Research Article |
Corresponding author: Yu Zhang ( biozy@alumni.ust.hk ) Academic editor: Pavel Stoev
© 2024 Ying Zhu, JiaJie Huang, Ronald Sluys, Yi Liu, Ting Sun, An-Tai Wang, Yu Zhang.
This 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.
Citation:
Zhu Y, Huang J, Sluys R, Liu Y, Sun T, Wang A-T, Zhang Y (2024) Integrative description of a new species of Dugesia (Platyhelminthes, Tricladida, Dugesiidae) from southern China, with its complete mitogenome and a biogeographic evaluation. Zoosystematics and Evolution 100(1): 167-182. https://doi.org/10.3897/zse.100.114016
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A new species of freshwater flatworm of the genus Dugesia from Guangdong Province in China is described through an integrative approach, including molecular and morphological data, as well as mitochondrial genome analysis. The new species, Dugesia ancoraria Zhu & Wang, sp. nov., is characterised by: (a) a highly asymmetrical penis papilla, provided with a hunchback-like dorsal bump; (b) a short duct between seminal vesicle and ejaculatory duct; and (c) a postero-ventral course of the ejaculatory duct, which opens to the exterior at the subterminal, ventral part of the penis papilla. The molecular phylogenetic tree obtained from the concatenated dataset of four DNA markers (18S rDNA, ITS-1, 28S rDNA, COI) facilitated determination of the phylogenetic position of the new species, which shares a sister-group relationship with a small clade, comprising D. notogaea Sluys & Kawakatsu, 1998 from Australia and D. bengalensis Kawakatsu, 1983 from India. The circular mitogenome of the new species is 17,705 bp in length, including 12 protein coding genes, two ribosomal genes, and 22 transfer RNAs. Via analysis of gene order of mitochondrial genomes, the presently available pattern of mitochondrial gene rearrangement in the suborder Continenticola is discussed.
biogeography, Dugesia, mitogenome, molecular phylogeny, taxonomy
The distributional range of freshwater planarians of the genus Dugesia Girard, 1850 covers a large part of the Old World and Australia (cf.
From the approximately 110 known species of Dugesia, thus far only 12 species have been recorded from China, namely, D. japonica Ichikawa & Kawakatsu, 1964; D. ryukyuensis Kawakatsu, 1976; D. sinensis Chen & Wang, 2015; D. umbonata Song & Wang, 2020; D. semiglobosa Chen & Dong, 2021; D. majuscula Chen & Dong, 2021; D. circumcisa Chen & Dong, 2021; D. verrucula Chen & Dong, 2021; D. constrictiva Chen & Dong, 2021; D. gemmulata Sun & Wang, 2022; D. adunca Chen & Sluys, 2022; and D. tumida Chen & Sluys, 2022. The present study adds a new species of Dugesia to the Chinese fauna by describing it through an integrative approach, involving morphological, molecular phylogenetic and mitogenomic analyses. Among these methods, morphological characters, especially the anatomy of the copulatory apparatus, form the main source for the description and identification of the new species.
Since the mitogenome is characterized by strict gene homology and uniparental inheritance without recombination, and contains genes that evolve at different rates, mitochondrial gene order is considered as a strong genetic marker for resolving the phylogenetic position of new species (
Specimens were collected from a narrow artificial canal running from Wenshan lake in Shenzhen city, Guangdong Province, China (22°31'55"N, 113°56'21"E) on 10 May 2021 (Fig.
