenbeck [26]. ML analysis was performed using PhyML 3.1 software. “JTT+I+G+F” was selected as the best suitable model by ProtTest v3.4.2 based on the Akaike information criterion [27] and was used for the BI and ML analyses. Phylograms were drawn using FigTree v.1.4.2 (http://tree.bio.ed.ac.uk/software/figtree).
cox1 sequence analysis
To determine the systematic relationship of the families in Caryophyllidea, BI analysis was performed using 20 cox1 sequences of the order Caryophyllidea and Gigantolina magna (GenBank accession No. JQ268545) as the outgroup.
Genome composition and organization
Sequencing of the CBCB mitogenome generated 4.08 Gb of raw data, from which approximately 7,577,818×2 clean reads were obtained following filtering and used for further assembly. The complete circular CBCB mitogenome (GenBank accession No. OP359069) was 14,273 bp and comprised 36 genes, including 12 PCGs (excluding atp8), 22 tRNA genes, 2 ribosomal RNA genes (rrnS and rrnL), and 2 noncoding regions (NCRs; control or AT-rich regions) (Fig. 1; Table 2). All 36 genes were transcribed in the forward direction. In C. brachycollis mitochondrial DNA, the AT-skews were all negative (−0.481 to −0.125), and the GC-skews were all positive (0.167 to 0.465) (Table 3), suggesting a bias toward T and G bases. The lengths of the 2 NCRs in CBCB were 845 and 423 bp, respectively, while those in CBCW were 641 and 871 bp, respectively (Table 2). The large NCR (LNCR) was located between tRNA-Leu2 and cox2, and the small NCR (SNCR) was located between tRNA-Gly and cox3 (Fig. 1). Alignment using BLAST revealed 100.0% nucleotide similarity with CBCW (GenBank accession No. NC_035430).
Composition of PCGs, ribosomal RNA genes, and tRNA genes
ATN was extensively used as the initiation codon, especially ATG. GTG is an uncommon start codon in tapeworms, but it was observed in cytb, nad1, and nad4L in this study (Table 2). Furthermore, TAA and TAG were frequently used as termination codons (TAG: cytb, atp6, nad3, nad4, and nad4L; TAA: nad6) (Table 2). Incomplete stop codons T and TA were also prevalent in termination, with cox1, cox3, and nad2 using T and cox2, nad1, and nad5 using TA (Table 2). The AT-skews of the 12 protein genes were all negative (−0.481 (nad3) to −0.181 (cox2)), and the GC-skews were all positive (0.167 (cox2) to 0.465 (nad4L)), suggesting a large T base bias in nad3, a G base tendency in nad4L, and a minor tendency of T+G bases in cox2.
The 22 tRNA genes ranged from 54 to 68 bp (Table 2). rrnL and rrnS were 951 and 712 bp, respectively, with an A+T content of 62.2% and 62.4%, respectively (Table 3).
Comparative analyses of CBCB and CBCW
Comparisons between the CBCB and CBCW mitogenome sequences revealed that CBCB was approximately 231 bp shorter than CBCW. In both CBCB (Fig. 1) and CBCW, the SNCR and LNCR were located in “tRNA-Gly and cox3” and “tRNA-Leu2 and cox2,” respectively. The size (cox2 and nad5) and the initiation/termination (cox2) codons of PCGs in CBCB and CBCW differed (Table 2). cox2 was 539 bp and 551 bp in CBCW and CBCB, respectively, while nad5 was 1,547 and 1,550 bp, respectively. The initiation/termination codons of cox2 were ATG/TAG and ATG/TA in CBCW and CBCB, respectively.
Comparison of the nucleotide sequences of PCGs between CBCB and CBCW revealed differences of 0% (nad4L) to 2.2% (cox3) (Table 4). Differences in the amino acid sequences of CBCB and CBCW ranged from 0% (nad4L) to 2.7% (cox2) (Table 4). nad4L typically shows interspecies variability. However, our study revealed that it was highly conserved in C. brachycollis. These findings suggested that cox2 might be a better molecular marker for identifying cryptic species within C. brachycollis.
