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Article

Mitogenomic and Phylogenetic Analyses of Lysmata lipkei (Crustacea: Decapoda: Lysmatidae)

by
Xixi Zhang
1,2,3,4,
Zhihuang Zhu
2,3,4,*,
Jianxin Wang
1,
Ge Shi
1,* and
Qi Lin
2,3,4,*
1
Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China
2
Fisheries Research Institute of Fujian, Xiamen 361013, China
3
Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Xiamen 361013, China
4
National and Local Joint Engineering Research Center of Marine Biological Seed Industry Technology, Xiamen 361013, China
*
Authors to whom correspondence should be addressed.
Fishes 2025, 10(4), 177; https://doi.org/10.3390/fishes10040177
Submission received: 1 March 2025 / Revised: 7 April 2025 / Accepted: 11 April 2025 / Published: 14 April 2025
(This article belongs to the Section Genetics and Biotechnology)
Browse Figures
Versions Notes

Abstract

This study aims to elucidate the characteristics of the mitogenome of Lysmata lipkei and investigate its phylogenetic relationships. Using both the Illumina NovaSeq 6000 (Illumina, Inc., San Diego, CA, USA) and PacBio Sequel II (Pacific Biosciences of California, Inc., Menlo Park, CA, USA) platforms, the complete mitogenome sequence of L. lipkei was determined. The mitogenome of L. lipkei was annotated, measuring 17,497 bp in length and comprising 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs). The nucleotide composition of the genome exhibited an AT bias of 63.4%. Among the PCGs, the most frequently used codon was UUA. All tRNAs, except for trnD, which lacks the TψC loop, were capable of forming the typical cloverleaf structure. Phylogenetic trees for Caridea were constructed using Bayesian Inference (BI) and Maximum Likelihood (ML) methods based on the nucleotide sequences of the 13 PCGs. Both methods yielded consistent topological structures, with L. lipkei showing the closest phylogenetic relationship to L. kuekenthali. Additionally, Lysmatidae, Thoridae, and Hippolytidae formed a monophyletic clade. This research not only filled the gap in mitogenome data for Lysmatidae but also provided novel molecular insights into Caridean phylogenetics.
Keywords:
shrimp; mitogenome; phylogeny
Key Contribution: The complete mitogenome sequence of Lysmata lipkei was achieved. The phylogenetic relationship within Lysmatidae was investigated.