After starvation for three days, total DNA was extracted from three sexual individuals using the E.Z.N.A.TM Mollusc DNA Isolation Kit (Omega, Norcross, GA, USA). Four gene fragments, namely 18S ribosomal gene (18S rDNA), 28S ribosomal gene (28S rDNA), ribosomal internal transcribed spacer-1 (ITS-1), and cytochrome C oxidase subunit I (COI), were amplified by polymerase chain reaction (PCR). We used 2×Taq Plus Master Mix II (Vazyme, China) to amplify 18S rDNA, 28S rDNA, ITS-1, and COI. Primers used for amplification and the PCR protocol are listed in Table
Gene | Primer | Sequence (5'-3') | Reference | PCR protocol |
---|---|---|---|---|
COI | COIEFMF | Forward: GGW GGK TTT GGW AAW TG | 94 °C 5 min, 35× (94 °C 50 s, 50 °C 45 s, 72 °C 45 s); 72 °C 7 min | |
COIRSong | Reverse: GWG CAA CAA CAT ART AAG TAT CAT | |||
ITS-1 | ITS9F | Forward: GTA GGT GAA CCT GCG GAA GG | Baguñà et al. 1999 | 98 °C 5 min, 30× (98 °C 30 s, 46 °C 45 s, 72 °C 30 s); 72 °C 7 min |
ITSR | Reverse: TGC GTT CAA ATT GTC AAT GAT C | |||
18S rDNA | 18S 1F | Forward: TAC CTG GTT GAT CCT GCC AGT AG | Carranza et al. 1996 | 94 °C 5 min, 40× (95 °C 50 s, 50 °C 45 s, 72 °C 50 s); 72 °C 7 min |
18S 9R | Reverse: GAT CCT TCC GCA GGT TCA CCT AC | |||
28S rDNA | 28S 1F | Forward: TAT CAG TAA GCG GAG GAA AAG | Álvarez-Presas et al. 2008 | 94 °C 5 min, 40× (94 °C 50 s, 52 °C 45 s, 72 °C 50 s); 72 °C 7 min |
28S 6R | Reverse: GGA ACC CCT TCT CCA CTT CAG T |
GenBank accession numbers of sequences for species taxa used in the phylogenetic analyses.
To determine the phylogenetic position of the new species within the genus Dugesia, we generated datasets consisting of marker gene sequences (18S rDNA, 28S rDNA, ITS-1, and COI; see Table
Nuclear ribosomal markers were aligned with MAFFT (online version 7: MAFFT alignment and NJ / UPGMA phylogeny (cbrc.jp),
Phylogenetic trees were constructed by Maximum Likelihood (ML) and Bayesian Inference (BI) methods. For ML, standard bootstrap analysis with 1,000 replications was performed by IQ-TREE v1.6.2 (
After having been starved for three days, the mitochondrial DNA of an asexual specimen of D. ancoraria was extracted (due to absence of sexual specimens at that time) using Animal mitochondrial DNA column extraction kit (PCR Grade; BioLebo Technology, Beijing China), followed by amplification of mitochondrial DNA using a REPLI-g Midi Kit (QIAGEN, Hilden, Germany). We compared the COI gene of the three sexual individuals with that of the asexual individual for mitochondrial extraction via megablast and, thus, found that they were perfectly identical. Paired-end sequencing was conducted on the Illumina Hiseq 2500 platform (BGI, Guangzhou, China). The mitogenome sequences were assembled using MitoFinder (
Species and corresponding GenBank accession numbers of mitochondrial genomes used for mitochondrial analysis.
Species | GenBank | Species | GenBank |
---|---|---|---|
Amaga expatria | MT527191 | Obama sp. | NC026978 |
Bipalium kewense | NC045216 | Obrimoposthia wandeli | NC050050 |
Crenobia alpina | KP208776 | Parakontikia ventrolineata | MT081960 |
Dugesia ancoraria* | OR400685 | Phagocata gracilis | KP090060 |
Dugesia japonica | NC016439 | Platydemus manokwari | MT081580 |
Dugesia constrictiva | OK078614 | Schmidtea mediterranea | JX398125 |
Dugesia ryukyuensis | AB618488 |
For the morphological analysis, the flatworms were starved for three days prior to the preparation of histological sections according to procedures described by
au: auricle; bc: bursal canal; ca: common atrium; cb: copulatory bursa; cm: circular muscle; d: diaphragm; db: distal bulge; du: duct; e: eye; ed: ejaculatory duct; esv: extension seminal vesicle; go: gonopore; hb: hunchback bump; ie: inner epithelium; lm: longitudinal muscle; lod: left oviduct; lvd: left vas deferens; ma: male atrium; od: oviduct; oe: outer epithelium; ov: ovary; pg: penis glands; ph: pharynx; pp: penis papilla; rod: right oviduct; rvd: right vas deferens; sg: shell glands; sv: seminal vesicle.
