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Article

The New Mitochondrial Genome of Hemiculterella wui (Cypriniformes, Xenocyprididae): Sequence, Structure, and Phylogenetic Analyses

by
Renyi Zhang
*,†,
Tingting Zhu
† and
Feng Yu
School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Genes 2023, 14(12), 2110; https://doi.org/10.3390/genes14122110
Submission received: 19 October 2023 / Revised: 19 November 2023 / Accepted: 20 November 2023 / Published: 22 November 2023
(This article belongs to the Section Animal Genetics and Genomics)
Browse Figures
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Abstract

:
Hemiculterella wui is an endemic small freshwater fish, distributed in the Pearl River system and Qiantang River, China. In this study, we identified and annotated the complete mitochondrial genome sequence of H. wui. The mitochondrial genome was 16,619 bp in length and contained 13 protein coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one control region. The nucleotide composition of the mitochondrial genome was 29.9% A, 25.3% T, 27.4% C, and 17.5% G, respectively. Most PCGs used the ATG start codon, except COI and ATPase 8 started with the GTG start codon. Five PCGs used the TAA termination codon and ATPase 8 ended with the TAG stop codon, and the remaining seven genes used two incomplete stop codons (T and TA). Most of the tRNA genes showed classical cloverleaf secondary structures, except that tRNASer(AGY) lacked the dihydrouracil loop. The average Ka/Ks value of the ATPase 8 gene was the highest, while the average Ka/Ks value of the COI gene was the lowest. Phylogenetic analyses showed that H. wui has a very close relationship with Pseudohemiculter dispar and H. sauvagei. This study will provide a valuable basis for further studies of taxonomy and phylogenetic analyses in H. wui and Xenocyprididae.

1. Introduction

Mitochondria are semi-autonomous organelles that exist widely in eukaryotic cells and possess their genome (called the mitochondrial genome) [1]. The mitochondrial genome is a covalently closed circular double-stranded DNA molecule that can independently encode some proteins for many biological processes [2]. The mitochondrial genomes of fish usually contain 37 genes, namely 13 protein coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs), in addition to a control region (CR) [3,4]. The CR is a non-coding region with the largest variation in the sequence and length of the entire mitochondrial genome and is generally found between the tRNAPro and tRNAPhe genes [5]. Because the mitochondrial genome has the advantages of simple structure, small molecular weight, self-replication, strict maternal inheritance, and a fast evolution rate, it has been widely used in fish phylogeny, species identification, population genetics, adaptive evolution, etc. [5,6].
The Xenocyprididae is one of the most species-rich families of Cypriniformes, comprising approximately 160 species belonging to 45 genera [7]. H. wui (Wang, 1935) is an endemic fish that is distributed in the Pearl River system, Poyang Lake system, and the Qiantang River system, China, and is used as a small economic species in local areas. The main characteristics of H. wui are that absence of spinous rays in the dorsal fin and a ventral ridge from the base of the pelvic fin to the anus [8]. The common name of H. wui is “LanDao” in China. However, little is known about H. wui, and previous research has focused mainly on resource investigation.
In this study, we first sequenced, annotated, and characterized the complete mitochondrial genome sequence of H. wui. A preliminary analysis of its genetic composition and structural characteristics was conducted to provide molecular insights into the taxonomic and phylogenetic structure of the family Xenocyprididae. On this basis, combined with data from the NCBI database, the phylogenetic relationship of Xenocyprididae in this family was analyzed. Our results reveal relevant information about the mitochondrial genomes of H. wui, as well as the evolutionary relationships of the Xenocyprididae, which will provide a valuable basis for further studies of the evolution of Hemiculterella and Xenocyprididae.