Phylogenetic analyses
The phylogeny of Caryophyllidea is currently unclear due to a lack of complete mitogenome sequences. To better clarify the phylogenetic relationships among the members of this order, 6 mitogenome sequences were phylogenetically analyzed using BI and ML methods. The BI and ML tree topologies were identical (Fig. 2). There were 2 main clades: 1 clade contained Caryophyllaeidae and Lytocestidae, and the other clade contained Capingentidae, Caryophyllaeidae, and Lytocestidae, indicating that families Caryophyllaeidae and Lytocestidae were paraphyletic. The mitochondrial DNA sequences of CBCB and CBCW grouped with short topological distance (BPP =1, BF=100) (Fig. 2), indicating that they were closely related. Furthermore, phylogenetic analyses of cox1 also showed that Caryophyllaeidae and Lytocestidae were paraphyletic and revealed a close evolutionary distance between CBCB and CBCW (Supplementary Fig. S2).
The complete mitogenome of CBCB was 14,273 bp and encoded 36 genes. The A+T base bias (73.2%) was significantly higher than the G+C base bias (26.8%). The AT-skew ([A-T]/[A+T]) and GC-skew ([G-C]/[G+C]) were useful methods to estimate compositional asymmetry [28].
Regarding the initiation codons, ATG was the most prevalent in 8 of the 12 PCGs (atp6, cox1, cox2, nad2, nad3, nad4, nad5, and nad6), and ATT was used in cox3. TAA and TAG have been reported as common termination codons [29,30] and were identified as frequent termination codons in our study. There were 22 tRNA genes in the CBCB mitogenome. Similar to tapeworms Breviscolex orientalis and Parabreviscolex niepini [31,32], most tRNA genes in CBCB presented as a typical ‘cloverleaf’ structure, excluding tRNA-SerAGN and tRNA-Arg, which lacked DHU arms. The rrnL was located between tRNA-Thr and tRNA-Cys, and rrnS between tRNA-Cys and tRNA-Leu1, similar to the arrangement in B. orientalis and Atractolytocestus huronensis [32].
Although the mitogenome sequence of CBCW was longer than that of CBCB, the arrangements of the 36 genes were the same and consistent with the order observed in most caryophyllideans [31,32]. Considering that the differences in mitogenome sequences between closely related nematode species are 10.0%–20.0% [33,34], and species-level variations in mammals are typically 2.0%–10.0% [35], the level of differences between CBCB and CBCW indicated that they were identical.
Comparison between the CBCB and CBCW mitogenomes revealed that cox2 is a reliable molecular marker for cryptic species identification. Furthermore, nad4L was highly conserved in C. brachycollis. This comparative mitogenomic analysis elucidated evolutionary and phylogenetic relationships among related species, enhancing the accuracy of taxonomic classification.
To summarize, our study determined and characterized the complete mitogenome sequence (14,273 bp) of CBCB, revealing that it was shorter than that of CBCW. The CBCB mitogenome provided evidence supporting a close phylogenetic relationship between C. brachycollis and other members of the Caryophyllidae family. Because only a limited number of specimens from a single geographic location were analyzed, future studies should include a broader sample to further assess intraspecific variations.