1. Introduction

Shrimps in the family Lysmatidae are small benthic crustaceans, typically measuring 2–5 cm in adult body length [1]. The carapace displays distinct chromatic patterns, featuring red, white, and orange stripes or patches [2]. These shrimps exhibit a wide geographical distribution, spanning tropical to temperate marine ecosystems, and are commonly found in intertidal to subtidal zones, where they often form symbiotic associations with anemones, coral reefs, macroalgae, or seagrass beds [3,4]. Molecular studies have revealed that the mitogenome in Lysmatidae measures approximately 15–22 kb in length, comprising 13 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), and 2 rRNA genes (rRNAs) [5]. As a crucial tool in molecular systematics research, the mitogenome is characterized by its compact structure, maternal inheritance, and high copy number [6]. In crustaceans, the mitogenome has been extensively applied to species identification, population genetics, and phylogenetic reconstruction [7,8]. Currently, studies have been conducted to elucidate the phylogenetic relationships within Caridea using the 13 PCGs. For instance, Tan et al. [9] revealed the sister group relationship between Palaemonidae and Alpheidae using Maximum Likelihood (ML) and Bayesian Inference (BI) methods. Sun et al. [10] analyzed the phylogenetic relationships of Caridean species in hydrothermal vent, seamount, freshwater, and shallow water habitats using ML and BI approaches, providing critical insights into the ecological adaptive evolution of this group.
Lysmata lipkei (Okuno and Fiedler, 2010) belongs to Arthropoda, Crustacea, Decapoda, Caridea, Lysmatidae, and Lysmata [11,12]. As a small marine ornamental shrimp widely distributed in the Indian and Pacific Oceans [13], L. lipkei has been identified as an invasive species in the Atlantic Ocean [14]. Its molecular data are of significant importance for species identification and invasive species detection [15]. Currently, L. lipkei lacks molecular data, and species identification primarily relies on morphological characteristics. However, the classification and identification of L. lipkei are challenging due to its high morphological similarity with closely related species, such as L. dispar and L. kuekenthali, in terms of carapace, abdomen, and appendage characteristics [16], making traditional morphological methods alone insufficient for species identification [17]. Furthermore, the evolutionary relationships between L. lipkei and other Lysmatidae species remain unclear. For instance, Alves et al. [14] constructed a phylogenetic tree of Lysmatidae based on the 16S rRNA gene fragment, which showed that the bootstrap support between L. lipkei and other species in Lysmatidae was less than 50%. This indicates that the information provided by a single gene fragment is limited and insufficient for comprehensively resolving its phylogenetic relationships. In contrast, mitogenomes contain richer genetic information and can provide more reliable molecular evidence for species identification and phylogenetic studies. Notably, the mitogenomes of species in the family Lysmatidae exhibit unique gene rearrangement patterns, which may be closely related to adaptive evolution or specific phylogenetic histories. For example, in Exhippolysmata ensirostris [18], the trnL2-cox2 arrangement replaces the typical cox2-trnL2 order, while in L. vittata [5], the positions of trnA and trnR are rearranged. These findings not only deepen the understanding of the genetic diversity within Lysmatidae but also provide important insights into their ecological adaptability and evolutionary mechanisms. Although the mitogenome sequences of seven species in Lysmatidae have been published [18,19,20,21,22], the phylogenetic position of Lysmatidae within Caridea remains controversial. For example, Cronin et al. [23] constructed an ML phylogenetic tree based on 13 PCGs, showing that Lysmatidae, Thoridae, and Hippolytidae are closely related and form a monophyletic clade, whereas Sun et al.’s BI and ML trees built using the same 13 PCGs revealed that Lysmatidae, Thoridae, and Hippolytidae do not cluster together as a monophyletic group [24]. Therefore, new molecular evidence is needed to address the phylogenetic controversies within Caridea. Currently, the mitogenome information of L. lipkei remains unavailable, and related studies have primarily focused on its morphological structures and ecological habits [13,25,26]. Thus, resolving the mitogenome of L. lipkei will not only help resolve its taxonomic controversies and increase the diversity but also provide molecular evidence for elucidating the phylogenetic relationships within Lysmatidae.
This study successfully obtained the mitogenome sequence of L. lipkei using second- and third-generation sequencing technology and conducted a comprehensive analysis of its structural features. The research focused on key characteristics, including the nucleotide composition, codon usage bias, and the secondary structures of tRNA genes within the mitogenome. Furthermore, based on the 13 PCGs, the study explored the phylogenetic relationships within Lysmatidae to resolve the taxonomic status of L. lipkei. The findings provide new molecular evidence and theoretical support for advancing the taxonomic research and understanding the evolutionary history of Lysmatidae.

2. Materials and Methods

2.1. Sampling, Identification, and DNA Extraction

The specimens analyzed in this study were collected in September 2023 from the coastal waters near Dachen Island (28.488615° N, 121.895701° E), Taizhou City, Zhejiang Province, China. Sampling was conducted by local fishermen during low tide in rocky reef habitats. The collection site is located within an ecotone where the Taiwan Warm Current converges with coastal currents, characterized by mixed sandy-mud substrates, surface water temperatures ranging from 23 to 26 °C, and salinity levels of 28–30‰. The specimens were immediately oxygen packed on-site and subsequently transported to the laboratory located in Xiamen, Fujian Province, China. Morphological identification confirmed the samples as L. lipkei. A voucher specimen (voucher number: FJOS23092) was preserved in the Collection of Ornamental Shrimp of the Fisheries Research Institute of Fujian. Muscle tissue was used for genomic DNA extraction, following the protocol outlined in the E.Z.N.A.® Tissue DNA Kit (Omega Bio-Tek, Norcross, GA, USA). To assess the quality of the extracted genomic DNA, its integrity was verified via 1% agarose gel electrophoresis, while its concentration and purity were determined using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Subsequently, the DNA was sent for sequencing with an Illumina NovaSeq 6000 (Illumina, Inc., San Diego, CA, USA) and PacBio Sequel II (Pacific Biosciences of California, Inc., Menlo Park, CA, USA) at Origin Gene Co. Ltd., Shanghai, China.

