Characterization of the complete mitochondrial genome of Desmaulus extinctorium (Littorinimorpha, Calyptraeoidea, Calyptraeidae) and molecular phylogeny of Littorinimorpha

Abstract

For the purpose of determining the placement of Calyptraeidae within the Littorinimorpha, we hereby furnish a thorough analysis of the mitochondrial genome (mitogenome) sequence of Desmaulus extinctorium. This mitogenome spans 16,605 base pairs and encompasses the entire set of 37 genes, including 13 PCGs, 22 tRNAs and two rRNAs, with an evident AT bias. Notably, tRNA^Ser1 and tRNA^Ser2 lack dihydrouracil (DHU) arms, resulting in an inability to form a secondary structure. Similarly, tRNA^Ala lacks a TΨC arm, rendering it incapable of forming a secondary structure. In contrast, the remaining tRNAs demonstrate a characteristic secondary structure reminiscent of a cloverleaf. A comparison with ancestral gastropods reveals distinct differences in three gene clusters (or genes), encompassing 15 tRNAs and eight PCGs. Notably, inversions and translocations represent the major types of rearrangements observed in D. extinctorium. Phylogenetic analysis demonstrates robust support for a monophyletic grouping of all Littorinimorpha species, with D. extinctorium representing a distinct Calyptraeoidea clade. In summary, this investigation provides the first complete mitochondrial dataset for a species of the Calyptraeidae, thus providing novel insights into the phylogenetic relationships within the Littorinimorpha.

Introduction

Mitochondria are double—membrane—coated organelles found in most eukaryotes. Although most of a cell’s DNA is contained in the nucleus, mitochondria have their own genome, known as the mitogenome. Attributable to its profoundly conserved characteristics, absence of extensive recombination, maternal inheritance, and elevated mutation rate [1–3], the mitogenome has found extensive utility in the realms of comparative and evolutionary genomics [4], species identification, population genetics [5], molecular evolution, and phylogenetic relationships [6,7]. In particular, phylogeny based on complete mitochondrial genomes have demonstrated improved resolution compared to phylogenetic trees inferred from partial gene fragments such as COI and 16S rRNA [8]. In recent years, mitochondrial genome sequencing and amplification techniques have rapidly developed, and mitochondrial genomes have been extensively utilized to reconstruct phylogenetic trees of different gastropods. For instance, Yang et al [9] sequenced the complete mitochondrial genomes of nine Nassariidae species and compared them with eight previously reported Nassariidae genomes, identifying the phylogenetic placement of these nine species within the gastropod clade. Genetic distance analysis and phylogenetic analysis both supported the distant relationship of Nassarius jacksonianus and Nassarius acuticostus to other Nassarius species. Furthermore, Yang et al [10] sequenced the complete mitochondrial genomes of two nassarids (Neogastropoda: Nassariidae: Nassarius), Nassarius glans and Nassarius siquijorensis, identifying the phylogenetic positions of these two species within Nassarius. In addition, Lee et al [11] reported the complete mitochondrial genome of Semisulcospira gottschei (Gastropoda: Caenogastropoda) and identified its phylogenetic relationship within Caenogastropoda. The study revealed that Semisulcospira gottschei is the closest relative to Semisulcospira coreana, and it was classified within the family Cerithioidea.

Desmaulus extinctorium is a marine snail that inhabits sandy substrates ranging from low intertidal to several metres subtidally. It belongs to the class Gastropoda, subclass Caenogastropoda, order Littorinimorpha, superfamily Calyptraeoidea, family Calyptraeidae, genus Desmaulus. Desmaulus extinctorium is abundant in southern China and Hongkong, with a widespread presence in the Indo-West Pacific region as well [12]. Previous research on this family has predominantly focused on morphology and growth [13–15]. Calyptraeid gastropods are known for their taxonomic challenges stemming from their simple, phenotypically variable shells [16]. As such, only a few studies have explored the phylogenetic analysis of this family. For instance, Cunha et al [17] conducted sequencing on a segment of the mitochondrial genome from the calyptraeoidean species Calyptraea chinensis, which belongs to the Littorinimorpha. Phylogenetic investigations have revealed that the Littorinimorpha does not form a monophyletic cluster. Meanwhile, Collin [18] examined how development modes influence the phylogeography and population dynamics of North Atlantic Crepidula (Gastropoda: Calyptraeidae). She created haplotype trees for each clade using 640 bp COI sequences. Examination of both the tree topology and AMOVA revealed that species undergoing direct development (hatching as benthic juveniles) displayed a more conspicuous population structure in comparison to those species undergoing planktonic development. Prior to our study, a complete mitochondrial genome of Calyptraeidae had not been uploaded to GenBank.