2. Materials and Methods

2.1. Sample Collection, DNA Extraction, and Illumina Sequencing

The fish samples were collected from the Duliujiang River, Guizhou Province, China, and preserved in anhydrous ethanol and stored at −20 °C. Genomic DNA was extracted from the muscle of a single specimen using the DNeasy Blood & Tissue Kit (Qiagen Inc., Hilden, Germany) according to the manufacturer’s protocol. Next-generation sequencing was performed at the DNA Stories Bioinformatics Center (Chengdu, Sichuan, China). Library construction and Illumina sequencing were carried out according to Zhang et al. [9].

2.2. Mitochondrial Genome Assembly, Annotation, and Sequence Analysis

Mitochondrial genome assembly was performed using GetOrganelle v. 1.7.7.0 [10]. Then, MitoAnnotator 3.94 [11] was used to annotate the mitochondrial genome. The tRNA second structures were predicted using the online tool MITOS Web Server [12]. The formulae AT skew = (A − T)/(A + T) and GC skew = (G − C)/(G + C) were used to calculate the asymmetric base composition of the mitochondrial genome sequence [13]. The proportions of mitochondrial genome nucleotides and relative synonymous codon usage (RSCU) were estimated using PhyloSuite v1.2.3 [14]. The rates of non-synonymous substitutions (Ka) and synonymous substitutions (Ks) for each PCG were calculated using DnaSP 6 [15].

2.3. Phylogenetic Analysis

To elucidate the phylogenetic position of H. wui, we constructed phylogenetic trees using a data set of 13 PCGs of 75 species in Xenocyprididae, plus Cyprinus carpio Linnaeus, 1758 and Gobiocypris rarus Ye & Fu, 1983 as outgroups (Table 1). We used PhyloSuite v1.2.3 [13] to extract mitochondrial genes and then align the 13 PCGs using MAFFT v7.0 [16]. The optimal partition scheme and evolutionary models were determined by PartitionFinder2 [17]. The Bayesian inference (BI) phylogenetic analysis was performed in MrBayes 3.2.6 [18], employing a partition model with 2 parallel runs and 2,000,000 generations. The initial 25% of the sampled data were excluded as burn-in. Maximum likelihood (ML) phylogenetic analysis was performed in IQ-TREE v1.6.12 [19] with 5000 ultrafast bootstraps [20]. The phylogenetic trees were generated and visualized using the online tool iTOL v6 (https://itol.embl.de/) (accessed on 26 September 2023).

3. Results and Discussion

3.1. Mitochondrial Genome Organization of H. wui

After assembly, annotation, and analysis, the mitochondrial genome (16,619 bp) of H. wui was determined in this study (GenBank Accession No.OR574832). The size of the complete mitochondrial genome of H. wui was almost the same as that of H. sauvagei Warpachowski, 1888 (16,618 bp). The mitochondrial genome of H. wui consisted of 13 PCGs, 2 rRNAs, 22 tRNAs, and a control region ‘D-loop’ (Figure 1; Table 2). Only 9 genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer (UCN), tRNAGlu, tRNAPro, and ND6) were encoded in the light strand, and the other genes were encoded in the heavy strand. The gene composition and order in H. wui were the same as in a typical fish mitochondrial genome [3,4,5].
There were 13 intergenic spacers found in the H. wui mitochondrial genome. The intergenic spacers varied in length from 1 bp to 32 bp (Table 2). The longest intergenic spacer was located between tRNAAsn and tRNACys (32 bp). Five gene overlaps were found in the H. wui mitochondrial genome. The minimum overlap region was located between tRNAThr and tRNAPro (1 bp), and the maximum overlap region was located between ATPase 8 and ATPase 6, ND4L and ND4 (7 bp). Mitochondrial gene overlap and gene spacers were common phenomena in teleost species [9,21].
The total nucleotide composition of the mitochondrial genome was 29.9% A, 25.3% T, 27.4% C, and 17.5% G, respectively, with a slight AT bias (55.2%) (Table 3). It was similar to other fish species in the Xenocyprididae family (Table 1). The highest A + T content was in the noncoding control region (64.4%) and the lowest A + T content was in the first codon position of PCGs (47.5%). The AT skew value was positive (0.084) in the mitochondrial genome of H. wui, while the GC skew value was negative (−0.22). It showed a preference for A and C bases compared to that for T and G bases.