2.2. Mitogenome Annotation and Analysis

Raw sequencing data were filtered to remove low-quality sequences. Illumina sequencing data was assembled using SPAdes v3.14.1 [27]. The assembled Illumina contigs were aligned to PacBio sequencing data using Minimap2 [28], and the aligned PacBio reads were subsequently extracted using Samtools v1.16.1 [29]. Mitogenome assembly was conducted from the PacBio data using Canu [30]. The final mitogenome sequence was polished using Pilon v1.23 [31] to correct base errors and determine the starting location and orientation of the assembly. MITOS Web Server [32] was utilized to identify tRNAs, rRNAs, and PCGs within the mitogenome. The circular mitogenome of L. lipkei was visualized using CGView [33]. Nucleotide composition, codon preference, and usage frequency of PCGs were analyzed using MEGA X [34]. We calculated the ENC (Effective Number of Codons) and GC3 (GC content at the third codon position) using EMBOSS [35]. The secondary structures of tRNA genes were predicted using both MITOS Web Server (http://mitos.bioinf.uni-leipzig.de/, accessed on 20 March 2024) [32] and tRNAscan-SE 2.0 [36].

2.3. Phylogenetic Tree Reconstruction

A dataset comprising 38 caridean shrimp mitogenomes (Table 1) was assembled from GenBank for phylogenetic reconstruction, using Aristeus virilis and Aristeus foliacea (Aristeidae) as outgroup taxa. The 13 PCG sequences were extracted and concatenated using PhyloSuite v1.2.3 [37]. Sequence alignment of the 13 PCGs was conducted with MAFFT v7.505 [38], followed by removal of ambiguous regions using Gblocks v0.91b [39]. Maximum likelihood (ML) analysis was implemented in IQ-TREE [40] using the optimal substitution model (GTR + F + I + G4) identified by ModelFinder v2.2.0 [41]. Bayesian Inference (BI) analysis was performed in MrBayes v3.2.7 [42] under the best-fit model (GTR + I + G + F), with four independent runs of 2,000,000 generations sampled every 1000 generations. The first 25% of samples were discarded as burn-in, and the remaining trees were used to construct a 50% majority-rule consensus tree with Bayesian posterior probabilities.

3. Results

3.1. Mitogenome Structure and Composition

The complete mitogenome of L. lipkei is a closed-circular molecule spanning 17,497 bp (GenBank accession number PQ863089). This genome encompassed a total of 37 genes, comprising 13 PCGs, 22 tRNAs, and 2 rRNAs. Among these genes, 23 genes were situated on the heavy strand (H strand), while 14 genes were positioned on the light strand (L strand) (Figure 1). Regarding nucleotide composition, the mitogenome was composed of A (32.0%), T (31.4%), G (14.4%), and C (22.2%), demonstrating a conspicuous AT bias. The cumulative AT content of the mitogenome stands at 63.4%. Calculated for the selected complete mitogenomes, the AT skew of the mitogenome was positive (0.008), while the GC skew was negative (−0.213), implying a higher abundance of Cs than Gs (Table 2).