The phylogenetic trees obtained by BI and ML from the concatenated dataset (with the order 18S rDNA–28S rDNA–ITS-1–COI) showed similar topologies and supported nodes (Fig.
Maximum likelihood phylogenetic tree topology inferred from the concatenated dataset (18S rDNA, ITS-1, 28S rDNA and COI). Numbers at nodes indicate support values (bootstrap/ posterior probability). Asterisks (*) indicate support values lower than 50% bs/0.50 pp, or posterior probability not applicable to this node, because of different topologies of trees generated by BI and ML methods. Scale bar: substitutions per site.
The complete, circular mitochondrial genome of Dugesia ancoraria is 17,705 bp in length, and includes 12 of the 13 protein-coding genes of mitochondrial genomes (atp8 was not found), two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes, which are arranged as follows: cox1-E-nad6-nad5-S2-D-R-cox3-I-Q-K-atp6-V-nad1-W-cox2-P-nad3-A-nad2-M-H-F-rrnS-L1-Y-G-S1-rrnL-L2-T-C-N-cob-nad4l-nad4. GC content is 23.77%, while a positive GC skew ([G-C]/[G+C] = 0.323) indicated the occurrence of more Gs than Cs (Fig.
Arrangement of the mitochondrial genome of Dugesia ancoraria. Outer circle: annotation of genes, with protein-coding genes, ribosomal RNAs and transfer RNAs represented by cyan, orange, and red, respectively. Intermediate circle: sequencing coverage, with green colour indicating coverage greater than 95% average coverage. Inner circle, with the blue colour indicating GC content and the thin orange circle indicating 50% of GC content. The picture in the middle represents an individual of D. ancoraria.
Both the ML and BI trees obtained from 12 protein coding genes (PCGs) have highly supported clades, excepting one node with a bootstrap support lower than 70%. Since the topologies of the ML and BI trees are basically identical, we integrated them into one phylogenetic tree. In the integrated tree, Crenobia alpina (Dana, 1766) and Phagocata gracilis (Haldeman, 1840) together form a clade that shares a sister-group relationship with a clade that is composed of two smaller clades, one comprising land planarians (Geoplanidae) and the other constituted by dugesiid freshwater planarians (Dugesiidae). The latter family forms a well-supported monophyletic group, in which D. ancoraria is sister to D. ryukyuensis with high support values (100% bs; 1.00 pp) (Fig.
Possible mechanisms of mitochondrial gene rearrangement in Continenticola estimated using CREx, with reference to phylogenetic relationships. On the left-hand side, phylogenetic tree obtained from Maximum likelihood and Bayesian analysis of the concatenated dataset for the protein-coding and rRNA genes within mitochondrial genomes; numbers at nodes indicate support values (pp/bs); Asterisks (*) indicate that bootstrap is not applicable to these nodes because of different topologies of trees generated by BI and ML methods. Pink lines connect species that share the same gene order. On the right-hand side, changes of gene order in mitochondrial genomes in several species of triclad; protein-coding genes in blue, tRNA genes in white, rRNA genes in grey; lines with different colours indicate transpositions of different genes; red lines indicate tandem duplication random loss (TDRL) events between species, while the orange colour indicates where TDRL events occurred.
The gene order of rRNAs, PCGs and tRNAs of D. ancoraria and other species used in our phylogenetic analysis are shown in Fig.