Author contributions

Conceptualization: Liu YL, Fu YT

Data curation: Liu YL, Zhang Y, Fu YT

Formal analysis: Zhang Y

Investigation: Liu YL

Methodology: Deng YP

Resources: Wang HM, Deng YP

Software: Wang HM

Supervision: Fu YT, Liu GH

Validation: Zhang Y, Fu YT, Liu GH

Writing – original draft: Liu YL, Zhang Y, Wang HM

Writing – review & editing: Deng YP

Conflict of interest

The authors declare no conflict of interest related to this study.

Acknowledgments

This study was supported in part, by the Training Programme for Excellent Young Innovators of Changsha (grant No. KQ2106044). The raw data have been deposited in GenBank (accession No. OP359069 and SRR34793993).

Supplementary material is available with this article at https://doi.org/10.3347/PHD.25044.
Fig. 1
Mitogenome organization of Caryophyllaeus brachycollis isolate from China. Gene scaling is approximate. CD, coding region; NCR1, long noncoding region; NCR2, short noncoding region; tRNA, transfer RNA; rRNA, ribosomal RNA.
phd-25044f1.jpg
Fig. 2
Inferred phylogenetic relationships among species in the order Caryophyllidea. The concatenated amino acid sequences of 12 mitochondrial protein-coding genes were analyzed utilizing maximum likelihood (ML) and Bayesian analysis (BI) methods, with Paruterina candelabraria as the outgroup. The Caryophyllaeus brachycollis form was isolated from carp tapeworm in Beijing in this study.
phd-25044f2.jpg
Table 1
Complete mitogenome sequences of the order Caryophyllidea used for phylogenetic analysis
Table 1
Family/order Species Size (bp) GenBank accession No.
Lytocestidae Khawia sinensis 13,759 NC034800
Atractolytocestys huronensis 15,130 NC035635

Caryophyllaeidae Caryophyllaeus brachycollis 14,504 NC035430
Parabreviscolex niepini 15,034 NC040117

Capingentidae Breviscolex orientalis 14,011 NC035634

Cyclophyllidea Paruterina candelabraria 13,634 NC039533
Table 2
Comparative organization of the complete mitogenome of Caryophyllaeus brachycollis isolates from Beijing and Wuhan, China
Table 2
Gene/region Positions Size (bp) No. of aa Ini/Ter codons Anticodons





CBCB CBCW CBCB CBCW CBCB CBCW CBCB CBCW CBCB/CBCW
cox3 1–643 1–643 643 643 214 214 ATT/T ATT/T

tRNA-His (H) 644–705 644–705 62 62 GTG

cytb 707–1825 707–1825 1,119 1,119 372 372 GTG/TAG GTG/TAG

nad4L 1828–2067 1828–2067 240 240 79 79 GTG/TAG GTG/TAG

nad4 2028–3260 2028–3260 1,233 1,233 410 410 ATG/TAG ATG/TAG

tRNA-Gln (Q) 3264–3318 3261–3322 55 63 TTG

tRNA-Phe (F) 3323–3377 3320–3382 55 63 GAA

tRNA-Met (M) 3378–3440 3378–3440 63 63 CAT

atp6 3444–3959 3444–3959 516 516 171 171 ATG/TAG ATG/TAG

nad2 3960–4830 3960–4830 871 871 290 290 ATG/T ATG/T

tRNA-Val (V) 4831–4890 4831–4890 60 60 TAC

tRNA-Ala (A) 4889–4949 4888–4949 61 62 TGC

tRNA-Asp (D) 4954–5014 4954–5014 61 61 GTC

nad1 5015–5907 5015–5908 893 894 297 297 GTG/TA GTG/TAG

tRNA-Asn (N) 5908–5975 5908–5975 68 68 GTT

tRNA-Pro (P) 5980–6040 5980–6040 61 61 TGG

tRNA-Ile (I) 6040–6103 6041–6102 64 62 GAT

tRNA-Lys (K) 6106–6165 6106–6165 60 60 GTT

nad3 6170–6517 6170–6517 348 348 115 115 ATG/TAG ATG/TAG

tRNA-Ser1 (S1) 6520–6574 6518–6575 55 58 GCT

tRNA-Trp (W) 6575–6638 6575–6638 64 64 TCA

cox1 6642–8178 6642–8201 1,537 1,537 512 512 ATG/T ATG/T

tRNA-Thr (T) 8183–8242 8183–8242 60 60 TGT

rrnL 8243–9193 8238–9191 951 954

tRNA-Cys 9194–9254 9192–9252 61 61 GCA

rrnS 9255–9966 9253–9965 712 713

tRNA-Leu1 (L1) 9967–10028 9966–10027 62 62 TAG

tRNA-Ser2 (S2) 10030–10093 10028–10093 64 66 TGA

tRNA-Leu2 (L2) 10095–10157 10094–10156 63 63 TAA

NCR1 10158–11002 10157–10797 845 641

cox2 11003–11553 10798–11336 551 539 183 179 ATG/TA ATG/TAG

tRNA-Glu (E) 11587–11646 11370–11429 60 60 TTC

nad6 11647–12105 11430–11888 459 459 152 152 ATG/TAA ATG/TAA

tRNA-Tyr (Y) 12113–12174 11896–11957 62 62 GTA

tRNA-Arg (R) 11183–12236 11966–12021 54 56 TCG

nad5 12237–13786 12023–13570 1,550 1,547 516 515 ATG/TA ATG/TA

tRNA-Gly (G) 13787–13850 13570–13633 64 64 TCC

NCR2 13851–14273 13634–14504 423 871

CBCB, Caryophyllaeus brachycollis isolates from Beijing; CBCW, C. brachycollis isolates from Wuhan.

