2urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7Eurn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727AZooKeysZK1313-29891313-2970Pensoft Publishers10.3897/zookeys.783.2467424674Research ArticleCestodaMolecular systematicsAsiaCharacterization of the complete mitochondrial genome of Parabreviscolexniepini Xi et al., 2018 (Cestoda, Caryophyllidea)XiBing-Wenbwxi_david@163.comhttps://orcid.org/0000-0002-0402-72811ZhangDong2LiWen-Xiang2YangBao-Juan1XieJun1Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 214081 Wuxi, ChinaFreshwater Fisheries Research Center, Chinese Academy of Fishery SciencesWuxiChinaInstitute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, ChinaInstitute of Hydrobiology, Chinese Academy of SciencesWuhanChina
Corresponding author: Bing-Wen Xi (xibw@ffrc.cn)
Academic editor: B. Georgiev
20180509201878397112FFF0FF95-462D-FFD1-BE25-7B5DFFA1FFFB08EFCF96-040C-4888-A30E-A7B744A41FAB14146502702201828052018Bing-Wen Xi, Dong Zhang, Wen-Xiang Li, Bao-Juan Yang, Jun XieThis is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.http://zoobank.org/08EFCF96-040C-4888-A30E-A7B744A41FAB
Parabreviscolexniepini is a recently described caryophyllidean monozoic tapeworm from schizothoracine fish on the Tibetan Plateau. In the present study, the complete mitochondrial genome of P.niepini is determined for the first time. The mitogenome is 15,034 bp in length with an A+T content of 59.6%, and consists of 12 protein-encoding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions. The secondary structure of tRNAs exhibit the conventional cloverleaf structure, except for trnS1(AGN) and trnR, which lack DHU arms. The anti-codon of trnS1(AGN) in the mitogenome of P.niepini is TCT. The two major non-coding regions, 567 bp and 1428 bp in size, are located between trnL2 and cox2, trnG and cox3, respectively. The gene order of P.niepini shows a consistent pattern with other caryophyllideans. Phylogenetic analysis based on mitogenomic data indicates that P.niepini has a close evolutionary relationship with tapeworms Breviscolexorientalis and Atractolytocestushuronensis.
Xi B-W, Zhang D, Li W-X, Yang B-J, Xie J (2018) Characterization of the complete mitochondrial genome of Parabreviscolex niepini Xi et al., 2018 (Cestoda, Caryophyllidea). ZooKeys 783: 97–112. https://doi.org/10.3897/zookeys.783.24674
Introduction
The Caryophyllidea is an ancient group of tapeworms, consisting of four families, 42 genera, and approximately 190 species parasitic in cypriniform and siluriform fishes in most zoogeographical regions (Scholz and Oros 2017). Some caryophyllideans, especially those in cyprinids (e.g. Khawiasinensis Hsü, 1935), cause severe fish diseases. The simplification and limited number of morphological characters cause species identification and taxonomic classification is problematic. Recent research found that the present classification of caryophyllideans could not reveal the natural phylogenetic relationships (Brabec et al. 2012; Xi et al. 2018). Further studies were desired to re-construct the taxonomic system. Maternal inheritance and rapid evolution have proven to be key factors in phylogenetic studies in tapeworms, making mitochondrial DNA a powerful marker for species identification (e.g. Brabec et al. 2012; Li et al. 2017).
Parabreviscolex Xi, Oros, Chen & Xie, 2018 is a recently erected genus in the family Capingentidae Hunter, 1930 (Cestoda: Caryophyllidea), with the type species Parabreviscolexniepini Xi, Oros, Chen & Xie, 2018 from schizothoracine fish on the Tibetan Plateau (Xi et al. 2018). The historical uplift of the Tibetan Plateau has caused significant differentiation of the Tibetan biotas, resulting in many endemic species. The evolution and adaptation processes of those species have attracted much attention. In this study, the complete mitogenome of P.niepini was sequenced, which may provide useful information for better understanding the evolution and taxonomy within caryophyllideans.