3.2. Protein Coding Genes and Codon Usage

There were 13 PCGs (ND1, ND2, ND3, ND4L, ND4, ND5, ND6, COI, COII, COIII, ATPase 6, ATPase 8, and Cyt b) in the mitochondrial genome and their total size was 11,422 bp (Table 3). Only ND6 was encoded on the light strand, while the rest of the PCGs were located on the heavy strand. The A + T content (54.6%) of PCGs was higher than the G + C content (45.4%). Most PCGs used the ATG start codon, but COI and ATPase 8 started with GTG. The GTG start codon for COI was observed in many other fish species [3], but the use of GTG as the start codon in ATPase 8 was a rare phenomenon. The termination codon TAA was used by five genes (COI, ND1, ND4L, ND5, and ND6). TAG was the stop codon of the ATPase 8 gene. The remaining 7 genes used two incomplete stop codons (T and TA). Incomplete stop codons can be transformed into complete stop codons by post-transcriptional modification, such as polyadenylation [22].
The RSCU value was a measure of codon usage preference in the genome. The number of codons and the RSCU of 13 PCGs are presented in Table 4 and Figure 2. A total of 3804 amino acid triplets were used in the 13 PCGs. The most commonly used amino acids were Leu, followed by Ala, Thr, Ile, and Gly. The least commonly used amino acid was Cys. The most commonly used codon was CUA, followed by UUC, AUU, and GCC. The least frequent codon was CGU, not including stop codons.

3.3. Ribosomal and Transfer RNA Genes

The mitochondrial genome of H. wui has two rRNAs (12S rRNA and 16S rRNA), both encoded in the heavy stand. They were close together in the genome, separated by a single tRNA. The 12S rRNA was located between tRNAPhe and tRNAVal with a length of 964 bp. The 16S rRNA was located between tRNAVal and tRNALeu (UUR) with a length of 1690 bp. The A + T content of the two rRNA was 53.70%. The two rRNA genes had a positive AT skew value of 0.245 and a negative GC skew value of −0.046 (Table 3).
Transfer RNA, also known as transfer ribonucleic acid, is often referred to as tRNA. As shown in Figure 3, we found that most tRNA genes had a typical cloverleaf secondary structure, except tRNASer(AGY) lacked the dihydrouracil loop (DHU loop). The tRNA genes varied in length from 68 bp (tRNACys) to 76 bp (tRNALeu (UUR) and tRNALys) and were scattered across the mitochondrial genome. The sum of the A + T content of all tRNAs was 55.8%. It showed a preference for AT bases. The AT skew and GC skew values were 0.029 and 0.056, respectively.

3.4. Control Region

The control region, also known as the AT rich region or D-loop, was 934 bp in length. It was located between tRNAPro and tRNAPhe, similar to a typical fish mitochondrial genome [3]. The nucleotide composition was 32.9% A, 31.5% T, 14.9% G, and 20.8% C (Table 3). This region had the highest AT content in the entire mitochondrial genome.

3.5. Selection Analysis

Among the 13 PCGs of the Xenocyprididae, the average value of Ka/Ks of ATPase 8 was the highest, while the average value of Ka/Ks of COI was the lowest (Figure 4). It implies that ATPase 8 might evolve more rapidly than other mitochondrial protein coding genes. Even under different selection pressures, the evolutionary patterns of 13 PCGs in Xenocyprididae were similar to those of Sinocyclocheilus (Fang, 1936) fishes [23] and Labeoninae [9]. Furthermore, the average Ka/Ks ratios of all PCGs were much lower than one, indicating that these genes were all under a strong purifying selection.