Littorinimorpha is a substantial order within Caenogastropoda (Class Gastropoda), encompassing 16 superfamilies according to the WoRMS database. Among marine snails, Caenogastropoda stands as the dominant group in terms of species numbers, diversity of habitats, ecological importance and behaviors. The current classification within Littorinimorpha was mainly established by Bouchet and Rocroi [19]. While Colgan et al [20] conducted an exhaustive phylogenetic investigation of Caenogastropoda, the interrelationships among families and superfamilies within the Caenogastropoda clade remain predominantly unresolved. The monophyly of both Littorinimorpha and Neogastropoda has been a topic of ongoing debate [21]. Cunha et al [22] conducted the sequencing of complete mitochondrial genomes for seven previously unanalyzed gastropod species. Subsequent phylogenetic analysis led to the rejection of the monophyletic status of Neogastropoda, attributed to the incorporation of Littorinimorpha lineages within this cluster. Additionally, Zhao et al. [23] sequenced the complete mitochondrial genomes of intermediate host snails for Schistosoma and performed a phylogenetic analysis, revealing that neither Neogastopoda nor Littorinimorpha were monophyletic groups. Consequently, further research is necessary to refine the phylogenetic relationship within Caenogastropoda. Riedel [24] established the superfamily Ficoidea, separate from the Tonnoidea, but based on the sequencing of the complete mitochondrial genome of Ficus variegata Wang et al. [25] demonstrated that it fits within the Tonnoidea. And then, Jiang et al [26] reconstructed the phylogenetic tree of Littorinimorpha by sequencing the complete mitochondrial genome of two species in the Stromboidea. The findings provided evidence for the existence of three significant clades within Littorinimorpha: 1) Stromboidea, Tonnoidea, Littorinoidea, and Naticoidea, 2) Rissooidea alongside Truncatelloidea, and 3) Vermetoidea.

In this investigation, we have accomplished the comprehensive sequencing of the mitogenome for D. extinctorium. Furthermore, an elucidation of the gene structure within the mitogenome of D. extinctorium has been presented, coupled with a phylogenetic scrutiny encompassing 51 species from the Littorinimorpha taxon. This analysis is predicated upon the nucleotide sequences of 13 PCGs. As an outcome of this study, there has been an augmentation of the mitochondrial genome repertoire for Littorinimorpha, along with the provision of data requisite for subsequent phylogenetic assessments within the Littorinimorpha clade.

Materials and methods

Sampling and DNA extraction

We obtained a specimen of D. extinctorium from Ningde, Fujian Province, China (27°04′812N, 120°24′158″E). The initial morphological classification of these samples involved expert consultation with taxonomists at Zhejiang Ocean University’s Marine Biological Museum. After collection, the specimen was rapidly submerged in absolute ethanol and stored at -20°C. To confirm its classification, we relied on morphological traits, and we preserved fresh tissues in absolute ethanol before DNA extraction. We used the salt-extraction technique [27] to isolate complete genomic DNA, which was then stored at -20°C.

Genome sequencing, assembly and annotation

The mitogenomes of D. extinctorium were sequenced by Origin gene Co. Ltd., situated in Shanghai, China, employing the Illumina HiSeq X Ten sequencing platform. HiSeq X Ten libraries were prepared, incorporating an insert size ranging from 300 to 500 base pairs, sourced from genomic DNA samples. Each library yielded approximately 10 gigabases of raw data. Preprocessing procedures encompassed the elimination of low-quality reads, adapters, sequences containing high proportions of ambiguous bases ("N" bases), and those with a length below 25 base pairs. For assembly, the NOVOPlasty software [28] (accessible at https://github.com/ndierckx/NOVOPlasty) was utilized. Annotation and manual refinement of the assembly were performed with reference to established mitogenome datasets. De novo assembled mitogenomes were generated using MITOS tools [29] (accessed through the MITOS Web Server at uni-leipzig.de). Validation of sequence accuracy was achieved through alignment against mitochondrial genes of other Calyptraeoidea species, complemented by confirmation via the COI barcode sequence and NCBI BLAST searches [30].

Reads were reconstructed using a de novo assembly program, and subsequent annotation of complete mitogenomes was conducted using Sequin version 16.0. The mitogenome map of D. extinctorium was visualized utilizing the online tool Poksee (accessible at https://proksee.ca) [31]. Secondary structures of tRNA genes were forecasted and illustrated through the MITOS Web Server. To gain insights into coding sequence characteristics, relative synonymous codon usage (RSCU) values and substitution saturation for the 13 protein-coding genes (PCGs) were computed utilizing DAMBE 5. Subsequent analysis of these values was executed using MEGA 7 [32]. Additionally, base compositional disparities and strand asymmetry among samples were assessed by evaluating GC-skews and AT-skews. These parameters were calculated using the following formulas: AT-skew = [A−T]/[A+T] and GC skew = [G−C]/[G+C]. Substitution saturation for the 13 PCGs was quantified using DAMBE 5 [33].