3.2. Protein Coding Genes

The collective length of 13 PCGs amounted to 11,133 bp. The individual PCGs exhibited a range of lengths spanning from 159 bp (atp8) to 1728 bp (nad5). Notably, the average AT content was 61.5%, ranging from 57.3% (cox1) to 76.7% (atp8). The AT-skew and GC-skew values were calculated as −0.174 and −0.01, respectively (Table 2). It was noteworthy that PCGs commence with the initiation codon ATG or ATA, except for cox1, which employed ATT as its start codon. Furthermore, the majority of PCGs terminated with TAA, whereas cox2 and nad4 used TAG as their respective stop codons, and cob and nad3 terminated with the incomplete stop codon T (Table 3).
In terms of amino acid utilization frequency, Leu was the most abundant, while Cys showed the lowest occurrence (Figure 2). The relative synonymous codon usage (RSCU) analysis of 13 PCGs in L. lipkei revealed UUA (Leu) as the most frequent codon and CGC (Arg) as the rarest (Figure 3). These genes exhibited a preferential use of codons terminating with A or T at the third nucleotide position. ENC plot analysis revealed that 13 PCGs possessed ENC values above 35, suggesting weak codon usage preference across these genes. Specifically, atp6, atp8, cox2, and cox3 showed ENC values close to the standard curve (with ENC ratios ranging from −0.05 to 0.05), indicating that their codon selection is mainly influenced by mutational pressure. Conversely, the ENC values of most genes substantially deviated from the standard curve, demonstrating that natural selection primarily drives codon usage bias in L. lipkei (Figure 4).

3.3. Transfer RNAs and Ribosomal RNAs

Among 22 tRNA genes, 14 genes were encoded by the heavy strand, while the remaining genes were encoded by the light strand. The tRNA genes ranged in length from 64 to 70 bp, accounting for 1475 bp of the mitogenome and exhibiting a strong AT bias (66%). AT-skew and GC-skew values were calculated at 0.006 and 0.078, respectively (Table 2). The trnD gene, due to the absence of the TψC loop, was unable to adopt a secondary structure. Other tRNAs successfully folded into classic cloverleaf secondary structures. In the folding process of the cloverleaf structure, there were 19 pairs of G-U mismatches. A-A mismatches were located on the amino acid acceptor arm of trnE. C-A mismatches were located on the anticodon arm and TψC arm of trnK. U-U mismatches were located on the amino acid acceptor arm of trnC and TψC arm of trnE (Figure 5).
Two rRNA genes were located on the light strand. The 12S rRNA (823 bp) and 16S rRNA (1330 bp) were separated by the trnV gene (Table 4). rRNA sequences displayed an AT content of 66.6%. AT-skew and GC-skew values were recorded as 0.025 and 0.280, respectively (Table 2).

3.4. Phylogenetic Relationships

Phylogenetic relationships were reconstructed using nucleotide sequences from 13 PCGs. The analysis specifically aimed to find the relationships within Lysmatidae, particularly focus on L. lipkei. The dataset included 38 shrimps, utilizing A. virilis and A. foliacea as outgroups. Both Maximum Likelihood (ML) and Bayesian Inference (BI) trees exhibited congruent topologies, although nodal support values differed between the two methods (Figure 6). BI analyses generated stronger nodal support, with posterior probabilities exceeding 0.95 for all nodes. The ML bootstrap support for the Thoridae–Hippolytidae clade was 69%, below the conventional 70% confidence threshold.
All nine families in the phylogenetic tree were monophyletic groups, supported by strong nodal support values. Specifically, Notostomus gibbosus and Oplophorus spinosus exhibited closer phylogenetic affinities, forming a distinct clade with Alvinocarididae. Alpheidae and Palaemonidae formed a sister group relationship. The analyzed specimen L. lipkei clustered consistently within Lysmatidae, demonstrating the closest affinity to L. kuekenthali. Lysmatidae, Thoridae, and Hippolytidae formed a clade with strong nodal support. Thoridae and Hippolytidae exhibit a sister group relationship; however, while BI demonstrates robust support (≥0.95) [61], the ML bootstrap value falls below the conventional confidence threshold (≥70%) [62]. This methodological discrepancy suggests that the phylogenetic relationship between these families requires further validation through more genes or genomes datasets to achieve more robust topological resolution (Figure 6).