3.6. Phylogenetic Analysis

We used a total of 75 species of Xenocyprididae to construct phylogenetic trees based on 13 PCGs in the mitochondrial genome, with C. carpio and G. rarus as outgroups. The two methods used to build the phylogenetic tree yielded similar topological structures (Figure 5). The phylogenetic trees showed that H. wui, P. dispar (Peters, 1881), and H. sauvagei, were clustered into a group (ML bootstrap value = 84%, Bayesian posterior probability = 0.5). The differences in external morphology between Pseudohemiculter Nichols & Pope, 1927 and Hemiculterella Warpachowski, 1888 are not obvious. The main difference is that the last unbranched dorsal fin ray of Pseudohemiculter is hard, whereas that of Hemiculterella is soft [7]. The monophyly of Hemiculterella, Pseudohemiculter, and Hemiculter was not supported. More extensive sampling and multilocus markers are required to understand the robust phylogenetic relationships of Pseudohemiculter, Hemiculterella, Hemiculter, and related genera.

4. Conclusions

In conclusion, we analyzed and described the characterization of the mitochondrial genome of H. wui and the phylogenetic relationship position in the Xenocyprididae, which will provide a valuable basis for further studies of H. wui and the evolutionary relationship of Xenocyprididae.

Author Contributions

Conceptualization, R.Z. and F.Y.; methodology, R.Z. and T.Z.; software, R.Z. and T.Z.; validation, R.Z., F.Y. and T.Z.; formal analysis, R.Z. and T.Z.; investigation, R.Z.; resources, R.Z.; data curation, R.Z. and T.Z.; writing—original draft preparation, R.Z., F.Y. and T.Z.; writing—review and editing, R.Z., F.Y. and T.Z.; visualization, R.Z. and T.Z.; supervision, R.Z.; project administration, R.Z.; funding acquisition, R.Z. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by Guizhou Provincial Science and Technology Foundation (Qiankehejichu [2018]1113) and new seedling plans of Guizhou Normal University, grant number Qianshi Xinmiao [2022]11.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Mitochondrial genome sequence data supporting the findings of this study are openly available from the GenBank of the National Center for Biotechnology Information (NCBI) at https://www.ncbi.nlm.nih.gov (accession number: OR574832) accessed on 18 October 2023.