Gene order analysis

In addition to the mitogenomes sequenced in this study, we obtained an additional 51 complete mitogenomes of Littorinimorpha from GenBank (Table 1) for comparative analyses. The gene arrangements of all 51 mitogenomes were compared with the ancestral Gastropoda, with the aim of identifying potential novel gene orders that have not been reported in previous studies. To ensure that observed gene order differences were not caused by mis-annotations, any mitogenomes in Littorinimorpha that deviated from the ancestral pattern underwent re-annotation using MITOS [29].

Table 1. List of species of Littorinimorpha analysed in this study and their GenBank accession numbers.

Superfamily	Family	Species	Accession no.	Size(bp)
Stromboidea	Strombidae	Aliger gigas[34]	MZ157283	15460
		Conomurex luhuanus[35]	NC_035726	15799
		Harpago chiragra[36]	MN885884	16404
		Laevistrombus canarium[37]	MT937083	15626
		Lambis lambis[36]	MH115428	15481
		Strombus pugilis[38]	MW244819	15809
		Tridentarius dentatus[38]	MW244820	15500
	Aporrhaidae	Aporrhais serresiana[38]	MW244817	15455
	Struthiolariidae	Struthiolaria papulosa[38]	MW244818	15475
	Seraphsidae	Terebellum terebellum[38]	MW244821	15478
	Rostellariidae	Tibia fusus	NC_065371	16083
		Varicospira cancellata[38]	MW244822	15864
	Xenophoridae	Xenophora japonica[38]	MW244823	15684
Truncatelloidea	Amnicolidae	Baicalia turriformis[39]	NC_035869	15127
		Godlewskia godlewskii[39]	NC_035870	15224
		Maackia herderiana[39]	NC_035871	15154
	Pomatiopsidae	Oncomelania hupensis	NC_013073	15182
		Tricula hortensis	NC_013833	15179
	Tateidae	Potamopyrgus antipodarum[40]	NC_070577	16846
		Potamopyrgus estuarinus[40]	NC_070576	16701
Tonnoidea	Bursidae	Bufonaria rana[41]	MT408027	15510
	Charoniidae	Charonia lampas	KU237290	15330
		Charonia tritonis	MT043269	15346
	Cassidae	Galeodea echinophora[21]	NC_028003	15388
	Cymatiidae	Monoplex parthenopeus[17]	NC_013247	15270
Naticoidea	Naticidae	Cryptonatica andoi[42]	NC_046598	15302
		Cryptonatica janthostoma[42]	NC_046704	15235
		Euspira gilva[42]	NC_046593	15315
		Euspira pila[42]	NC_046703	15244
		Glossaulax reiniana[43]	NC_041162	15254
		Mammilla mammata[42]	NC_046597	15319
		Mammilla kurodai[42]	NC_046596	15309
		Naticarius hebraeus[21]	NC_028002	15384
		Neverita didyma[42]	NC_046594	15629
		Notocochlis gualteriana[42]	NC_046705	15176
		Paratectonatica tigrina[42]	NC_050661	15201
		Polinices sagamiensis[42]	NC_046595	15383
		Tanea lineata[42]	NC_050662	15156
Cypraeoidea	Cypraeidae	Cypraea tigris[44]	MK783263	16177
		Erronea errones	NC_066082	15422
Vermetoidea	Vermetidae	Dendropoma gregarium[45]	NC_014580	15641
		Eualetes tulipa[45]	NC_014585	15078
		Thylacodes squamigerus[45]	NC_014588	15544
Ficoidea	Ficidae	Ficus variegata	NC_056153	15736
Littorinoidea	Littorinidae	Littoraria ardouiniana	NC_066085	16261
		Littoraria intermedia	NC_064397	16194
		Littoraria melanostoma	NC_064398	16149
		Littoraria sinensis[46]	MN496138	16420
		Littorina brevicula[47]	NC_050987	16356
		Littorina saxatilis	NC_030595	16887
		Melarhaphe neritoides[48]	MH119311	15676
Calyptraeoidea	Calyptraeidae	Desmaulus extinctorium	OQ511529	16572
Outgroup		Donax variegatus[49]	NC_035986	17195
		Donax vittatus[49]	NC_035987	17070

Phylogenetic analysis

Exploring the evolutionary relationships within the Littorinimorpha clade involved an analysis of 13 PCGs. These genes were sourced from a comprehensive dataset that included 51 complete mitogenome sequences. The mitogenome sequences were retrieved from the GenBank database (https://www.ncbi.nlm.nih.gov/genbank/). To provide additional context, two species from the Donacidae family were also included as representatives of the outgroup. The assessment of phylogenetic relationships utilized both Maximum Likelihood (ML) and Bayesian Inference (BI) methodologies [50–52].

