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Zhang X, Li C, Jiang L, Qiao G, Chen J. Characteristics and Comparative Analysis of Mitochondrial Genomes of the Aphid Genus Hyalopterus Koch (Hemiptera: Aphididae: Aphidinae). INSECTS 2024; 15:389. [PMID: 38921104 PMCID: PMC11204073 DOI: 10.3390/insects15060389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/18/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024]
Abstract
Using Illumina sequencing technology, we generated complete mitochondrial genomes (mitogenomes) of three constituent species of the aphid genus Hyalopterus Koch, Hyalopterus amygdali (Blanchard), Hyalopterus arundiniformis Ghulamullah, and Hyalopterus pruni (Geoffroy). The sizes of the Hyalopterus mitogenomes range from 15,306 to 15,410 bp, primarily due to variations in the length of non-coding regions. The Hyalopterus mitogenomes consist of 37 coding genes arranged in the order of the ancestral insect mitogenome, a control region, and a repeat region between trnE and trnF. According to the COI-based analysis, one previously reported mitogenome of H. pruni should be assigned to H. arundiniformis. The gene order, nucleotide composition, and codon usage in the Hyalopterus mitogenomes are highly conserved and similar to those of other species of Aphidinae. The tandem repeat units differ in nucleotide composition, length, and copy number across three Hyalopterus species. Within the widespread Eurasian species H. arundiniformis, variation in repeat units among different geographic populations is observed, indicating that the repeat region may provide valuable insights for studying the intraspecific diversification of aphids. Phylogenetic analyses based on 28 complete mitogenomes of Aphidinae supported the monophyly of Aphidinae, Aphidini, Macrosiphini, and two subtribes of Aphidini. Hyalopterus was monophyletic. H. amygdali and H. pruni formed a sister group, while H. arundiniformis was placed basally. Characterization of the mitogenomes of Hyalopterus provides valuable resources for further comparative studies and for advancing our understanding of the aphid mitogenome architecture.
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Affiliation(s)
- Xiaolu Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cailing Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liyun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
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Dial DT, Weglarz KM, Brunet BMT, Havill NP, von Dohlen CD, Burke GR. Whole-genome sequence of the Cooley spruce gall adelgid, Adelges cooleyi (Hemiptera: Sternorrhyncha: Adelgidae). G3 (BETHESDA, MD.) 2023; 14:jkad224. [PMID: 37766465 PMCID: PMC10755206 DOI: 10.1093/g3journal/jkad224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
The adelgids (Adelgidae) are a small family of sap-feeding insects, which, together with true aphids (Aphididae) and phylloxerans (Phylloxeridae), make up the infraorder Aphidomorpha. Some adelgid species are highly destructive to forest ecosystems such as Adelges tsugae, Adelges piceae, Adelges laricis, Pineus pini, and Pineus boerneri. Despite this, there are no high-quality genomic resources for adelgids, hindering advanced genomic analyses within Adelgidae and among Aphidomorpha. Here, we used PacBio continuous long-read and Illumina RNA-sequencing to construct a high-quality draft genome assembly for the Cooley spruce gall adelgid, Adelges cooleyi (Gillette), a gall-forming species endemic to North America. The assembled genome is 270.2 Mb in total size and has scaffold and contig N50 statistics of 14.87 and 7.18 Mb, respectively. There are 24,967 predicted coding sequences, and the assembly completeness is estimated at 98.1 and 99.6% with core BUSCO gene sets of Arthropoda and Hemiptera, respectively. Phylogenomic analysis using the A. cooleyi genome, 3 publicly available adelgid transcriptomes, 4 phylloxera transcriptomes, the Daktulosphaira vitifoliae (grape phylloxera) genome, 4 aphid genomes, and 2 outgroup coccoid genomes fully resolves adelgids and phylloxerans as sister taxa. The mitochondrial genome is 24 kb, among the largest in insects sampled to date, with 39.4% composed of noncoding regions. This genome assembly is currently the only genome-scale, annotated assembly for adelgids and will be a valuable resource for understanding the ecology and evolution of Aphidomorpha.
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Affiliation(s)
- Dustin T Dial
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | | | - Bryan M T Brunet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada K1A 0C6
| | - Nathan P Havill
- USDA Forest Service, Northern Research Station, Hamden, CT 06514, USA
| | | | - Gaelen R Burke
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
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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 (Basel) 2023; 14:2110. [PMID: 38136932 PMCID: PMC10742607 DOI: 10.3390/genes14122110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
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.