Conflicts of Interest

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

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Genes 14 02110 g001
Figure 1. Circular map of the H. wui mitochondrial genome.
Figure 1. Circular map of the H. wui mitochondrial genome.
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Figure 2. Relative synonymous codon usage (RSCU) of the mitochondrial genome for H. wui.
Figure 2. Relative synonymous codon usage (RSCU) of the mitochondrial genome for H. wui.
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Figure 3. Predicted secondary structures of 22 tRNAs in the mitochondrial genome of H. wui.
Figure 3. Predicted secondary structures of 22 tRNAs in the mitochondrial genome of H. wui.
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Figure 4. Ka/Ks values for 13 PCGs from 75 mitochondrial genomes of Xenocyprididae.
Figure 4. Ka/Ks values for 13 PCGs from 75 mitochondrial genomes of Xenocyprididae.
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Figure 5. The phylogeny of H. wui with other species of Xenocyprididae based on the concatenated nucleotide sequences of 13 PCGs. The Maximum likelihood bootstrap values and Bayesian posterior probabilities are superimposed on each node.
Figure 5. The phylogeny of H. wui with other species of Xenocyprididae based on the concatenated nucleotide sequences of 13 PCGs. The Maximum likelihood bootstrap values and Bayesian posterior probabilities are superimposed on each node.
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Table 1. Species information for phylogenetic analysis.
Table 1. Species information for phylogenetic analysis.
No.SpeciesGenBank Accession No.Size (bp)A%T%G%C%A + T%AT SkewGC Skew
1Anabarilius brevianalis Zhou & Cui, 1992MK757491.116,61028.324.618.728.452.90.070−0.205
2Anabarilius duoyiheensis Li, Mao & Lu, 2002NC_068241.116,61428.924.918.427.953.80.074−0.205
3Anabarilius grahami (Regan, 1908)MF370204.116,61228.924.818.327.953.70.077−0.208
4Anabarilius liui (Chang, 1944) MG702493.116,60828.524.418.528.552.90.077−0.212
5Ancherythroculter kurematsui (Kimura, 1934)NC_029707.116,62131.224.916.227.756.10.112−0.263
6Ancherythroculter lini Luo, 1994NC_027741.116,61630.824.716.528.055.50.109−0.259
7Ancherythroculter nigrocauda Yih & Wu, 1964NC_021414.116,62331.224.816.227.856.00.114−0.262
8Ancherythroculter wangi (Tchang, 1932)NC_037405.116,62231.224.816.227.856.00.113−0.264
9Aphyocypris arcus (Lin, 1931)NC_015540.116,61731.427.115.725.758.50.074−0.241
10Aphyocypris chinensis Günther, 1868NC_008650.116,60630.727.716.525.158.40.053−0.207
11Aphyocypris kikuchii (Oshima, 1919)NC_019620.116,60130.827.716.525.058.50.052−0.206
12Aphyocypris lini (Weitzman & Chan, 1966)NC_062821.116,61330.426.916.626.057.30.061−0.221
13Aphyocypris moltrechti (Regan, 1908)NC_019621.116,61731.227.416.025.558.60.066−0.229
14Aphyocypris normalis Nichols & Pope, 1927NC_015538.116,61931.227.015.925.858.20.073−0.237
15Aphyocypris pulchrilineata Zhu, Zhao & Huang, 2013MK387702.116,61030.526.616.626.257.10.069−0.224
16Candidia barbata (Regan, 1908)NC_037156.116,60830.326.916.726.157.20.059−0.219
17Candidia pingtungensis Chen, Wu & Hsu, 2008NC_028596.116,61229.926.917.126.256.80.053−0.211
18Chanodichthys dabryi (Bleeker, 1871)NC_021418.116,62231.525.015.927.656.50.116−0.268