The ML analysis, carried out with IQ-TREE 1.6.2, involved 1000 ultrafast likelihood bootstrap replicates. The choice of optimal models was guided by the Bayesian Information Criterion (BIC), leading to the adoption of the GTR + F + R6 model for each partition. We conducted Bayesian Inference (BI) analyses using the MrBayes 3.2 software, and model selection was facilitated by MrMTgui [53], a tool that connects PAUP, ModelTest, and MrModelTest across different platforms. For model selection, we chose the best-fit model (GTR + I + G) based on AIC results obtained from MrModelTest 2.3 [54]. Bayesian analyses were then performed in MrBayes, utilizing parameter values from either MrModelTest or ModelTest (nst = 6, rates = invgamma) [55]. The Bayesian analyses utilized Markov Chain Monte Carlo (MCMC) sampling, involving two independent runs of three hot chains and one cold chain. These chains ran simultaneously for 2,000,000 generations, with sampling intervals set at 1000 steps and a relative burn-in rate of 25%. We assessed the convergence of independent runs by examining the mean standard deviation of split frequencies (< 0.01). Finally, the resulting phylogenetic trees were visualized and edited using Figure Tree v.1.4.3 software [56].

Results discussion

Genome structure and composition

The complete mitogenome sequence of D. extinctorium constitutes a prototypical closed-circular molecule spanning 16,605 bp in length (GenBank accession number OQ511529). This genome encompasses a total of 37 genes, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (16S rRNA and 12S rRNA), and a concise non-coding region. This structural arrangement aligns consistently with the composition observed in the majority of previously investigated mollusks [57–59]. All these genes have been discerned and are depicted in Fig 1 and Table 2. Among the 37 genes, the majority are localized on the heavy (H-) strand, except for eight tRNAs (tRNA-Phe, His, Pro, Leu, Val, Gln, Cys, and Tyr). (Fig 1. Maps of the mitochondrial genomes of D. extinctorium.)

Fig 1. Maps of the mitochondrial genomes of D. extinctorium.

Table 2. Mitochondrial genome organization of D. extinctorium.

Gene	Direction	Position	Length/bp		Start/Stop codon	Intergenic Nucleotide(bp)	Anticodon
COX1	H	1	1551	1551	ATT/TAA	22
COX2	H	1574	2266	693	ATG/TAA	46
tRNA Asp	H	2313	2382	70		82	GTC
ATP8	H	2465	2623	159	ATG/TAA	57
ATP6	H	2681	3376	696	ATG/TAA	26
tRNA Met	L	3403	3468	66		8	CAT
tRNA Tyr	L	3477	3542	66		4	GTA
tRNA Cys	L	3547	3612	66		0	GCA
tRNA Trp	L	3613	3679	67		-2	TCA
tRNA Gln	L	3678	3743	66		4	TTG
tRNA Gly	L	3748	3813	66		-1	TCC
tRNA Glu	L	3813	3882	70		80	TTC
12S rRNA	H	3963	4858	896		-1
tRNA Val	H	4858	4925	68		-10	TAC
16S rRNA	H	4916	6279	1364		13
tRNA Leu1	H	6293	6364	72		4	TAG
tRNA Leu2	H	6369	6438	70		0	TAA
NAD1	H	6439	7383	945	ATG/TAA	12
tRNA Pro	H	7396	7463	68		6	TGG
NAD6	H	7470	7973	504	ATG/TAA	16
Cytb	H	7990	9129	1140	ATG/TAA	17
tRNA Ser2	H	9147	9212	66		0	TGA
NAD4l	H	9213	9515	303	ATG/TAG	80
NAD4	H	9596	10900	1305	ATG/TAA	10
tRNA His	H	10911	10976	66		0	GTG
NAD5	H	10977	12848	1872	ATG/TAG	10
tRNA Phe	H	12859	12924	66		12	GAA
tRNA Thr	L	13573	13640	68		104	TGT
COX3	H	13745	14524	780	ATG/TAA	29
tRNA Lys	H	14554	14628	75		13	TTT
tRNA Ala	H	14684	14734	51		17	TGC
tRNA Arg	H	14752	14821	70		21	TCG
tRNA Asn	H	14843	14912	70		23	GTT
tRNA Ile	H	14936	15005	70		0	GAT
NAD3	H	15010	15366	357	ATG/TAG	1
tRNA Ser1	H	15416	15483	68		2	GCT
NAD2	H	15484	16572	1089	ATG/TAA	36

The longest gene, ND5, stretches across 1872 base pairs, whereas the shortest is tRNA^Ala, comprising a mere 51 base pairs. The D. extinctorium mitogenome comprises four regions displaying overlap. Of these, one involves a 10 bp overlap with tRNA^Val, and the remaining three exhibit overlaps shorter than 10 bp with tRNA^Trp (2 bp), tRNA^Gly (1 bp), and 16S rRNA (1 bp). Additionally, the D. extinctorium mitogenome accommodates 1393 bp of intergenic spacers distributed across 28 regions, ranging in size from 3 to 648 bp (Table 2).