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Gao Y, Zhang J, Wang Q, Liu Q, Tang B. The Complete Mitochondrial Genome of Box Tree Moth Cydalima perspectalis and Insights into Phylogenetics in Pyraloidea. Animals (Basel) 2023; 13:ani13061045. [PMID: 36978586 PMCID: PMC10044125 DOI: 10.3390/ani13061045] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/15/2023] Open
Abstract
To resolve and reconstruct phylogenetic relationships within Pyraloidea based on molecular data, the mitochondrial genome (mitogenome) was widely applied to understand phylogenetic relations at different taxonomic levels. In this research, a complete mitogenome of Cydalima perspectalis was recorded, and the phylogenetic position of C. perspectalis was inferred based on the sequence in combination with other available sequence data. According to the research, the circular mitochondrial genome is 15,180 bp in length. It contains 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), 13 typical protein-coding genes (PCGs), and a non-coding control region. The arrangement of a gene of the C. perspectalis mitogenome is not the same as the putative ancestral arthropod mitogenome. All of the PCGs are initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which is undertaken by CGA. Five genes have incomplete stop codons that contain only ‘T’. All tRNA genes display a typical clover–leaf structure of mitochondrial tRNA, except for trnS1 (AGN). The control region contained an ‘ATAGG(A)’-like motif followed by a poly-T stretch. Based on the mitochondrial data, phylogenetic analysis within Pyraloidea was carried out using Bayesian inference (BI) and maximum likelihood (ML) analyses. Phylogenetic analysis showed that C. perspectalis is more closely related to Pygospila tyres within Spilomelinae than those of Crambidae and Pyraloidea.
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Affiliation(s)
- Yichang Gao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Centre for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224007, China
| | - Jie Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Centre for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224007, China
| | - Qinghao Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Centre for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224007, China
| | - Qiuning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Centre for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224007, China
- Correspondence: (Q.L.); (B.T.); Tel./Fax: +86-515-88233991 (B.T.)
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Centre for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224007, China
- Correspondence: (Q.L.); (B.T.); Tel./Fax: +86-515-88233991 (B.T.)
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Wei Z, Huang X, Shi A. First mitochondrial genome of subfamily Julodinae (Coleoptera, Buprestidae) with its phylogenetic implications. Zookeys 2023; 1139:165-182. [PMID: 36761279 PMCID: PMC9860506 DOI: 10.3897/zookeys.1139.96216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Complete mitochondrial genomes of three species of the family Buprestidae were sequenced, annotated, and analyzed in this study. To explore the mitogenome features of the subfamily Julodinae and verify its phylogenetic position, the complete mitogenome of Julodisvariolaris was sequenced and annotated. The complete mitogenomes of Ptosimachinensis and Chalcophorajaponica were also provided for the phylogenetic analyses within Buprestidae. Compared to the known mitogenomes of Buprestidae species varied from 15,499 bp to 16,771 bp in length, three newly sequenced mitogenomes were medium length (15,759-16,227 bp). These mitogenomes were encoded 37 typical mitochondrial genes. Among the three studied mitogenomes, Leu2 (L2), Ser2 (S2), and Pro (P) were the three most frequently encoded amino acids. Within the Buprestidae, the heterogeneity in sequence divergences of Agrilinae was highest, whereas the sequence homogeneity of Chrysochroinae was highest. Moreover, phylogenetic analyses were performed based on nucleotide matrix (13 PCGs + 2 rRNAs) among the available sequenced species of Buprestidae using Bayesian Inference and Maximum Likelihood methods. The results showed that the Julodinae was closely related to the subfamily Polycestinae. Meanwhile, the genera Melanophila, Dicerca, and Coomaniella were included in Buprestinae, which was inconsistent with the current classification system of Buprestidae. These results could contribute to further studies on genetic diversity and phylogeny of Buprestidae.
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Affiliation(s)
- Zhonghua Wei
- The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University, 637009, Nanchong, Sichuan Province, ChinaChina West Normal UniversityNanchongChina
| | - Xuyan Huang
- The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University, 637009, Nanchong, Sichuan Province, ChinaChina West Normal UniversityNanchongChina
| | - Aimin Shi
- The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University, 637009, Nanchong, Sichuan Province, ChinaChina West Normal UniversityNanchongChina
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Dan ZC, Guan DL, Jiang T, Wang H, Zhao L, Xu SQ. Evolution of Gene Arrangements in the Mitogenomes of Ensifera and Characterization of the Complete Mitogenome of Schizodactylus jimo. Int J Mol Sci 2022; 23:ijms232012094. [PMID: 36292953 PMCID: PMC9603354 DOI: 10.3390/ijms232012094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
Gene arrangement (relative location of genes) is another evolutionary marker of the mitogenome that can provide extensive information on the evolutionary mechanism. To explore the evolution of gene arrangements in the mitogenome of diversified Ensifera, we sequenced the mitogenome of the unique dune cricket species found in China and used it for phylogenetic analysis, in combination with 84 known Ensiferan mitogenomes. The mitogenome of Schizodactylus jimo is a 16,428-bp circular molecule that contains 37 genes. We identified eight types of gene arrangement in the 85 ensiferan mitogenomes. The gene location changes (i.e., gene translocation and duplication) were in three gene blocks: I-Q-M-ND2, rrnl-rns-V, and ND3-A-R-N-S-E-F. From the phylogenetic tree, we found that Schizodactylus jimo and most other species share a typical and ancient gene arrangement type (Type I), while Grylloidea has two types (Types II and III), and the other five types are rare and scattered in the phylogenetic tree. We deduced that the tandem replication–random loss model is the evolutionary mechanism of gene arrangements in Ensifera. Selection pressure analysis revealed that purifying selection dominated the evolution of the ensiferan mitochondrial genome. This study suggests that most gene rearrangements in the ensiferan mitogenome are rare accidental events.
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