19Chanodichthys erythropterus (Basilewsky, 1855)MN105126.116,62331.025.116.327.656.10.106−0.255
20Chanodichthys mongolicus (Basilewsky, 1855)NC_008683.116,62231.224.916.227.856.10.113−0.264
21Chanodichthys recurviceps (Richardson, 1846)NC_024277.116,62231.424.816.127.856.20.117−0.266
22Ctenopharyngodon idella (Valenciennes, 1844)NC_010288.116,60931.926.215.626.358.10.098−0.253
23Culter alburnus Basilewsky, 1855NC_013616.116,62231.224.816.227.856.00.114−0.262
24Culter compressocorpus (Yih & Chu, 1959)NC_024183.116,62331.125.116.327.556.20.105−0.254
25Culter oxycephaloides Kreyenberg & Pappenheim, 1908KY404014.116,61931.324.816.127.956.10.117−0.269
26C. carpio Linnaeus, 1758 NC_018035.11658131.924.815.727.556.70.125−0.272
27Distoechodon compressus (Nichols, 1925)NC_067894.116,62131.425.416.027.256.80.107−0.260
28Distoechodon tumirostris Peters, 1881NC_011208.116,62031.425.416.027.256.80.106−0.261
29Elopichthys bambusa (Richardson, 1845)NC_024834.116,61930.127.216.925.857.30.049−0.209
30G. rarus Ye & Fu, 1983NC_018099.116,60129.527.617.225.757.10.034−0.198
31Hemiculter bleekeri Warpachowski, 1888NC_029831.116,61529.325.617.827.354.90.067−0.211
32Hemiculter leucisculus (Basilewsky, 1855)NC_022929.116,61730.425.417.127.255.80.090−0.228
33Hemiculter nigromarginis Fang, 1942NC_036740.116,62130.425.417.127.155.80.089−0.228
34Hemiculterella sauvagei Warpachowski, 1888NC_026693.116,61829.925.617.427.055.50.078−0.216
35H. wui (Wang, 1935)OR57483216,61929.925.317.527.455.20.084−0.22
36Hemigrammocypris neglecta (Stieler, 1907)NC_015548.116,61531.226.316.725.857.50.085−0.215
37Hypophthalmichthys molitrix (Valenciennes, 1844)NC_010156.116,62031.825.615.826.957.40.109−0.261
38Hypophthalmichthys nobilis (Richardson, 1845)NC_010194.116,62131.625.315.927.156.90.111−0.259
39Ischikauia steenackeri (Sauvage, 1883)NC_008667.116,62031.425.116.127.456.50.111−0.261
40Macrochirichthys macrochirus (Valenciennes, 1844)NC_015551.11685732.526.115.226.258.60.108−0.266
41Megalobrama amblycephala Yih, 1955NC_010341.116,62331.224.716.227.955.90.117−0.265
42Megalobrama skolkovii (Basilewsky, 1855)NC_024422.116,62031.224.716.227.955.90.116−0.266
43Megalobrama terminalis (Richardson, 1846)NC_018816.116,62331.124.816.327.855.90.113−0.26
44Metzia formosae (Oshima, 1920)NC_022458.116,61431.425.616.226.857.00.102−0.246
45Metzia lineata (Pellegrin, 1907)NC_031541.116,61432.126.915.625.459.00.089−0.241
46Metzia longinasus Gan, Lan & Zhang, 2009NC_024729.116,61431.926.215.726.258.10.098−0.251
47Metzia mesembrinum (Jordan & Evermann, 1902)NC_023797.116,61132.026.815.725.558.80.088−0.238
48Mylopharyngodon piceus (Richardson, 1846)NC_011141.116,60932.024.515.727.856.50.132−0.278
49Nipponocypris koreanus (Kim, Oh & Hosoya, 2005)NC_025286.116,61530.026.817.126.156.80.056−0.209
50Nipponocypris sieboldii (Temminck & Schlegel, 1846)NC_008653.116,61630.125.816.927.255.90.078−0.233
51Nipponocypris temminckii (Temminck & Schlegel, 1846)NC_027664.116,61530.326.516.826.356.80.067−0.221
52Ochetobius elongatus (Kner, 1867)NC_025646.116,61331.025.416.327.456.40.099−0.255
53Opsariichthys acutipinnis (Bleeker, 1871)NC_028595.116,61528.226.618.027.254.80.030−0.204
54Opsariichthys bidens Günther, 1873NC_008744.116,61127.226.719.127.153.90.010−0.174