4. Discussion

4.1. Mitogenome

Among the eight published species in the family Lysmatidae, mitogenome rearrangements were observed in three species, indicating that such genomic rearrangements are relatively prevalent within this family (Figure 7). For instance, a specific case in E. ensirostris demonstrated a gene order of trnL2-cox2, as opposed to the more common cox2-trnL2 arrangement [18]. Additionally, in the mitogenome of L. vittata, the positions of two tRNA genes (trnA and trnR) have been observed to undergo translocation [5]. Notably, the mitogenome of L. lipkei spanned a total length of 17,497 bp and encoded 37 genes, with its gene arrangement and orientation remaining consistent with ancestral types, indicating a high level of conservation. Further analysis revealed that the proportion of AT bases in this mitogenome is significantly higher compared to CG bases, a characteristic that was widely observed within Caridea [8]. The interspecific divergence in AT content mainly results from the accumulation of simple sequence repeats within non-coding genomic regions [63]. A higher AT content not only reduces the stability of the DNA double helix, thereby facilitating more efficient transcription processes [64], but also significantly decreases the energy expenditure required during DNA replication [65]. For PCGs, the initiation codons are typically in the ATN form, while the termination codons were predominantly TAN or the incomplete codon T, the latter often requiring the addition of an A at the 3′ end through post-transcriptional modification of mRNA to form a complete termination signal [66]. In the mitogenome of L. lipkei, nearly all 22 tRNA genes exhibit a standard cloverleaf structure, with the exception of trnD, which lacks the TψC loop; it is relatively common for certain tRNAs to fail to form a cloverleaf structure. For example, the trnT of E. ensirostris also lacks the TψC loop.

4.2. Phylogenetic Analysis

The Caridea represents one of the most diverse decapod groups, ranking second in species richness [67]. Phylogenetic relationships in Caridea have attracted substantial research interest, as advances in mitogenome sequencing have reshaped phylogenetic frameworks. This study confirmed monophyly in nine Caridean families. Notably, Alpheidae and Palaemonidae formed a sister group, a conclusion supported by multiple studies [20,46,68,69]. Additionally, consistent with previous findings, Alvinocarididae, Acanthephyridae, and Oplophoridae form a clade with strong nodal support [10]. Importantly, this research also confirmed a close relationship among Hippolytidae, Lysmatidae, and Thoridae, with sister relationship between Hippolytidae and Thoridae. However, the specific sister relationships among these three families remained contentious within the academic community. These discrepancies may arise from differences in methodologies and the diversity of species samples used in phylogenetic analyses. For instance, Cronin et al. [23] reconstructed a ML phylogeny based on 13 PCGs, recovering Lysmatidae, Thoridae, and Hippolytidae as a monophyletic clade. Conversely, Zhu et al. [5], employing both ML and BI on 13 PCGs, suggested a paraphyletic relationship between Hippolytidae and Thoridae, with Lysmatidae placed outside this grouping. Sun et al. [24], also using 13 PCGs with ML and BI analyses, proposed that these three families do not form a paraphyletic assemblage. In this study, however, the sister relationship of Hippolytidae and Thoridae showed low bootstrap support in ML analyses, suggesting this relationship requires confirmation through additional data. In light of this, the taxonomic status of Hippolytidae, Lysmatidae, and Thoridae within Caridea warrants further investigation, and additional research is needed to clarify the phylogenetic positions of the various families within Caridea.