Materials and methodsSpecimen collection and DNA extraction
Parabreviscolexniepini were collected from the schizothoracine fish Schizopygopsisyounghusbandi Regan, 1905 in the Yarlung Tsangpo River at Linzhi (29°39'N, 94°21'E), Tibet, China, and the specimens were fixed in 100% ethanol and stored at Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences. Total genomic DNA was extracted using a TIANamp Micro DNA Kit (Tiangen Biotech, Beijing, China), according to the manufacturer’s instructions. DNA was stored at -20 °C for further molecular analyses.
PCR and DNA sequencing
The whole mitogenome was amplified with primers designed based on closely related tapeworms (Suppl. material 1). PCR reactions were performed in a 20 µL reaction mixture, containing 7.4 µL dd H2O, 10 µL 2×PCR buffer (Mg2+, dNTP plus, Takara, China), 0.6 µL of each primer (10 µM), 0.4 µL ExTaq polymerase (Takara, China), and 1 µL DNA template (200 ng/µL). Amplification was conducted as follows: initial denaturation at 95 °C for 2 min, followed by 40 cycles at 95 °C for 10 sec, 46 °C – 53 °C for 30 sec (annealing temperature depending on the primers used, see Suppl. material 1), and 68 °C for 90 sec, and final extension at 68 °C for 10 min. PCR products were sequenced bidirectionally at Sangon Biotech (Shanghai, China) using the primer walking strategy.
Sequence annotation and analyses
The amplified fragments were quality-proofed, and BLASTN (Altschul et al. 1990) to confirm the fragments were the actual target sequence. The complete mitochondrial genomic sequence of P.niepini was assembled manually in a stepwise manner using the DNAstar v7.1 program (Burland 2000). To determine the gene boundaries, it was aligned against the reference mitogenomic sequences of Atractolytocestushuronensis Anthony, 1958 (KY486754) using the program MAFFT 7.149 (Katoh and Standley 2013) integrated with Geneious (Kearse et al. 2012). The mitogenome was annotated and characterized mainly following previous descriptions (Zhang et al. 2017a, b; Zou et al. 2017; Li et al. 2018). Protein-coding genes (PCGs) were found by searching for ORFs (employing genetic code 9, an echinoderm mitochondrial genome) and checking the nucleotide alignments against the reference genome in Geneious. All tRNAs were identified, and confirmed with ARWEN (Laslett and Canback 2008) and MITOS (Bernt et al. 2013) web servers. Similarly, rrnL and rrnS were initially found using MITOS and their boundaries were determined by the alignments with the reference genome in Geneious. The NCBI submission file and tables with statistics for mitogenomes were generated using a GUI-based program, MitoTool (Zhang 2016b). Tandem Repeats Finder (Benson 1999) was employed to find tandem repeats in the non-coding regions. A nucleotide composition table was then used to make the broken line graph of A+T content in ggplot2 (Hadley 2009). Codon usage and relative synonymous codon usage (RSCU) for twelve protein-encoding genes (PCGs) of P.niepini was computed and sorted using MitoTool, and finally imported to ggplot2 to draw the RSCU figure. Ggplot2 was used to draw scatter diagrams for the principal component analysis (PCGs) and nucleotide skews. Input files for the PCGs of codon usage pattern, as well as analyses of amino acid usage pattern and nucleotide skews, were generated by MitoTool. PASW 18.0 (Allen and Bennett 2010) was used to conduct a principal component analysis and generate data for the scatter diagram.
Phylogeny and gene order
Phylogenetic analyses were undertaken using nucleotide sequences of all 36 genes of the newly sequenced mitogenome of P.niepini and 36 selected cestodes mitogenomes available in the GenBank (Suppl. material 2). The mitogenomic sequences of Khawiasinensis (NC_034800/KR676560) and Caryophyllaeusbrachycollis Janiszewska, 1953 (NC_035430/KT028770) from the common carp, sequenced and deposited in GenBank by the same researchers (Feng et al. 2017), were reassigned herein as Khawia sp. 1 and Khawia sp. 2, respectively, because the species identifications were questionable. Caryophyllaeusbrachycollis mainly infests the cyprinid Barbus and Abramis in European countries, while its occurrence in China is rare (Barčák et al. 2014). We considered that the researchers have misidentified the two common tapeworms Khawiasinensis and Khawiajaponensis (Yamaguiti, 1934) from the common carp.