55Opsariichthys evolans (Jordan & Evermann, 1902)NC_033948.116,61628.226.618.027.254.80.029−0.203
56Opsariichthys pachycephalus Günther, 1868NC_033949.116,60627.926.818.327.154.70.020−0.194
57Opsariichthys uncirostris (Temminck & Schlegel, 1846)NC_008652.116,61327.226.718.927.253.90.008−0.181
58Parabramis pekinensis (Basilewsky, 1855)NC_022678.116,62231.124.816.327.855.90.113−0.261
59Parazacco spilurus (Günther, 1868)NC_023786.116,61230.426.916.626.057.30.062−0.220
60Plagiognathops microlepis (Bleeker, 1871)NC_022711.116,62330.625.216.927.355.80.097−0.236
61Pseudobrama simoni (Bleeker, 1864)NC_022852.116,61831.627.215.725.558.80.075−0.238
62P. dispar (Peters, 1881)NC_020435.116,62030.325.517.127.155.80.086−0.224
63Pseudohemiculter hainanensis (Boulenger, 1900)NC_065693.116,64729.724.817.528.054.50.089−0.230
64Pseudolaubuca engraulis (Nichols, 1925)NC_020462.116,61227.125.919.527.553.00.023−0.171
65Pseudolaubuca sinensis Bleeker, 1864NC_026712.116,61729.625.817.626.955.40.069−0.209
66Sinibrama macrops (Günther, 1868)NC_020013.116,62630.724.716.627.955.40.110−0.253
67Sinibrama melrosei (Nichols & Pope, 1927)NC_063731.116,61930.725.516.627.256.20.092−0.242
68Sinibrama taeniatus (Nichols, 1941)NC_026119.116,62331.325.816.126.857.10.097−0.248
69Sinibrama wui (Rendahl, 1933)NC_068747.116,62630.724.616.728.055.30.110−0.253
70Squaliobarbus curriculus (Richardson, 1846)NC_019652.116,61931.225.016.127.756.20.111−0.264
71Toxabramis houdemeri Pellegrin, 1932NC_029348.116,61830.825.316.627.356.10.098−0.243
72Toxabramis swinhonis Günther, 1873NC_029249.116,62231.226.516.126.157.70.081−0.237
73Xenocypris davidi Bleeker, 1871NC_013072.116,63031.325.416.227.256.70.104−0.254
74Xenocypris fangi Tchang, 1930NC_056130.116,61931.225.316.227.356.50.105−0.255
75Xenocypris yunnanensis Nichols, 1925NC_035954.116,63031.325.416.127.256.70.104−0.255
76Zacco acanthogenys (Bleeker, 1871)NC_028546.116,61129.127.217.626.056.30.033−0.192
77Zacco platypus (Temminck & Schlegel, 1846)NC_023105.116,61129.027.217.826.156.20.032−0.190
Table 2. Organization and characterization of the H. wui mitochondrial genome.
Table 2. Organization and characterization of the H. wui mitochondrial genome.
GeneStrandLocation (bp)Size (bp)Intergenic NucleotideAnticodonStart/Stop Codons
tRNAPheH1–69690GAA
12S rRNAH70–10339640
tRNAValH1034–1105720TAC
16S rRNAH1106–279516900
tRNALeu (UUR)H2796–2871761TAA
ND1H2873–38479754 ATG/TAA
tRNAIleH3852–392372−2GAT
tRNAGlnL3922–3992711TTG
tRNAMetH3994–4062690CAT
ND2H4063–510710450 ATG/T
tRNATrpH5108–5178711TCA
tRNAAlaL5180–5248691TGC
tRNAAsnL5250–53227332GTT
tRNACysL5355–5422681GCA
tRNATyrL5424–5494711GTA
COIH5496–704615510 GTG/TAA
tRNASer (UCN)L7047–7117713TGA
tRNAAspH7121–71947413GTC
COIIH7208–78986910 ATG/T
tRNALysH7899–7974761TTT
ATPase 8H7976–8140165−7 GTG/TAG
ATPase 6H8134–88166830 ATG/TA
COIIIH8817–96017850 ATG/TA
tRNAGlyH9602–9673720TCC
ND3H9674–10,0223490 ATG/T
tRNAArgH10,023–10,092700TCG
ND4LH10,093–10,389297−7 ATG/TAA
ND4H10,383–11,76413820 ATG/TA
tRNAHisH11,765–11,833690GTG
tRNASer (AGY)H11,834–11,902691GCT
tRNALeu (CUN)H11,904–11,976730TAG
ND5H11,977–13,8121836−4 ATG/TAA
ND6L13,809–14,3305220 ATG/TAA
tRNAGluL14,331–14,399694TTC
Cyt bH14,404–15,54411410 ATG/T
tRNAThrH15,545–15,61672−1TGT
tRNAProL15,616–15,685700TGG