Table 3
Nucleotide composition and skews of the Caryophyllaeus brachycollis mitogenome
Table 3
Gene Nucleotide frequency A+T (%) AT-skew GC-skew
A (%) G (%) T (%) C (%)
atp6 16.7 25.0 42.2 16.1 58.9 −0.434 0.297
cox1 21.7 23.0 40.3 15.0 62.0 −0.230 0.212
cox2 25.4 22.1 36.7 15.8 62.1 −0.181 0.167
cox3 18.7 24.9 40.4 16.0 59.1 −0.368 0.217
cytb 22.0 23.2 39.9 14.9 61.9 −0.289 0.218
nad1 19.6 25.9 41.8 12.8 61.4 −0.361 0.339
nad2 16.6 26.5 45.8 11.0 62.4 −0.467 0.411
nad3 16.1 25.3 46.0 12.6 62.1 −0.481 0.333
nad4 20.8 22.4 41.7 15.1 62.5 −0.335 0.195
nad4L 19.6 26.2 44.6 9.6 64.2 −0.390 0.465
nad5 20.1 23.4 42.5 13.9 62.6 −0.357 0.254
nad6 20.0 22.9 42.3 14.8 62.3 −0.357 0.214
rrnS 27.0 23.9 35.4 13.8 62.4 −0.135 0.269
rrnL 27.2 22.7 35.0 15.0 62.2 −0.125 0.203
22 tRNAs 25.9 24.8 34.3 15.0 60.2 −0.139 0.246
Total 23.7 22.6 39.5 14.2 63.2 −0.250 0.227
Table 4
Nucleotide and amino acid sequence differences between the isolates from Beijing, China and Wuhan, China mitogenomes
Table 4
Gene/region NT sequence length NT difference (%) No. of AA AA difference (%)




CBCB CBCW CBCB/CBCW CBCB CBCW CBCB/CBCW
atp6 516 516 1.7 171 171 1.2

cox1 1,537 1,537 0.8 512 512 1.0

cox2 551 539 1.5 183 179 2.7

cox3 643 643 2.2 214 214 1.4

cytb 1,119 1,119 1.3 372 372 0.3

nad1 893 894 0.6 297 297 0.7

nad2 871 871 0.6 290 290 0.3

nad3 348 348 0.3 115 115 0.9

nad4 1,233 1,233 1.4 397 410 0.7

nad4L 240 240 0.0 79 79 0.0

nad5 1,550 1,547 1.0 516 515 0.8

nad6 459 459 1.1 152 152 1.3

rrnS 712 713 1.7 - - -

rrnL 951 954 0.8 - - -

All 22tRNAs 1,339 1,361 2.1 - - -

NT, nucleotide; AA, amino acid; CBCB, Caryophyllaeus brachycollis isolates from Beijing; CBCW, C. brachycollis isolates from Wuhan.

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Complete mitogenome sequence of Caryophyllaeus brachycollis (Cestoda: Caryophyllidae) from China: Characterization and phylogenetic analyses of Caryophyllidea
Parasites Hosts Dis. 2025;63(4):317-326.   Published online November 19, 2025
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Complete mitogenome sequence of Caryophyllaeus brachycollis (Cestoda: Caryophyllidae) from China: Characterization and phylogenetic analyses of Caryophyllidea
Parasites Hosts Dis. 2025;63(4):317-326.   Published online November 19, 2025
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Complete mitogenome sequence of Caryophyllaeus brachycollis (Cestoda: Caryophyllidae) from China: Characterization and phylogenetic analyses of Caryophyllidea
Image Image
Fig. 1 Mitogenome organization of Caryophyllaeus brachycollis isolate from China. Gene scaling is approximate. CD, coding region; NCR1, long noncoding region; NCR2, short noncoding region; tRNA, transfer RNA; rRNA, ribosomal RNA.
Fig. 2 Inferred phylogenetic relationships among species in the order Caryophyllidea. The concatenated amino acid sequences of 12 mitochondrial protein-coding genes were analyzed utilizing maximum likelihood (ML) and Bayesian analysis (BI) methods, with Paruterina candelabraria as the outgroup. The Caryophyllaeus brachycollis form was isolated from carp tapeworm in Beijing in this study.
Complete mitogenome sequence of Caryophyllaeus brachycollis (Cestoda: Caryophyllidae) from China: Characterization and phylogenetic analyses of Caryophyllidea