Two trematode species, Dicrocoeliumdendriticum (Rudolphi, 1819) (NC_025280) and Dicrocoeliumchinensis Tang & Tang, 1978 (NC_025279), were used as outgroups. The nucleotide sequences for all 12 PCGs, two rRNAs and 22 tRNAs were extracted from GenBank files. The PCGs were translated into amino acid sequences (employing genetic code 9) using MitoTool, and aligned in batches with MAFFT integrated into another GUI-based program BioSuite (Zhang 2016a) using codon-alignment mode. RNAs were aligned with structural alignment mode using the Q-INS-i algorithm incorporated into MAFFT-with-extensions software. BioSuite was then used to concatenate these alignments and remove ambiguously aligned fragments from the concatenated alignments by another plug-in program, Gblocks 0.91b (Talavera and Castresana 2007). Phylogenetic analyses were conducted using maximum likelihood (ML) and Bayesian inference (BI) methods. Selection of the most appropriate evolutionary model for the dataset was carried out using ModelFinder (Kalyaanamoorthy et al. 2017). Based on the Bayesian information criterion, GTR+I+G was chosen as the optimal model for both analyses. ML analysis was performed in RaxML GUI (Silvestro and Michalak 2011) using a ML + rapid bootstrap (BP) algorithm with 1000 replicates. BI analysis was performed in MrBayes 3.2.6 (Ronquist et al. 2012) with default settings, and 6×106 metropolis-coupled MCMC generations.
Selection analyses
To determine lineage-specific positively selected sites in individual mitochondrial PCGs, a branch-site model incorporated by CodeML within PAML package (Yang 2007) was used. The resultant ML and/or BI tree (unrooted tree with outgroups removed) was employed for the analysis. The alternative model, MA fixes ω at 1 for each branch except for the specified branch leading to P.niepini (foreground branch), wherein ω is presumed to be greater than 1. The first null model MAnull fixes ω at 1 for every branch in the tree, whereas the second null model M1a fixes ω at 1 for every branch except for the foreground branch, where ω is assumed to be in the range 0 to 1. The null model and alternative model were compared via a likelihood ratio test (LRT), and positive selection was confirmed when P<0.05. Comparing MA to MAnull can estimate positive selection, while comparing MA to M1a can identify instances of relaxation of selective constraints as well as positive selection (Láruson 2017). The posterior probabilities value (≥ 95%) of Bayes Empirical Bayes (BEB) method was used to identify for positively selected sites (Yang 2005).
ResultsGenome organization and base composition
The closed-circular mitochondrial genome of Parabreviscolexniepini is 15,034 bp in size (GenBank accession number: MG674140). The mitogenome is composed of 12 protein-encoding genes (PCGs), 22 tRNA genes, two rRNA genes, two non-coding regions, and it lacks the atp8 gene (NCR) (Fig. 1). As is common in flatworms, all genes are transcribed from the same strand (Le et al. 2002). Eight overlapping regions and 16 intergenic regions were found in the genome (Table 1). In accordance with other caryophyllidean species, the A+T content of the whole genome (59.6%) and its elements are lower than in the segmented cestodes (Fig. 2d). The mitogenome of P.niepini exhibits G-skew and T-skew, which is also the case in other cestodes (Fig. 2a). However, the unsegmented cestodes appear to exhibit less mutation bias than segmented cestodes (lower GC-skew and higher AT-skew values, Fig. 2a).
Circular representation of the mitochondrial genome of Parabreviscolexniepini. Different colors were used to indicated protein-coding genes (12) (red), tRNAs (22) (yellow), rRNAs (2) (green), and non-coding regions (grey). Tapeworm was stained with iron acid carmine.
a The comparison of nucleotide skewness of the full genomes for the mitogenome of Parabreviscolexniepini and other cestodes b, c Principal component (PC) analysis of the codon usage and amino acid usage in the PCGs of P.niepini and other cestodes. The first PC (PC1) and the second PC (PC2) of the codon usage and amino acid usage accounted for 96.7% and 98.08% of the variability, respectively. d G+T content of complete genomes and their individual elements. The six caryophyllideans are represented by triangles in a-c. Abbreviations: AH: Atractolytocestushuronensis; BO: Breviscolexorientalis; Ksp2: Khawia sp. 2; KSK: Khawiasinensis; Ksp1: Khawia sp. 1; PN: Parabreviscolexniepini.
https://binary.pensoft.net/fig/227011
Annotated mitochondrial genome of Parabreviscolexniepini.