Control regionH15,686–16,6199340
Table 3. List of the nucleotide composition, AT skew, and GC skew of the H. wui mitochondrial genome.
Table 3. List of the nucleotide composition, AT skew, and GC skew of the H. wui mitochondrial genome.
RegionsSize (bp)A%T%G%C%A + T%G + C%AT SkewGC Skew
Full genome16,61929.925.317.527.455.244.90.084−0.22
PCGs11,42227.627.017.128.354.645.40.011−0.248
1st codon position380426.521.026.426.147.552.50.1160.005
2nd codon position380418.540.513.727.359.041.0−0.374−0.333
3rd codon position380437.919.411.131.657.342.70.322−0.478
ATPase 668327.129.614.528.856.743.3−0.044−0.331
ATPase 816535.823.612.128.559.440.60.204−0.403
COI155126.628.218.626.654.845.2−0.028−0.178
COII69129.826.016.627.555.844.10.067−0.246
COIII78527.327.617.128.054.945.1−0.007−0.243
Cyt b114128.026.215.930.054.245.90.032−0.308
ND197526.824.917.530.851.748.30.036−0.274
ND2104528.322.917.231.651.248.80.107−0.294
ND334925.828.717.228.454.545.6−0.053−0.245
ND4L138229.127.015.928.056.143.90.037−0.275
ND429725.925.316.532.351.248.80.013−0.324
ND5183630.426.014.429.256.443.60.077−0.34
ND652214.039.132.014.953.146.9−0.4730.363
rRNAs265433.420.322.124.253.746.30.245−0.046
tRNAs156628.727.123.320.855.844.10.0290.056
Control region93432.931.514.920.864.435.70.022−0.165
Table 4. Codon number in the H. wui mitochondrial PCGs.
Table 4. Codon number in the H. wui mitochondrial PCGs.
Amino AcidCodonCountRSCUAmino AcidCodonCountRSCU
Phe (F)UUU740.66Tyr (Y)UAU450.79
UUC1511.34 UAC691.21
Leu (L)UUA940.91stop codonUAA53.33
UUG260.25 UAG10.67
CUU1111.07His (H)CAU220.42
CUC920.89 CAC821.58
CUA2242.16Gln (Q)CAA841.73
CUG740.71 CAG130.27
Ile (I)AUU1491.06Asn (N)AAU480.79
AUC1320.94 AAC731.21
Met (M)AUA1121.29Lys (K)AAA611.54
AUG610.71 AAG180.46
Val (V)GUU500.83Asp (D)GAU170.44
GUC520.86 GAC611.56
GUA1051.74Glu (E)GAA841.63
GUG350.58 GAG190.37
Ser (S)UCU350.88Cys (C)UGU100.77
UCC671.68 UGC161.23
UCA771.93Trp (W)UGA1041.72
UCG70.18 UGG170.28
Pro (P)CCU290.54Arg (R)CGU60.32
CCC591.09 CGC150.79
CCA1021.89 CGA392.05
CCG260.48 CGG160.84
Thr (T)ACU500.66Ser (S)AGU150.38
ACC991.32 AGC380.95
ACA1281.7stop codonAGA00
ACG240.32 AGG00
Ala (A)GCU480.57Gly (G)GGU300.49
GCC1491.77 GGC460.75
GCA1121.33 GGA1091.79
GCG280.33 GGG590.97
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Zhang, R.; Zhu, T.; Yu, F. The New Mitochondrial Genome of Hemiculterella wui (Cypriniformes, Xenocyprididae): Sequence, Structure, and Phylogenetic Analyses. Genes 2023, 14, 2110. https://doi.org/10.3390/genes14122110

AMA Style

Zhang R, Zhu T, Yu F. The New Mitochondrial Genome of Hemiculterella wui (Cypriniformes, Xenocyprididae): Sequence, Structure, and Phylogenetic Analyses. Genes. 2023; 14(12):2110. https://doi.org/10.3390/genes14122110

Chicago/Turabian Style

Zhang, Renyi, Tingting Zhu, and Feng Yu. 2023. "The New Mitochondrial Genome of Hemiculterella wui (Cypriniformes, Xenocyprididae): Sequence, Structure, and Phylogenetic Analyses" Genes 14, no. 12: 2110. https://doi.org/10.3390/genes14122110

APA Style

Zhang, R., Zhu, T., & Yu, F. (2023). The New Mitochondrial Genome of Hemiculterella wui (Cypriniformes, Xenocyprididae): Sequence, Structure, and Phylogenetic Analyses. Genes, 14(12), 2110. https://doi.org/10.3390/genes14122110

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