Complete mitogenome sequences of the order Caryophyllidea used for phylogenetic analysis

Family/order Species Size (bp) GenBank accession No.
Lytocestidae Khawia sinensis 13,759 NC034800
Atractolytocestys huronensis 15,130 NC035635

Caryophyllaeidae Caryophyllaeus brachycollis 14,504 NC035430
Parabreviscolex niepini 15,034 NC040117

Capingentidae Breviscolex orientalis 14,011 NC035634

Cyclophyllidea Paruterina candelabraria 13,634 NC039533

Comparative organization of the complete mitogenome of Caryophyllaeus brachycollis isolates from Beijing and Wuhan, China

Gene/region Positions Size (bp) No. of aa Ini/Ter codons Anticodons





CBCB CBCW CBCB CBCW CBCB CBCW CBCB CBCW CBCB/CBCW
cox3 1–643 1–643 643 643 214 214 ATT/T ATT/T

tRNA-His (H) 644–705 644–705 62 62 GTG

cytb 707–1825 707–1825 1,119 1,119 372 372 GTG/TAG GTG/TAG

nad4L 1828–2067 1828–2067 240 240 79 79 GTG/TAG GTG/TAG

nad4 2028–3260 2028–3260 1,233 1,233 410 410 ATG/TAG ATG/TAG

tRNA-Gln (Q) 3264–3318 3261–3322 55 63 TTG

tRNA-Phe (F) 3323–3377 3320–3382 55 63 GAA

tRNA-Met (M) 3378–3440 3378–3440 63 63 CAT

atp6 3444–3959 3444–3959 516 516 171 171 ATG/TAG ATG/TAG

nad2 3960–4830 3960–4830 871 871 290 290 ATG/T ATG/T

tRNA-Val (V) 4831–4890 4831–4890 60 60 TAC

tRNA-Ala (A) 4889–4949 4888–4949 61 62 TGC

tRNA-Asp (D) 4954–5014 4954–5014 61 61 GTC

nad1 5015–5907 5015–5908 893 894 297 297 GTG/TA GTG/TAG

tRNA-Asn (N) 5908–5975 5908–5975 68 68 GTT

tRNA-Pro (P) 5980–6040 5980–6040 61 61 TGG

tRNA-Ile (I) 6040–6103 6041–6102 64 62 GAT

tRNA-Lys (K) 6106–6165 6106–6165 60 60 GTT

nad3 6170–6517 6170–6517 348 348 115 115 ATG/TAG ATG/TAG

tRNA-Ser1 (S1) 6520–6574 6518–6575 55 58 GCT

tRNA-Trp (W) 6575–6638 6575–6638 64 64 TCA

cox1 6642–8178 6642–8201 1,537 1,537 512 512 ATG/T ATG/T

tRNA-Thr (T) 8183–8242 8183–8242 60 60 TGT

rrnL 8243–9193 8238–9191 951 954

tRNA-Cys 9194–9254 9192–9252 61 61 GCA

rrnS 9255–9966 9253–9965 712 713

tRNA-Leu1 (L1) 9967–10028 9966–10027 62 62 TAG

tRNA-Ser2 (S2) 10030–10093 10028–10093 64 66 TGA

tRNA-Leu2 (L2) 10095–10157 10094–10156 63 63 TAA

NCR1 10158–11002 10157–10797 845 641

cox2 11003–11553 10798–11336 551 539 183 179 ATG/TA ATG/TAG

tRNA-Glu (E) 11587–11646 11370–11429 60 60 TTC

nad6 11647–12105 11430–11888 459 459 152 152 ATG/TAA ATG/TAA

tRNA-Tyr (Y) 12113–12174 11896–11957 62 62 GTA

tRNA-Arg (R) 11183–12236 11966–12021 54 56 TCG

nad5 12237–13786 12023–13570 1,550 1,547 516 515 ATG/TA ATG/TA

tRNA-Gly (G) 13787–13850 13570–13633 64 64 TCC