5. Conclusions

This study sequenced and characterized the mitogenome of L. lipkei (17,497 bp), containing 13 PCGs, 22 tRNAs, and 2 rRNAs. Characteristic features include an AT-biased nucleotide composition (63.4%), ATN initiation codons in PCGs, and the lack of the TψC loop in trnD. Phylogenetic analysis within Caridea, based on 13 PCGs, demonstrated a close evolutionary relationship between L. lipkei and L. kuekenthali, while Hippolytidae, Lysmatidae, and Thoridae formed a distinct cluster. The research clarifies the evolutionary position of L. lipkei within Lysmatidae; provides a complete genomic reference for its molecular identification; offers new molecular evidence to resolve the phylogenetic relationships among Hippolytidae, Lysmatidae, and Thoridae; and enriches the mitogenome database of crustaceans. Additionally, the mitogenome of L. lipkei could be utilized for eDNA metabarcoding, particularly considering the species’ invasive characteristics.

Author Contributions

Conceptualization, Z.Z. and Q.L.; methodology, Z.Z. and X.Z.; software, X.Z.; validation, G.S. and J.W.; formal analysis, X.Z. and Z.Z.; investigation, X.Z. and Z.Z.; resources, Z.Z.; data curation, Z.Z. and X.Z.; writing—original draft preparation, X.Z.; writing—review and editing, Z.Z.; visualization, J.W.; supervision, Z.Z. and J.W.; project administration, J.W., G.S. and Q.L.; funding acquisition, Z.Z. All authors have read and agreed to the published version of the manuscript.

Funding

This study was supported by the special fund of marine and Fishery Structure Adjustment in Fujian (No. 2017HYJG03, No. 2020HYJG01, and No. 2020HYJG08), Fujian province marine service and fishery high-quality development special fund project (FJHY-YYKJ-2022-1-7), Xiamen marine and fishery development special fund youth science and technology innovation project (23YYST0710CA14), and Basic Research Special Program for Public Welfare Research Institutes under the Provincial Department of Science and Technology of Fujian Province (2024R1013007).

Institutional Review Board Statement

The animal study protocol was approved by Application Format for Ethical approval for science and technology (Research involving animals) of Fisheries Research Institute of Fujian (protocol code FRIF21-2502-02).

Informed Consent Statement

Not applicable.

Data Availability Statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI under the accession no. PQ863089. The associated BioProject, BioSample, and SRA numbers are PRJNA1208241, SAMN46171225, SRR31939564 (Illumina), and SRR31939563 (PacBio), respectively.

Acknowledgments

We thank Origin Gene Co. Ltd., Shanghai, China, for sequencing the samples with Illumina NovaSeq 6000 and PacBio Sequel II.

Conflicts of Interest

The authors declare no conflicts of interest.