Regarding nucleotide composition, the D. extinctorium mitogenome is comprised of A (27.73%), T (42.47%), G (18.08%), and C (11.71%), demonstrating a conspicuous AT bias. These findings parallel not only those observed in numerous mollusks [60,61] but also in certain crustaceans like crabs and lobsters [62,63]. The cumulative A + T (%) content of the mitogenomes stands at 70.20%. Calculated for the selected complete mitogenomes, the AT-skew of the D. extinctorium mitogenome is negative (−0.210), while the GC-skew is positive (0.214), implying a higher abundance of Ts and Cs than As and Gs. These outcomes align with those identified in specific Neritidae species [57].

Transfer RNAs, ribosomal RNAs

Similar to the prevailing pattern in many invertebrate species [64,65], the mitogenome of D. extinctorium harbors a total of 22 tRNA genes. Among these, fourteen are encoded by the heavy strand (H-), while the remaining ones are encoded by the light strand (L-). Across the entire mitogenome, the size of tRNA molecules spans from 51 to 75 bp, collectively encompassing a length of 1485 bp, characterized by a pronounced AT bias (70.23%). The AT-skew and GC-skew values are recorded as– 0.014 and 0.158, respectively, signifying a subtle inclination towards adenine usage and a conspicuous predilection for guanine usage (Table 3). The tRNA^Ser1 and tRNA^Ser2, due to the absence of dihydrouracil (DHU) arms, along with tRNA^Ala, due to the lack of a TΨC arm, are unable to adopt a secondary structure. Conversely, other tRNAs possess the capacity to fold into a conventional clover-leaf secondary structure. Notably, the structural variation observed in tRNA^Ser1 corresponds with the tRNA^Ser1 configuration documented in other invertebrate mitogenomes [66]. Moreover, G-C mismatches are evident in all tRNAs except tRNA^Leu2, tRNA^Met, tRNA^Trp, and tRNA^Tyr. (Fig 2. Secondary structure of the tRNA genes in the mitogenome of D. extinctorium. The tRNAs are labeled with the abbreviations of their corresponding amino acids. Blue dots indicate normal conditions and yellow dots indicate base mismatches.).

Table 3. Nucleotide contents of the coding and non-coding regions of the mitochondrial genome of D. extinctorium, indicating AT-, GC-skew ratios.

Region	Size(bp)	A (%)	T (%)	G (%)	C (%)	A+T (%)	AT-skew	GC-skew
Mitogenome	16608	27.73	42.47	18.08	11.72	70.20	-0.210	0.213
COX1	1551	23.92	43.13	20.05	12.89	67.05	-0.287	0.217
COX2	693	27.13	38.96	20.49	13.42	66.09	-0.179	0.209
ATP8	159	27.67	44.65	15.72	11.95	72.32	-0.235	0.136
ATP6	696	23.13	46.70	16.67	13.51	69.83	-0.337	0.105
COX3	780	21.67	42.31	22.31	13.72	63.98	-0.323	0.238
NAD3	357	19.89	47.90	20.73	11.48	67.79	-0.413	0.287
NAD1	945	24.02	45.29	18.20	12.49	69.31	-0.307	0.186
NAD5	1872	26.82	42.63	16.61	13.94	69.45	-0.228	0.087
NAD4	1305	25.21	46.13	16.86	11.80	71.34	-0.293	0.176
NAD4l	303	26.73	43.89	19.80	9.57	70.62	-0.243	0.348
NAD6	504	26.39	46.43	18.65	8.53	72.82	-0.275	0.372
Cytb	1140	24.39	44.39	17.81	13.42	68.78	-0.291	0.140
NAD2	1089	25.34	46.37	18.64	9.64	71.71	-0.293	0.318
tRNAs	1485	34.61	35.62	17.24	12.53	70.23	-0.014	0.158
rRNAs	2260	34.91	38.14	17.08	9.87	73.05	-0.044	0.268
PCGs	11394	24.84	44.25	18.47	12.44	69.09	-0.281	0.195

Fig 2. Secondary structure of the tRNA genes in the mitogenome of D. extinctorium.