Gene
Position
Size
Intergenic nucleotides
Codon
Anti-codon
From
To
Start
Stop
cox3
1
643
643
ATG
T
trnH
644
706
63
GTG
cytb
710
1798
1089
3
ATG
TAG
nad4L
1802
2062
261
3
ATG
TAG
nad4
2023
3255
1233
-40
ATG
TAG
trnQ
3252
3309
58
-4
TTG
trnF
3314
3378
65
4
GAA
trnM
3374
3436
63
-5
CAT
atp6
3440
3955
516
3
ATG
TAG
nad2
3960
4832
873
4
ATG
TAG
trnV
4835
4896
62
2
TAC
trnA
4895
4955
61
-2
TGC
trnD
4960
5021
62
4
GTC
nad1
5022
5915
894
GTG
TAG
trnN
5915
5980
66
-1
GTT
trnP
5984
6045
62
3
TGG
trnI
6045
6109
65
-1
GAT
trnK
6114
6175
62
4
CTT
nad3
6185
6523
339
9
GTG
TAG
trnS1
6522
6580
59
-2
TCT
trnW
6581
6646
66
TCA
cox1
6650
8210
1561
3
ATG
T
trnT
8208
8273
66
-3
TGT
rrnL
8274
9226
953
trnC
9227
9286
60
GCA
rrnS
9287
9993
707
trnL1
9994
10059
66
TAG
trnS2
10063
10125
63
3
TGA
trnL2
10127
10190
64
1
TAA
cox2
10758
11330
573
567
ATG
TAG
trnE
11331
11391
61
TTC
nad6
11392
11850
459
GTG
TAG
trnY
11859
11923
65
8
GTA
trnR
11925
11982
58
1
TCG
nad5
11983
13542
1560
GTG
TAA
trnG
13543
13606
64
TCC
Protein-coding genes and codon usage
Coalesced PCGs were 9999 bp in size, the lowest A+T content (56.6%) in all selected eucestodes (Suppl. material 2), which is also reflected in individual PCGs from 54% (nad3) to 63.2% (nad4L) (Suppl. material 3). ATG is the most commonly used initial codon for eight PCGs; exceptions are nad1, nad3, nad6, and nad5, which use GTG. Among the terminal codons, nine out of 12 are TAG, while nad5 uses TAA, cox3, and cox1 uses abbreviated stop codons (T--) (Table 1).
Codon usage, RSCU, and codon family proportion (corresponding to the amino acid usage) of P.niepini was investigated (Suppl. material S5). The four most abundant codon families (Phe, Val, Leu2, and Gly) encompass 38.41% of all codon families. Among these codon families, G+T-rich codons are favored over synonymous codons with lower G+T content in P.niepini (Suppl. material S5). This G+T preference corresponds well with the relatively high G+T content (Suppl. material S3) as well as G and T preference in the skewness analysis for PCGs (Suppl. material S2). Additionally, the principal component analyses (PCGs) suggested that the overall amino acid usage patterns of the unsegmented cestodes (except for KhawiasinensisKY486753) were apparently different from segmented cestodes (Fig. 2c). Noteworthy, in contrast to segmented cestodes, which have notably heightened A+T content at the 3rd codon position, these unsegmented cestodes (except KhawiasinensisKY486753) exhibit lower and/or similar A+T content to other elements of the mitogenome (Fig. 2d).