NCR2 13851–14273 13634–14504 423 871

CBCB, Caryophyllaeus brachycollis isolates from Beijing; CBCW, C. brachycollis isolates from Wuhan.

Nucleotide composition and skews of the Caryophyllaeus brachycollis mitogenome

Gene Nucleotide frequency A+T (%) AT-skew GC-skew
A (%) G (%) T (%) C (%)
atp6 16.7 25.0 42.2 16.1 58.9 −0.434 0.297
cox1 21.7 23.0 40.3 15.0 62.0 −0.230 0.212
cox2 25.4 22.1 36.7 15.8 62.1 −0.181 0.167
cox3 18.7 24.9 40.4 16.0 59.1 −0.368 0.217
cytb 22.0 23.2 39.9 14.9 61.9 −0.289 0.218
nad1 19.6 25.9 41.8 12.8 61.4 −0.361 0.339
nad2 16.6 26.5 45.8 11.0 62.4 −0.467 0.411
nad3 16.1 25.3 46.0 12.6 62.1 −0.481 0.333
nad4 20.8 22.4 41.7 15.1 62.5 −0.335 0.195
nad4L 19.6 26.2 44.6 9.6 64.2 −0.390 0.465
nad5 20.1 23.4 42.5 13.9 62.6 −0.357 0.254
nad6 20.0 22.9 42.3 14.8 62.3 −0.357 0.214
rrnS 27.0 23.9 35.4 13.8 62.4 −0.135 0.269
rrnL 27.2 22.7 35.0 15.0 62.2 −0.125 0.203
22 tRNAs 25.9 24.8 34.3 15.0 60.2 −0.139 0.246
Total 23.7 22.6 39.5 14.2 63.2 −0.250 0.227

Nucleotide and amino acid sequence differences between the isolates from Beijing, China and Wuhan, China mitogenomes

Gene/region NT sequence length NT difference (%) No. of AA AA difference (%)




CBCB CBCW CBCB/CBCW CBCB CBCW CBCB/CBCW
atp6 516 516 1.7 171 171 1.2

cox1 1,537 1,537 0.8 512 512 1.0

cox2 551 539 1.5 183 179 2.7

cox3 643 643 2.2 214 214 1.4

cytb 1,119 1,119 1.3 372 372 0.3

nad1 893 894 0.6 297 297 0.7

nad2 871 871 0.6 290 290 0.3

nad3 348 348 0.3 115 115 0.9

nad4 1,233 1,233 1.4 397 410 0.7

nad4L 240 240 0.0 79 79 0.0

nad5 1,550 1,547 1.0 516 515 0.8

nad6 459 459 1.1 152 152 1.3

rrnS 712 713 1.7 - - -

rrnL 951 954 0.8 - - -

All 22tRNAs 1,339 1,361 2.1 - - -

NT, nucleotide; AA, amino acid; CBCB, Caryophyllaeus brachycollis isolates from Beijing; CBCW, C. brachycollis isolates from Wuhan.

Table 1 Complete mitogenome sequences of the order Caryophyllidea used for phylogenetic analysis
Table 2 Comparative organization of the complete mitogenome of Caryophyllaeus brachycollis isolates from Beijing and Wuhan, China

CBCB, Caryophyllaeus brachycollis isolates from Beijing; CBCW, C. brachycollis isolates from Wuhan.

Table 3 Nucleotide composition and skews of the Caryophyllaeus brachycollis mitogenome
Table 4 Nucleotide and amino acid sequence differences between the isolates from Beijing, China and Wuhan, China mitogenomes

NT, nucleotide; AA, amino acid; CBCB, Caryophyllaeus brachycollis isolates from Beijing; CBCW, C. brachycollis isolates from Wuhan.