Order Tricladida Lang, 1884
Suborder Continenticola Carranza, Littlewood, Clough, Ruiz-Trillo, Baguñà & Riutort, 1998
Family Dugesiidae Ball, 1974
Genus Dugesia Girard, 1850
Holotype : PLA-0251, a narrow artificial canal of Wenshan lake, Shenzhen city, Guangdong Province, China, 22°31'55"N, 113°56'21"E, 10 May 2021, coll. MY Xia and co-workers, sagittal sections on 14 slides.
Paratypes : PLA-0252, ibid., sagittal sections on 12 slides; PLA-0253, ibid., transverse sections on 35 slides; RMNH.VER.21525.1, ibid., sagittal sections on 12 slides.
Specimens were collected from a narrow artificial canal running from Wenshan lake (22°31'55"N, 113°56'21"E), which is located in Shenzhen city, Guangdong Province, China (Fig.
Dugesia ancoraria is characterised by the following characters: highly asymmetrical penis papilla, provided with a hunchback-like dorsal bump; vasa deferentia opening symmetrically into the mid-lateral section of the more or less ellipsoidal seminal vesicle, which may give rise to a narrow dorsal extension; long and narrow duct connecting seminal vesicle with small diaphragm; ejaculatory duct with a subterminal opening through the ventral surface of the penis papilla; asymmetrical oviducal openings, with the right oviduct opening into a section of the bursal canal that bends ventrally to communicate with the common atrium; the left oviduct opens into the bursal canal at the point where the latter meets the common atrium.
The specific epithet is derived from Latin adjective ancorarius, of the anchor, and alludes to the penis papilla, which has a hunchback-shape, reminiscent of an anchor, more or less.
Sexualized specimens measured 8.43–9.11 mm in length and 1.13–1.18 mm in width (n = 4; Fig.
The ground colour of the dorsal surface is brown, dotted with dark brown and white specks; ventral surface much paler than dorsal surface; the body margin is pale (Fig.
The cylindrical pharynx is positioned at about 1/2 of the body and measures about 1/5 of the total body length; the mouth opening is situated at the posterior end of the pharyngeal pocket. The musculature of the pharynx consists of an outer, subepithelial layer of circular muscle, followed by a layer of longitudinal muscle, while the inner musculature is composed of a thick, subepithelial layer of circular muscle, followed by 2–3 layers of longitudinal muscle. The gonopore is situated at about 1/5 of the length of the body, as measured from the posterior body margin (Fig.
The globular ovaries are located at 1/6 – 1/7 of the distance between the brain and the root of pharynx. From the ovaries, the nucleated oviducts run ventrally in a caudal direction and open separately and asymmetrically into the female reproductive apparatus. Posterior to the gonopore, the right oviduct turns antero-medially and then opens into a section of the bursal canal that bends ventrally to communicate with the common atrium. The left oviduct opens into the bursal canal at the point where the latter meets the common atrium. (Figs
Dugesia ancoraria, holotype PLA-0101, sagittal sections, anterior to the right. A. Photomicrograph showing copulatory bursa, ejaculatory duct, penis papilla, and seminal vesicle; B. Photomicrograph showing copulatory bursa, bursal canal, and gonopore; C. Photomicrograph showing copulatory bursa, and bursal canal. Scale bars: 100 μm.
A large sac-shaped copulatory bursa is situated immediately behind the pharyngeal pocket and occupies the entire dorso-ventral space; it is lined with a layer of vacuolated, nucleated cells (Figs
The bursal canal is lined by a nucleated, columnar glandular epithelium, which is underlain with a layer of longitudinal muscles, followed by 1–4 layers of circular muscles. Along the ventral coat of muscle, ectal reinforcement is present in the form of a single layer of longitudinal muscle running from about the opening of the canal into the common atrium to about 1/3 of the length of the bursal canal (Fig.