Transfer and ribosomal RNA genes
The two rRNAs, rrnL, and rrnS are 953 and 707 bp in size, with 59.6% and 60.4% A+T content, respectively (Suppl. material S3). All 22 commonly found tRNAs are present in the mitochondrial genome of P.niepini, ranging from 58 bp (trnQ and trnR) to 66 bp in size (trnN, trnW, trnT and trnL1), and adding up to 1381 bp in total coalesced length (Table 1 and Suppl. material S2). All of the secondary structures (predicted by MITOS and ARWEN) exhibit the conventional cloverleaf structure, except for trnS1(AGN) and trnR, which lack DHU arms. The unorthodox trnS1(AGN) and trnR were also found in the Caryophyllidea (Li et al. 2017) and the Anoplocephalidae (Guo 2016). Additionally, the anti-codon of trnS1(AGN) in the mitogenome of P.niepini is TCT, in contrast to other eucestodes, which use GCT, except for Khawiasinensis (KY486753) (Suppl. material S4).
Non-coding regions
The two major non-coding regions (NCR), 567 bp (NCR1) and 1428 bp (NCR2) in size, are located between trnL2 and cox2 and between trnG and cox3, respectively. The positions of the two NCR are consistently reported in other unsegmented tapeworms (see fig. s3 of Li et al. 2017). They have apparently higher A+T content (76.5% for NCR1 and 72.6% for NCR2) than other parts of the genome (Suppl. material S3). The NCR1 contain five tandem repeats (TRs), with two truncated TRs (repeat unit 1 and 5) and one T insertion in repeat unit 2 (Fig. 3). Two highly repetitive regions (HRR) were found in NCR2. HRR1 possess seven TRs, identical in size (40 bp). Repeat units 1–3 are identical in nucleotide composition. In comparison to the repeat units 1–3, repeat unit 4 differed in three nucleotides, while unit 5 and 6 differed in five nucleotides (Fig. 3). HRR2 possess 20 TRs, repeat units 1–19 are identical in size (57 bp) and nucleotide composition, whereas unit 20 is 46 bp long (Fig. 3).
Tandem repeats in two main non-coding regions of Parabreviscolexniepini.
https://binary.pensoft.net/fig/227012Phylogeny and gene order
The phylogenetic topology constructed using BI and ML methods show concordant branches and high statistical support. All bootstrap support values (BS) are higher than 68 and Bayesian posterior probabilities (BPP) are higher than 0.96. Parabreviscolexniepini exhibits the closest phylogenetic relationship with Breviscolexorientalis Kulakovskaya, 1962 and Atractolytocestushuronensis with robust support (Fig. 4). Moreover, the similarity of the codon usage pattern (Fig. 2b) lends further support to the phylogenetic affinity of P.niepini, B.orientalis and A.huronensis. The mitochondrial gene arrangement of P.niepini (Fig. 1) shows a consistent pattern in the Caryophyllidea, and obviously differs from the segment tapeworms (fig. S3 of Li et al. 2017).
Phylogenetic tree of five cestode orders inferred from maximum likelihood analysis with concatenated nucleotide sequence of all 36 genes (12 PCGs, 2 rRNAs, and 22 tRNAs). Bootstrap (BS)/bayesian posterior probability (BPP) support values are shown above the nodes, only BS < 100 and BPP < 1 are displayed. Scale bar represents the estimated number of substitutions per site.
The branch-site model tests based on the criteria of posterior probabilities ≥ 95% in the BEB analyses and in the likelihood ratio test (LRT) (P<0.05), found the amino acid positions V(6) and H(49) of P.niepinicytb (Suppl. material S6, Table 2) were under positive selection. Moreover, several sites in nad4, nad5, and cox3 were also identified to exhibit relaxed selective pressure (Table 2).
Summary of branch-site model analyses for genes cytb, nad4, nad5, nad2, cox3 and cox1 of Parabreviscolexniepini.