The tRNAs are labeled with the abbreviations of their corresponding amino acids. Blue dots indicate normal conditions and yellow dots indicate base mismatches.

The sizes of the 12S rRNA and 16S rRNA components are 896 bp and 1364 bp, respectively, typically demarcated by tRNA^Val (Table 2). These dimensions align comparably with those observed in other invertebrate species. The A-T content of the rRNAs is determined to be 73.05%. AT-skew and GC-skew values are recorded as– 0.044 and 0.268, respectively, indicating a modest tendency towards adenine utilization and a marked preference for guanine utilization (Table 3). The control region (CR), positioned between tRNA^Thr and tRNA^Phe, spans a length of 648 bp.

PCGs and codon usage

The result presents the initiation and termination codons for all Protein-Coding Genes (PCGs) within D. extinctorium in Table 3. The mitochondrial genome of D. extinctorium encompasses a total of 13 PCGs, comprising a cytochrome b (Cytb), two ATPases (ATP6 and ATP8), three cytochrome oxidases (COI–III), and seven NADH dehydrogenases (ND1–6 and ND4L). This configuration aligns with the established structural pattern observed in the Muricidae family [64]. The collective length of these 13 PCGs amounts to 11,484 bp. Within this set, the individual PCGs exhibit a range of lengths spanning from 159 to 1,872 bp. Notably, the average A+T content stands at 69.13%, with variations across the spectrum from 63.98% (COIII) to 72.82% (ND6) (Table 2). The AT-skew and GC-skew values are calculated as -0.281 and 0.195, respectively (Table 4). It is noteworthy that all PCGs commence with the initiation codon ATG, except for ND4, which employs ATT as its start codon. Furthermore, the majority of PCGs terminate with TAA, whereas ND4L, ND5, and ND5 employ TAG as their respective stop codons (Table 4). Examining the amino acid utilization in D. extinctorium, tRNA^Phe emerges as the most frequently employed, while tRNA^His is the least prevalent (Fig 2). Relative synonymous codon usage (RSCU) values for the 13 PCGs in D. extinctorium are presented in Table 4 and Fig 3. Among these, UUA (Leu) ranks as the most frequently encountered codon, whereas CUC (Leu) stands as the least common codon. (Fig 3. Codon usage patterns in the mitogenome of D. extinctorium. CDspT, codons per thousand codons. Codon families are provided on the x-axis (A) and the relative synonymous codon usage (RSCU) (B)).

Table 4. Relative synonymous codon usage (RSCU) in the mitogenomes of D. extinctorium.

Codon	Count	RSCU	Codon	Count	Codon	Codon	Count	RSCU	Codon	Count	Codon
GCU(A)	84.0	2.11	CCU(P)	64.0	2.08	AGA(S)	85.0	1.17	CAU(H)	57.0	1.54
GCC(A)	19.0	0.48	CCC(P)	19.0	0.62	AGG(S)	83.0	1.14	CAC(H)	17.0	0.46
GCA(A)	41.0	1.03	CCA(P)	27.0	0.88	AUU(I)	293.0	1.70	ACU(T)	97.0	2.38
GCG(A)	15.0	0.38	CCG(P)	13.0	0.42	AUC(I)	52.0	0.30	ACC(T)	20.0	0.49
UGU(C)	123.0	1.43	CAA(Q)	53.0	1.15	AAA(K)	179.0	1.39	ACA(T)	34.0	0.83
UGC(C)	49.0	0.57	CAG(Q)	39.0	0.85	AAG(K)	79.0	0.61	ACG(T)	12.0	0.29
GAU(D)	112.0	1.75	CGU(R)	35.0	1.77	UUA(L)	336.0	2.66	GUU(V)	182.0	2.25
GAC(D)	16.0	0.25	CGC(R)	5.0	0.25	UUG(L)	160.0	1.27	GUC(V)	33.0	0.41
GAA(E)	95.0	1.43	CGA(R)	18.0	0.91	CUU(L)	126.0	1.00	GUA(V)	66.0	0.82
GAG(E)	38.0	0.57	CGG(R)	21.0	1.06	CUC(L)	26.0	0.21	GUG(V)	42.0	0.52
UUU(F)	512.0	1.65	UCU(S)	113.0	1.55	CUA(L)	67.0	0.53	UGA(W)	115.0	1.11
UUC(F)	108.0	0.35	UCC(S)	44.0	0.60	CUG(L)	43.0	0.34	UGG(W)	92.0	0.89
GGU(G)	102.0	1.47	UCA(S)	83.0	1.14	AUA(M)	135.0	1.19	UAU(Y)	240.0	1.56
GGC(G)	41.0	0.59	UCG(S)	31.0	0.43	AUG(M)	91.0	0.81	UAC(Y)	68.0	0.44
GGA(G)	65.0	0.94	AGU(S)	100.0	1.37	AAU(N)	189.0	1.65	UAA(*)	174.0	1.25
GGG(G)	70.0	1.01	AGC(S)	43.0	0.59	AAC(N)	40.0	0.35	UAG(*)	105.0	0.75

Fig 3. Codon usage patterns in the mitogenome of D. extinctorium. CDspT, codons per thousand codons.