The large, near-globular testicular follicles are situated dorsally and extend posteriorly from a short distance behind the brain to well beyond the copulatory apparatus. The male atrium comprises most of the dorso-ventral space of the body (Figs
Dugesia ancoraria, paratype RMNH.VER.21525.1, sagittal sections. A. Photomicrograph showing ejaculatory duct, penis papilla, and seminal vesicle; B. Photomicrograph showing copulatory bursa, common atrium, and gonopore; C. Photomicrograph showing copulatory bursa, and bursal canal. Scale bars: 100 μm.
The vasa deferentia have expanded to form spermiducal vesicles that are packed with sperm. At the level of the penis bulb, the ducts recurve, while decreasing in diameter, run postero-medially for some distance and, thereafter, recurve anteriad before opening separately into the mid-lateral portion of the seminal vesicle (Figs
The male atrium is lined by a nucleated epithelium. The dorsal part of the male atrium is surrounded by a layer of circular muscle, followed by 1–2 layers of longitudinal muscle, while a subepithelial layer of circular muscle, followed by a layer of longitudinal muscle constitutes the musculature on the ventral part of the atrium. The male atrium communicates with the common atrium via a broad opening. The common atrium is lined with a nucleated epithelium, which is underlain by 2–3 layers of circular muscle (Figs
In our phylogenetic tree (Fig.
In the phylogenetic trees obtained from the concatenated dataset (Fig.
With respect to the geographical distribution within China of other species of Dugesia, in relation to the distribution of D. ancoraria, the following should be noted. Dugesia japonica has a wide distribution, as it has been reported from the eastern, southern and northern regions of China, while the remaining 11 species are found only in southern China. Among these species, D. semiglobosa and D. majuscula were documented in Hainan province, D. circumcisa and D. adunca in Guangxi province, with these two provinces being relatively close to the locality of D. ancoraria in Guangdong. Dugesia tumida and D. sinensis occur also in Guangdong Province, while they share only a very distant relationship with the new species D. ancoraria. Other species, like D. umbonata, were found in Jiangsu province and D. gemmulata in Guizhou. Although these two species are geographically far distant from each other, they share a close relationship.
The close relationship between Chinese D. ancoraria and Australian D. notogaea, with the latter being the sister-species of Malaysian D. bengalensis, is interesting from a historical biogeographic perspective. This pattern of relationships basically agrees with that uncovered by
In our mitogenome analysis, trnT was the only tRNA that could not be automatically annotated by MITOS. However, through translating nucleotides of 12 PCGs to amino acid with Expacy (http://web.expasy.org/translate/), 63 sites of threonine, which is coded by ACN, were found. These results thus support the existence of trnT, which is required for the reading of the triplet of the genetic code (ACN). Therefore, we annotated trnT manually, based on homology comparisons with other species in the family Dugesiidae. Specifically, we aligned the complete mitogenome of D. ancoraria with three species belonging to family Dugesiidae, namely D. japonica, D. ryukyuensis and D. constrictiva and found a homologous sequence (60 bp) among these five species, which is particularly conserved at 5’ end (AGAA) and 3’ end (TTCTT). In addition, the position of trnT of all reported species belonging to Dugesiidae is very conserved and is situated between trnL2 and trnC. Interestingly, the putative trnT in D. ancoraria is also located between trnL2 and trnC, providing another line of evidence in support of the annotation. Furthermore, we predicted the secondary structure of trnT manually and presented this through RNAalifold WebServer (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi) and were surprised to find that the predicted result is not a typical cloverleaf structure with an absence of the DHU stem. By comparing the free energy between the two predicted structures, we found that the free energy with DHU stem (-1.20 kcal/mol) is higher than the one without DHU stem (-4.50 kcal/mol). The absence of the DHU stem in trnT also occurred in several other species of Tricladida, such as Dugesia japonica, D. ryukyuensis, Crenobia alpina, Obama sp. and Schmidtea mediterranea. (