Gene
Null model
Parameter estimated
P value
Positively selected sites (BEB analysis)
Site class
0
1
2a
2b
cytb
Model A null
proportion
0.86659
0.0458
0.08322
0.0044
p < 0.05*
6V 0.970/49H 0.975
background w
0.02999
1
0.02999
1
foreground w
0.02999
1
13.90314
13.90314
nad4
M1a
proportion
0.77596
0.18941
0.02783
0.00679
p < 0.05*
146S 0.974
background w
0.0505
1
0.0505
1
foreground w
0.0505
1
11.95711
11.95711
nad5
M1a
proportion
0.66652
0.24542
0.06436
0.0237
p < 0.01**
117A 0.961/212T 0.966/
background w
0.0584
1
0.0584
1
303M 0.991
foreground w
0.0584
1
2.01044
2.01044
nad2
M1a
proportion
0.80968
0.09257
0.08772
0.01003
p < 0.01**
background w
0.03581
1
0.03581
1
foreground w
0.03581
1
97.38901
97.38901
cox3
M1a
proportion
0.76066
0.06085
0.16527
0.01322
p < 0.01**
32A 0.954/65S0.989/
background w
0.03801
1
0.03801
1
105Y 0.996/184T 0.957
foreground w
0.03801
1
2.15924
2.15924
cox1
M1a
proportion
0.93133
0.04455
0.02301
0.0011
p < 0.01**
background w
0.01974
1
0.01974
1
foreground w
0.01974
1
2.28474
2.28474
cytb
M1a
proportion
0.86658
0.0458
0.08322
0.0044
p < 0.01**
6V 0.970/49H 0.975
background w
0.02999
1
0.02999
1
foreground w
0.02999
1
13.90396
13.90396
Discussion
The different evolution rate of individual genes render phylogenetic analysis of cestode complicated or unreliable for some taxa; however, the complete mtDNA data was considered to provide the best interrelationship estimate (Waeschenbach et al. 2012). So far, the amount of mitogenome data available was limited. In this study, we sequenced and characterized the sixth mitogenome of caryophyllidean. The phylogenetic analysis constructed here placed caryophyllideans in the basal clade of eucestodes, and supported the position of unsegmented tapeworms as the earliest divergent group. In the caryophyllidean clade, the family Lytocestidae was found to be polyphyletic group, with lingeages Khawia spp. and Atractolytocestushuronensis recovered as distantly related. Atractolytocestushuronensis clustered robustly with Parabreviscolexniepini and Breviscolexorientalis of the family Capingentidae. Thus, further study is needed to recircumscribe the Lytocestidae.
The mitogenome of P.niepini showed the consistent characters of unsegmented tapeworms determined by Li et al. (2017), and differed significantly from the segmented tapeworms in codon usage and gene order. The unsegmented caryophyllideans consisted of two clades according to the fish hosts, cypriniform and siluriform (Xi et al. 2018). The tapeworms sequenced in the present study were all collected from cypriniform fishes; however, specimens from catostomid fishes have never been reported. Further studies are required to determine the similarity of the mitogenome of caryophyllideans from catostomid fish.
Conclusions
In this study, the complete mitogenome of the tapeworm Parabreviscolexniepini from a schizothoracine fish Schizopygopsisyounghusbandi was sequenced, annotated, and characterized. The mitogenome organization analysis indicated that it possessed a similar pattern to those caryophyllideans deposited in the GenBank database. Phylogenetic analysis based on mitogenomic data further confirmed the taxonomic validity of P.niepini, and its closest evolutionary relationship with Breviscolexorientalis and Atractolytocestushuronensis.
Acknowledgments
This work was supported by the Natural Sciences Foundation of China (31302222), the earmarked fund for China Agriculture Research System (CARS-45).