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Fishes 10 00177 g001
Figure 1. Mitogenome structure of L. lipkei. The genes outside the map were coded on the H strand, whereas the genes on the inside of the map were coded on the L strand. The middle black circle displays the GC content, and the inside purple and green circle displays the GC skew [27].
Figure 1. Mitogenome structure of L. lipkei. The genes outside the map were coded on the H strand, whereas the genes on the inside of the map were coded on the L strand. The middle black circle displays the GC content, and the inside purple and green circle displays the GC skew [27].
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Figure 2. Amino acid count in the mitogenome of L. lipkei.
Figure 2. Amino acid count in the mitogenome of L. lipkei.
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Figure 3. Relative synonymous codon usage (RSCU) in the mitogenome of L. lipkei.
Figure 3. Relative synonymous codon usage (RSCU) in the mitogenome of L. lipkei.
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Figure 4. ENC plot analysis of L. lipkei.
Figure 4. ENC plot analysis of L. lipkei.
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Figure 5. Secondary structure for the tRNAs of L. lipkei mitogenome. The yellow box indicates a C-A mismatch, the green box indicates a U-U mismatch, the purple box indicates an A-A mismatch, the red box indicates a G-U mismatch, and the blue box represents the trnD gene lacking the TψC loop.
Figure 5. Secondary structure for the tRNAs of L. lipkei mitogenome. The yellow box indicates a C-A mismatch, the green box indicates a U-U mismatch, the purple box indicates an A-A mismatch, the red box indicates a G-U mismatch, and the blue box represents the trnD gene lacking the TψC loop.
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Figure 6. Phylogenetic tree inferred from nucleotide sequences of 13 PCGs of the mitogenome using BI methods and ML methods.
Figure 6. Phylogenetic tree inferred from nucleotide sequences of 13 PCGs of the mitogenome using BI methods and ML methods.
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Figure 7. Mitochondrial gene rearrangement within Lysmatidae. The red box indicates translocation, and the blue box indicates duplication, translocation, and inversion.
Figure 7. Mitochondrial gene rearrangement within Lysmatidae. The red box indicates translocation, and the blue box indicates duplication, translocation, and inversion.
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Table 1. List of shrimps analyzed in this study.
Table 1. List of shrimps analyzed in this study.
IDOrganismFamilyLength (bp)AT (%)Reference
NC 059935Notostomus gibbosusAcanthephyridae17,59060.3[43]
NC 038068Alpheus hoplochelesAlpheidae15,73560.6[44]
NC 038116Alpheus japonicusAlpheidae16,61965.1[45]
NC 041151Alpheus inopinatusAlpheidae15,78961.2
NC 047307Synalpheus microneptunusAlpheidae15,60364.6[46]
NC 079948Alpheus brevicristatusAlpheidae15,70562.6
NC 018778Alvinocaris chelysAlvinocarididae15,91063.4[47]
NC 037487Shinkaicaris leurokolosAlvinocarididae15,90365.9[48]
NC 042497Alvinocaris longirostrisAlvinocarididae16,02262.2
NC 051948Chorocaris paulexaAlvinocarididae15,90965.7
NC 035411Stygiocaris styliferaAtyidae15,81266.3
NC 035412Halocaridinides fowleriAtyidae15,97764.3
NC 036335Typhlatya miravetensisAtyidae15,86566.2[49]
NC 038067Caridina multidentataAtyidae15,82563.4[50]
NC 067571Caridina longshanAtyidae15,55665.1
NC 070241Atyopsis moluccensisAtyidae15,93362.5[51]
MK681888Exhippolysmata ensirostrisLysmatidae16,35064.4[18]
MW836830Lysmata sp. 1 LQZ-2020Lysmatidae16,75864.5
NC 049878Lysmata vittataLysmatidae22,00371.5[21]
NC 050676Lysmata amboinensisLysmatidae16,73564.1[19]
NC 060421Lysmata debeliusLysmatidae16,75767.1[20]
NC 064049Lysmata boggessiLysmatidae17,34567.1[22]
PQ043512Lysmata kuekenthaliLysmatidae17,54069.0
PQ863089Lysmata lipkeiLysmatidae17,49763.4This study
NC 059714Oplophorus spinosusOplophoridae17,34665.6[52]
NC 046034Anchistus australisPalaemonidae15,39668.4[53]
NC 061664Periclimenes brevicarpalisPalaemonidae16,67360.3[54]
NC 072240Palaemon tenuidactylusPalaemonidae15,73567.0[55]
NC 073543Palaemon macrodactylusPalaemonidae15,74468.1[55]
NC 082428Palaemon modestusPalaemonidae15,73467.6
NC 086649Palaemon australisPalaemonidae15,90564.9
NC 086964Gnathophyllum americanumPalaemonidae15,84266.3[56]
NC 045223Lebbeus groenlandicusThoridae17,39964.8[57]
NC 051930Thor amboinensisThoridae15,55373.1[58]
NC 081991Latreutes anoplonyxHippolytidae16,42069.0[59]
NC 050677Saron marmoratusHippolytidae16,33067.9[51]
NC 039154Aristeus virilisAristeidae15,93664.6[60]
NC 039153Aristaeomorpha foliaceaAristeidae15,92666.0[60]
Table 2. Mitogenome organization of L. lipkei.
Table 2. Mitogenome organization of L. lipkei.
RegionsSize (bp)T (%)C (%)A (%)G (%)AT (%)GC (%)AT SkewGC Skew
Mitogenome17,49731.422.232.014.463.436.60.008−0.213
PCGs11,13336.119.525.419.161.538.6−0.174−0.010
tRNAs147532.815.733.218.366.034.00.0060.078
rRNAs215332.512.034.121.466.633.40.0250.280
Table 3. PCG organization of L. lipkei.
Table 3. PCG organization of L. lipkei.
GeneStrandLength (bp)AT SkewGC SkewAT (%)GC (%)Start CodonStop Codon
atp6+675−0.117−0.26261.139ATGTAA
atp8+159−0.082−0.18976.723.2ATATAA
cob+1135−0.139−0.185941ATGT
cox1+1500−0.114−0.09157.342.7ATTTAA
cox2+687−0.071−0.12461.238.8ATGTAG
cox3+789−0.175−0.13558.741.3ATGTAA
nad1−945−0.2330.25161.338.7ATGTAA
nad2+1017−0.147−0.31760.939.2ATATAA
nad3+355−0.214−0.20664.635.5ATAT
nad4−1341−0.2710.36362.837.3ATGTAG
nad4l−285−0.2530.35963.936.2ATGTAA
nad5−1728−0.1870.25664.435.7ATGTAA
nad6+519−0.223−0.3376436ATGTAA
Table 4. RNA organization of L. lipkei.
Table 4. RNA organization of L. lipkei.
GeneStrandLength (bp)AT SkewGC SkewAT (%)GC (%)Anticodon
rrnL−13300.050.30469.330.7
rrnS−823−0.020.24862.237.8
trnA+640.1062.537.6UGC
trnC−6400.09165.634.4GCA
trnD+6400.16781.218.7GUC
trnE+690−0.04869.630.4UUC
trnF−670.0830.26371.628.3GAA
trnG+670.064−0.270.129.8UCC
trnH−6500.5388020GUG
trnI+670.0530.17256.843.3GAU
trnK+690.050.03457.942UUU
trnL1−690.0480.25960.939.1UAG
trnL2+65−0.023066.133.8UAA
trnM+690−0.2415842CAU
trnN+670.091−0.04365.734.3GUU
trnP−690.020.57128.9UGG
trnQ−690.0590.22273.926UUG
trnR+65−0.25−0.0349.350.8UCG
trnS1+69−0.122059.440.6UCU
trnS2+70−0.0980.15872.927.1UGA
trnT+64−0.042−0.1257525UGU
trnV−68−0.070.2863.236.7UAC
trnW+690.045−0.263.736.2UCA
trnY−660.0770.25959.141GUA
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Zhang, X.; Zhu, Z.; Wang, J.; Shi, G.; Lin, Q. Mitogenomic and Phylogenetic Analyses of Lysmata lipkei (Crustacea: Decapoda: Lysmatidae). Fishes 2025, 10, 177. https://doi.org/10.3390/fishes10040177

AMA Style

Zhang X, Zhu Z, Wang J, Shi G, Lin Q. Mitogenomic and Phylogenetic Analyses of Lysmata lipkei (Crustacea: Decapoda: Lysmatidae). Fishes. 2025; 10(4):177. https://doi.org/10.3390/fishes10040177

Chicago/Turabian Style

Zhang, Xixi, Zhihuang Zhu, Jianxin Wang, Ge Shi, and Qi Lin. 2025. "Mitogenomic and Phylogenetic Analyses of Lysmata lipkei (Crustacea: Decapoda: Lysmatidae)" Fishes 10, no. 4: 177. https://doi.org/10.3390/fishes10040177

APA Style

Zhang, X., Zhu, Z., Wang, J., Shi, G., & Lin, Q. (2025). Mitogenomic and Phylogenetic Analyses of Lysmata lipkei (Crustacea: Decapoda: Lysmatidae). Fishes, 10(4), 177. https://doi.org/10.3390/fishes10040177

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