Codon families are provided on the x-axis (A) and the relative synonymous codon usage (RSCU) (B).

Gene re-arrangement

Rearrangements in mitochondrial gene order present an autonomous dataset for resolving evolutionary relationships. Shared patterns of mitogenome gene order rearrangements among distinct taxonomic groups are likely indicative of common ancestry rather than products of convergent evolution [6,67]. In comparison to the ancestral gastropod gene arrangement, significant rearrangements are evident in the mitogenome of D. extinctorium. As illustrated in Fig 4, a minimum of three gene clusters (or genes) differ notably from the conventional arrangement, encompassing 15 tRNA genes (M, Y, C, W, Q, G, E, V, L, P, S, H, F, and T), as well as eight protein-coding genes (16S rRNA, 12S rRNA, NAD1, NAD6, Cytb, NAD4L, NAD4, and NAD5). The rearrangement of these three gene clusters (or genes) is detailed as follows (Fig 4): (1) The M-Y-C-W-Q-G-E cluster has relocated downstream of ATP6; (2) The T cluster has shifted downstream of F; (3) The F-ND5-H-ND4-ND4L-S-Cytb-ND6-P-ND1-L-16S-V-12S underwent inversion and translocation. (Fig 4. Comparison of mitochondrial gene rearrangements of the D. extinctorium. The green squares represent PCGs, the yellow squares represent tRNAs, and the orange squares represent rRNAs. The position at the top indicates that it is encoded in the H chain, and the position at the bottom indicates that it is encoded in the L chain.)

Fig 4. Comparison of mitochondrial gene rearrangements of the D. extinctorium.

The green squares represent PCGs, the yellow squares represent tRNAs, and the orange squares represent rRNAs. The position at the top indicates that it is encoded in the H chain, and the position at the bottom indicates that it is encoded in the L chain.

Furthermore, mitochondrial gene rearrangements have frequently been linked to heightened rates of evolution [68]. Prior investigations have identified a notable positive correlation in mitochondrial genomes between rates of gene order rearrangement and accelerated evolutionary rates [69]. Intriguingly, when compared to the extensive gene rearrangements observed in Lottiidae, Littorinimorpha exhibits minimal differences in genetic order, with the exception of Vermetoidea [70]. We postulate that this circumstance could be attributed to the relatively modest variations in genome size among Littorinimorpha species, ranging from 15,127 bp to 17,195 bp (Tab 1), while the mitochondrial genome size within Lottiidae spans from 16,319 bp to 26,835 bp. Further investigations are warranted to scrutinize this association within a broader spectrum of Gastropoda groups.

In the context of gene rearrangement patterns, three primary categories are recognized [71]: (1) shuffling, where genes migrate from their original locations to adjacent positions on the same strand, typically without traversing protein-coding genes; (2) translocation, in which genes traverse several genes, often including protein-coding genes, relocating from their original positions to new sites; (3) inversion, involving the switch of genes from one strand to the other. Based on the characteristics of mitochondrial sequences, our analysis suggests that inversion and translocation are the predominant types of rearrangements observed in D. extinctorium.

Furthermore, we conducted a comparative examination of the gene order in D. extinctorium against other superfamilies within Littorinimorpha. With the exception of Vermetoidea, the gene order across other superfamilies remains largely consistent. Notably, in Vermetoidea, significant deviations in gene order primarily pertain to tRNAs. In addition, the M-Y-C-W-Q-G-E cluster within the mitochondrial genome of Vermetoidea has undergone inversion, a phenomenon observed in other gastropod mitochondrial genomes [72], resulting in disruption and rearrangement. Intriguingly, a remarkably similar set of genes undergoes rearrangement in the common ancestor of Caenogastropoda, although the integrity of the M-Y-C-W-Q-G-E cluster is maintained [22,73,74]. These findings align with the conclusions drawn from gene order-based phylogenetic analysis, underscoring the utility of comparing mitochondrial gene rearrangements as a valuable tool in phylogenetic studies.