ReferencesAllenPJBennettK (2010) PASW statistics by SPSS: A practical guide: Version 18.0. Cengage Learning Press, Melbourne, 266–270.AltschulSFGishWMillerWMyersEWLipmanDJ (1990) Basic local alignment search tool.215(3): 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2BarčákDOrosMHanzelováVScholzT (2014) Phenotypic plasticity in Caryophyllaeusbrachycollis Janiszewska, 1953 (Cestoda: Caryophyllidea): does fish host play a role? Systematic Parasitology 88(2): 153–166. https://doi.org/10.1007/s11230-014-9495-2BensonG (1999) Tandem repeats finder: a program to analyze DNA sequences.27(2): 573–580. https://doi.org/10.1093/nar/27.2.573BerntMDonathAJühlingFExternbrinkFFlorentzCFritzschGPützJMiddendorfMStadlerPF (2013) MITOS: improved de novo metazoan mitochondrial genome annotation.69(2): 313–319. https://doi.org/10.1016/j.ympev.2012.08.023BrabecJScholzTKrálová-HromadováIBazsalovicsováEOlsonPD (2012) Substitution saturation and nuclear paralogs of commonly employed phylogenetic markers in the Caryophyllidea, an unusual group of non-segmented tapeworms (Platyhelminthes).42: 259–267. https://doi.org/10.1016/j.ijpara.2012.01.005BurlandTG (2000) DNASTAR’s Lasergene sequence analysis software. In: MisenerSKrawetzSA (Eds) Bioinformatics methods and protocols.132: 71–91.EspostiMDDe VriesSCrimiMGhelliAPatarnelloTMeyerA (1993) Mitochondrial cytochrome b: evolution and structure of the protein.1143(3): 243–271. https://doi.org/10.1016/0005-2728(93)90197-NFengYFengHLFangYHSuYB (2017) Characterization of the complete mitochondrial genome of Khawiasinensis belongs among platyhelminths, cestodes.177: 35–39. https://doi.org/10.1016/j.exppara.2017.04.005GuoA (2016) Monieziabenedeni and Monieziaexpansa are distinct cestode species based on complete mitochondrial genomes.166: 287–292. https://doi.org/10.1016/j.actatropica.2016.11.032HadleyW (2009) Springer-Verlag, New York, 182 pp. https://doi.org/10.1007/978-0-387-98141-3KalyaanamoorthySMinhBQWongTKFvon HaeselerAJermiinLS (2017) ModelFinder: fast model selection for accurate phylogenetic estimates.14(6): 587–589. https://doi.org/10.1038/nmeth.4285KatohKStandleyDM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability.30(4): 772–780. https://doi.org/10.1093/molbev/mst010KearseMMoirRWilsonAStones-HavasSCheungMSturrockSBuxtonSCooperADuranCThiererTAshtonBMeintjesPDrummondA (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.28(12): 1647–1649. https://doi.org/10.1093/bioinformatics/bts199LárusonÁJ (2017) Rates and relations of mitochondrial genome evolution across the Echinoidea, with special focus on the superfamily Odontophora.7(13): 4543–4551. https://doi.org/10.1002/ece3.3042LaslettDCanbackB (2008) ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences.24(2): 172–175. https://doi.org/10.1093/bioinformatics/btm573LeTHBlairDMcManusDP (2002) Mitochondrial genomes of parasitic flatworms.18(5): 206–213. https://doi.org/10.1016/S1471-4922(02)02252-3LiWXZhangDBoyceKXiBWZouHWuSGLiMWangGT (2017) The complete mitochondrial DNA of three monozoic tapeworms in the Caryophyllidea: a mitogenomic perspective on the phylogeny of eucestodes. Parasites & Vectors 10(1): 314. https://doi.org/10.1186/s13071-017-2245-yRonquistFTeslenkoMvan der MarkPAyresDLDarlingAHöhnaSLargetBLiuLSuchardMAHuelsenbeckJP (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.61(3): 539–542. https://doi.org/10.1093/sysbio/sys029ScholzTOrosM (2017) Caryophyllidea van Beneden in Carus, 1863. In: CairaJNJensenK (Eds) Planetary Biodiversity Inventory (2008–2016): Tapeworms from vertebrate bowels of the earth., 47–64.SilvestroDMichalakI (2011) raxmlGUI: a graphical front-end for RAxML.12(4): 335–337. https://doi.org/10.1007/s13127-011-0056-0TalaveraGCastresanaJ (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.56(4): 564–577. https://doi.org/10.1080/10635150701472164WaeschenbachAWebsterBLLittlewoodDTJ (2012) Adding resolution to ordinal level relationships of tapeworms (Platyhelminthes: Cestoda) with large fragments of mtDNA.63(3): 834–47. https://doi.org/10.1016/j.ympev.2012.02.020XiBWOrosMChenKXieJ (2018) A new monozoic tapeworm, Parabreviscolexniepini n. g., n. sp. (Cestoda: Caryophyllidea), from schizothoracine fishes (Cyprinidae: Schizothoracinae) in Tibet, China.117: 347–354. https://doi.org/10.1007/s00436-017-5682-9YangZ (2007) PAML 4: phylogenetic analysis by maximum likelihood.24(8): 1586–1591. https://doi.org/10.1093/molbev/msm088YangZWongWSNielsenR (2005) Bayes empirical bayes inference of amino acid sites under positive selection.22(4): 1107–1118. https://doi.org/10.1093/molbev/msi097ZhangD (2016a) BioSuite software. https://github.com/dongzhang0725/BioSuiteZhangD (2016b) MitoTool software. https://github.com/dongzhang0725/MitoToolZhangDZouHWuSGLiMJakovlicIZhangJChenRWangGTLiWX (2017a) Sequencing, characterization and phylogenomics of the complete mitochondrial genome of Dactylogyruslamellatus (Monogenea: Dactylogyridae).29: 1–12. https://doi.org/10.1017/S0022149X1700089XZhangDZouHWuSGLiMJakovlićIZhangJChenRWangGTLiWX (2017b) Sequencing of the complete mitochondrial genome of a fish-parasitic flatworm Paratetraonchoidesinermis (Platyhelminthes: Monogenea): tRNA gene arrangement reshuffling and implications for phylogeny. Parasites & Vectors 10(1): 462. https://doi.org/10.1186/s13071-017-2404-1ZouHJakovlicIChenRZhangDZhangJLiWXWangGT (2017) The complete mitochondrial genome of parasitic nematode Camallanuscotti: extreme discontinuity in the rate of mitogenomic architecture evolution within the Chromadorea class. BMC Genomics 18(1): 840. https://doi.org/10.1186/s12864-017-4237-xSupplementary materials10.3897/zookeys.783.24674.suppl114146941937EF6C-B4CA-59C9-91D5-5144586D0409
Table S1. Primers used to amplify and sequence the mitochondrial genomes of Parabreviscolexniepini
Data type: molecular data
https://binary.pensoft.net/file/227014This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.Bing-Wen Xi, Dong Zhang, Wen-Xiang Li, Bao-Juan Yang, Jun Xie10.3897/zookeys.783.24674.suppl2141469685B8D40A-CC93-55AB-8521-BC3FECF3E176
Table S2. The list of cestodes species and outgroups used for comparative mitogenomic and phylogenetic analyses
Data type: molecular data
https://binary.pensoft.net/file/227015This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.Bing-Wen Xi, Dong Zhang, Wen-Xiang Li, Bao-Juan Yang, Jun Xie10.3897/zookeys.783.24674.suppl314146982E7808E5-6478-58EF-9AE9-E40219454DDD
Table S3. Nucleotide composition and skewness of different elements of the studied mitochondrial genome
Data type: molecular data
https://binary.pensoft.net/file/227016This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.Bing-Wen Xi, Dong Zhang, Wen-Xiang Li, Bao-Juan Yang, Jun Xie10.3897/zookeys.783.24674.suppl414147004484DCBF-27CA-5ED6-9CDB-0670F21652E1
Figure S1. Sequence alignment of trnS1 for Parabreviscolexniepini and other cestodes
Data type: molecular data
Explanation note: The position of the anticodon sequences was indicated.
https://binary.pensoft.net/file/227017This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.Bing-Wen Xi, Dong Zhang, Wen-Xiang Li, Bao-Juan Yang, Jun Xie10.3897/zookeys.783.24674.suppl51414702F5D5F5A2-9FEB-5B36-98BF-8D5761A4325C
Figure S2. Relative Synonymous Codon Usage (RSCU) of Parabreviscolexniepini
Data type: molecular data
Explanation note: Codon families are labelled on the x-axis. Values on the top of the bars denote amino acid usage.
https://binary.pensoft.net/file/227018This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.Bing-Wen Xi, Dong Zhang, Wen-Xiang Li, Bao-Juan Yang, Jun Xie10.3897/zookeys.783.24674.suppl614147044A453A61-8868-53DE-BCEB-4AA44700483F
Figure S3. Amino acid alignment for sites under positive selection for cytb
Data type: molecular data
Explanation note: The positions of each site are denoted on the top. An asterisk * denotes sites with posterior probability value ≥ 0.95 in Bayes Empirical Bayes (BEB) analysis.
https://binary.pensoft.net/file/227019This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.Bing-Wen Xi, Dong Zhang, Wen-Xiang Li, Bao-Juan Yang, Jun Xie