In addition, some common features can be discovered in the mitochondrial gene order of the investigated species. Among the five species of Geoplanidae, locations of trnT are variable, in that transpositions of trnT occur in each of two adjacent species in the mitogenome tree, from B. kewense to P. ventrolineata. Besides, trnF is located at 3’ downstream of nad4, with the only exception being Crenobia alpina. The gene rearrangement of the maricolan Obrimoposthia wandeli differs considerably from species belonging to the suborder Continenticola. Therefore, transformation of gene order in O. wandeli to species of the Continenticola may require multiple rearrangements, including reversals, transpositions, and TDRL. Similarly, several TDRL events are required to go from the Geoplanoidea gene order to those of the Dugesiidae species. It is also noteworthy that two species (D. ancoraria and D. constrictiva) with identical mitochondrial gene order occur in two separate clades. Since gene rearrangements appear to be rare events that may not arise independently in separate lineages (
A highly asymmetrical penis papilla with both a proximal as well as distal dorsal bumps is the most characteristic feature of Dugesia ancoraria. Similar bumps are known only from D. gibberosa Stocchino & Sluys, 2017. However, in D. gibberosa the penis papilla has a different, ventro-caudal orientation, while its ejaculatory duct opens terminally at the tip of the papilla, in contrast to the subterminal opening in D. ancoraria. Moreover, in D. gibberosa the bursal canal is surrounded by a very thick layer of circular muscle, while its ectal reinforcement extends more than halfway along the bursal canal. In contrast, the bursal canal musculature in D. ancoraria is thinner and the ectal reinforcement weakly developed. Furthermore, D. ancoraria and D. gibberosa are far removed from each other in the phylogenetic tree (Fig.
Our molecular analyses, particularly the concatenated dataset, showed that D. ancoraria shares a sister-group relationship with Australian D. notogaea and Malaysian D. bengalensis. Morphologically, all three species have an asymmetrical penis papilla, with the dorsal lip being thicker than ventral lip, and a duct between seminal vesicle and ejaculatory duct. In addition, D. ancoraria and D. notogaea share the condition in which the oviducts open asymmetrically into the bursal canal. However, there are also clear differences between these three species. For example, in D. bengalensis and D. ancoraria, the ejaculatory duct has a subterminal opening at the tip of the penis papilla, whereas D. notogaea exhibits a terminal opening. In D. bengalensis and D. notogaea, the vasa deferentia open through the postero-lateral roof of the seminal vesicle, whereas in D. ancoraria the ducts open into the mid-lateral portion of the vesicle.
Although D. gibberosa is the only other species with two clear dorsal bumps on the penis papilla, there are a number of Dugesia species that deserve some comparison with D. ancoraria, viz., D. astrocheta Marcus, 1958, D. austroasiatica Kawakatsu, 1985, and D. tamilensis Kawakatsu, 1980. Dugesia astrocheta has a clear, proximal hunchback bump on its very asymmetrical penis papilla, while there is also some indication of a distal bump or bulge (cf.
This study was supported by grants from Cultivation of Guangdong College Students’ Scientific and Technological Innovation (“Climbing Program” Special Funds; grant no. pdjh2023b0449), China Undergraduate Training Program for Innovation and Entrepreneurship (grant no. S202210590072) and the Shenzhen University Innovation Development Fund (grant no. 2021258), as well as grants from the Scientific and Technical Innovation Council of Shenzhen Government (grant nos. jcyj20210324093412035 and kcxfz20201221173404012) and Special Program of Key Sectors in Guangdong Universities (grant no. 2022ZDZX4040). We are grateful to Meng-yu Xia for assistance with sample collection.
Bayesian inference phylogenetic tree topology
Data type: docx
Explanation note: Bayesian inference phylogenetic tree topology inferred from the concatenated dataset (18S rDNA, IT-1, 28S DNA and COI). Numbers at nodes indicate support values (posterior probability). Scare bar: substitutions per site.