Phylogenetic relationships

In this current study, we conducted an analysis of phylogenetic relationships using the sequences of 13 protein-coding genes (PCGs). The primary objective was to gain insights into the interrelationships within the Littorinimorpha clade, focusing on D. extinctorium. Additionally, we included 51 other well-known Littorinimorpha species in our analysis, with Donax variegatus and Donax vittatus serving as outgroups. Both the Maximum Likelihood (ML) tree and the Bayesian Inference (BI) tree revealed consistent topological structures, although they exhibited varying degrees of support values. Notably, BI generally yielded higher support values, with most nodes having a support value of 1. In contrast, the support values in ML, except for three nodes in the Stromboidea superfamily, were below 70, and the majority of other branches had support values above 90. Consequently, we present and display only one topology (ML) with both support values. (Fig 5. The phylogenetic tree was inferred from the nucleotide sequences of 13 mitogenome PCGs using BI and ML methods. Numbers on branches indicate posterior probability (BI) and bootstrap support (ML)).

Fig 5. The phylogenetic tree was inferred from the nucleotide sequences of 13 mitogenome PCGs using BI and ML methods.

Numbers on branches indicate posterior probability (BI) and bootstrap support (ML).

Among the 19 families encompassed within our phylogenetic tree, each individual family constitutes a monophyletic clade, bolstered by elevated nodal support values. Phylogenetic analysis showed that nine superfamilies within the Littorinimorpha show the following relationship: ((((((Naticoidea + Littorinoidea) + Truncatelloidea) + Tonnoidea + Ficoidea + Cypraeoidea) +Stromboidea) + Calyptraeoidea) + Vermetoidea), and all nine of them are monophyletic groups, some previous studies have shown that this is plausible [75,76], and Naticoidea and Littorinoidea are the closest sisters to each other. Additionally, phylogenetic tree showed that (Tonnoidea + Ficoidea + Cypraeoidea) formed a clade which showing were sister groups in this tree, while D. extinctorium alone forms a Calyptraeoidea clade, and (Calyptraeoidea + (Stromboidea + (Tonnoidea + Ficoidea + Cypraeoidea) + Truncatelloidea + (Naticoidea + Littorinoidea))) formed a clade. Vermetoidea is placed at the basal position of the monophyletic Littorinimorpha, this is consistent with previous research [73], and this can also be related to the results of gene re-arrangements, only the Vermetoidea has a significantly different genetic sequence from the rest of the species, so Vermetoidea is at the bottom of the phylogenetic tree. Stromboidea is the superfamily containing the largest number of families, it is a highly diverse group. Stromboidea is currently understood to comprise six extant families: Aporrhaidae, Rostellariidae, Seraphsidae, Strombidae, Struthiolariidae and Xenophoridae. Within each superfamily, each family forms a distinct clade. The results of phylogenetic relationships in the superfamil were consistent with the findings of Irwin et al [38]. In our study, Naticidae is the family of which most species have been included, representing a large number of genera. The Littorinidae are its sister group, of which a substantial number of species has been included in our study, however only representing a selection of the genera.

Conclusion

In this investigation, we conducted the sequencing of the mitogenome of D. extinctorium employing next-generation sequencing techniques, thus yielding novel mitochondrial data pertinent to Calyptraeidae. An exhaustive examination of the mitogenome of D. extinctorium revealed its substantial resemblance to other representatives of the Littorinimorpha order, characterized by several notable features, including AT-skew and a codon usage bias, among others. Comparative analysis with the ancestral gastropod indicated a noteworthy rearrangement in the gene order of the D. extinctorium mitogenome. The Littorinimorpha exhibited four distinct rearrangement patterns, with their rearrangement similarity consistently mirroring their phylogenetic relationships. Our phylogenetic tree displayed both congruities and disparities when compared to preceding studies. Phylogenetic analyses indicated the formation of an exclusive Calyptraeoidea clade by D. extinctorium, whereas (Calyptraeoidea + (Stromboidea + (Tonnoidea + Ficoidea + Cypraeoidea) + Truncatelloidea + (Naticoidea + Littorinoidea))) constituted a distinct clade. Despite a limited number of species available for a robust phylogenetic analysis, our phylogeny garnered statistical support and aspires to provide a rational framework for future phylogenetic inquiries within the realm of Calyptraeoidea. These findings not only offer insights into the gene arrangement characteristics within Littorinimorpha mitogenomes but also establish the groundwork for further explorations into the phylogenetic aspects of Littorinimorpha.

Data Availability

The datasets analysed during the current study are available in the National Center for Biotechnology Information, and the GenBank accession numbers of the mtgenome of D. extinctorium is OQ511529.

Funding Statement

This research was financially supported by the Project of Bureau of Science and Technology of Zhoushan (No. 2021C21017), the National Key R&D Program of China (2019YFD0901204) and NSFC Projects of International Cooperation and Exchanges (42020104009). There was no additional external funding received for this study.