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Xiong Z, He D, Guang X, Li Q. Novel tRNA Gene Rearrangements in the Mitochondrial Genomes of Poneroid Ants and Phylogenetic Implication of Paraponerinae (Hymenoptera: Formicidae). Life (Basel) 2023; 13:2068. [PMID: 37895449 PMCID: PMC10608118 DOI: 10.3390/life13102068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/04/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Ants (Formicidae) are the most diverse eusocial insects in Hymenoptera, distributed across 17 extant subfamilies grouped into 3 major clades, the Formicoid, Leptanilloid, and Poneroid. While the mitogenomes of Formicoid ants have been well studied, there is a lack of published data on the mitogenomes of Poneroid ants, which requires further characterization. In this study, we first present three complete mitogenomes of Poneroid ants: Paraponera clavata, the only extant species from the subfamily Paraponerinae, and two species (Harpegnathos venator and Buniapone amblyops) from the Ponerinae subfamily. Notable novel gene rearrangements were observed in the new mitogenomes, located in the gene blocks CR-trnM-trnI-trnQ-ND2, COX1-trnK-trnD-ATP8, and ND3-trnA-trnR-trnN-trnS1-trnE-trnF-ND5. We reported the duplication of tRNA genes for the first time in Formicidae. An extra trnQ gene was identified in H. venator. These gene rearrangements could be explained by the tandem duplication/random loss (TDRL) model and the slipped-strand mispairing model. Additionally, one large duplicated region containing tandem repeats was identified in the control region of P. clavata. Phylogenetic analyses based on protein-coding genes and rRNA genes via maximum likelihood and Bayes methods supported the monophyly of the Poneroid clade and the sister group relationship between the subfamilies Paraponerinae and Amblyoponinae. However, caution is advised in interpreting the positions of Paraponerinae due to the potential artifact of long-branch attraction.
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Affiliation(s)
- Zijun Xiong
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;
- BGI Research, Wuhan 430074, China
| | - Ding He
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark;
| | | | - Qiye Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;
- BGI Research, Wuhan 430074, China
- BGI Research, Shenzhen 518083, China;
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2
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Hebert PDN, Bock DG, Prosser SWJ. Interrogating 1000 insect genomes for NUMTs: A risk assessment for estimates of species richness. PLoS One 2023; 18:e0286620. [PMID: 37289794 PMCID: PMC10249859 DOI: 10.1371/journal.pone.0286620] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/22/2023] [Indexed: 06/10/2023] Open
Abstract
The nuclear genomes of most animal species include NUMTs, segments of the mitogenome incorporated into their chromosomes. Although NUMT counts are known to vary greatly among species, there has been no comprehensive study of their frequency/attributes in the most diverse group of terrestrial organisms, insects. This study examines NUMTs derived from a 658 bp 5' segment of the cytochrome c oxidase I (COI) gene, the barcode region for the animal kingdom. This assessment is important because unrecognized NUMTs can elevate estimates of species richness obtained through DNA barcoding and derived approaches (eDNA, metabarcoding). This investigation detected nearly 10,000 COI NUMTs ≥ 100 bp in the genomes of 1,002 insect species (range = 0-443). Variation in nuclear genome size explained 56% of the mitogenome-wide variation in NUMT counts. Although insect orders with the largest genome sizes possessed the highest NUMT counts, there was considerable variation among their component lineages. Two thirds of COI NUMTs possessed an IPSC (indel and/or premature stop codon) allowing their recognition and exclusion from downstream analyses. The remainder can elevate species richness as they showed 10.1% mean divergence from their mitochondrial homologue. The extent of exposure to "ghost species" is strongly impacted by the target amplicon's length. NUMTs can raise apparent species richness by up to 22% when a 658 bp COI amplicon is examined versus a doubling of apparent richness when 150 bp amplicons are targeted. Given these impacts, metabarcoding and eDNA studies should target the longest possible amplicons while also avoiding use of 12S/16S rDNA as they triple NUMT exposure because IPSC screens cannot be employed.
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Affiliation(s)
- Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dan G. Bock
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Sean W. J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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Xu S, Li W, Liu Q, Wang Y, Li X, Duan X, He J, Song F. The mitochondrial genome of Binodoxys acalephae (Hymenoptera: Braconidae) with unique gene rearrangement and phylogenetic implications. Mol Biol Rep 2023; 50:2641-2649. [PMID: 36639523 PMCID: PMC10011326 DOI: 10.1007/s11033-022-08232-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/22/2022] [Indexed: 01/15/2023]
Abstract
BACKGROUND Species in the subfamily Aphidiinae from the Braconidae of Hymenoptera are endoparasitic wasps that exclusively utilize aphids as hosts. Some Aphidiinae species are widely used as biological agents. However, there were only one species with determined complete mitochondrial genome from this subfamily. METHODS AND RESULTS In this study, we sequenced and annotated the mitochondrial genome (mitogenome) of Binodoxys acalephae, which was 15,116 bp in size and contained 37 genes. The start codon of 13 protein-coding genes was ATN, and the complete stop codon TAA and TAG was widely assigned to 11 protein-coding genes. The lrRNA contains 43 stem-loop structures, and srRNA contains 25 stem-loop structures. Translocation and inversion of tRNA genes was found to be dominant in B. acalephae. In contrast to Aphidius gifuensis from the same subfamily Aphidiinae, inverted tRNALeu1 was translocated to the gene cluster between tRNALeu2 and COX2, and the control region between tRNAIle and tRNAMet was deleted in the mitogenome of B. acalephae. Within Braconidae, gene clusters tRNATrp-tRNACys-tRNATyr and CR-tRNAIle-tRNAGln-tRNAMet were hotspots for gene rearrangement. Phylogenetic analysis showed that both Bayesian and maximum-likelihood methods recovered the monophyly of Aphidiinae and suggested that Aphidiinae formed sister clades with the remaining subfamilies. The phylogenetic analyses of nine subfamilies supported the monophyly of Cyclostomes and Noncyclostomes in Braconidae. CONCLUSION The arrangement of mitochondrial genes and the phylogenetic relationships among nine Braconidae subfamilies were constructed better to understand the diversity and evolution of Aphidiinae mitogenomes.
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Affiliation(s)
- Shiwen Xu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193 Beijing, China
| | - Weiwei Li
- Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
- Yunnan Agricultural University, 650201 Kunming, China
| | - Qiannan Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193 Beijing, China
| | - Yunming Wang
- Yuxi Branch, Yunnan Tobacco Company, 653100 Yuxi, China
| | - Xiaoling Li
- Yuxi Branch, Yunnan Tobacco Company, 653100 Yuxi, China
| | - Xiaoqian Duan
- Yuxi Branch, Yunnan Tobacco Company, 653100 Yuxi, China
| | - Jia He
- Institute of Plant Protection, Academy of Ningxia Agriculture and Forestry Science, 750002 Yinchuan, China
- Ningxia Key Laboratory of Plant Disease and Pest Control, 750002 Yinchuan, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193 Beijing, China
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Triant DA, Pearson WR. Comparison of detection methods and genome quality when quantifying nuclear mitochondrial insertions in vertebrate genomes. Front Genet 2022; 13:984513. [PMID: 36482890 PMCID: PMC9723244 DOI: 10.3389/fgene.2022.984513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 11/03/2022] [Indexed: 01/27/2024] Open
Abstract
The integration of mitochondrial genome fragments into the nuclear genome is well documented, and the transfer of these mitochondrial nuclear pseudogenes (numts) is thought to be an ongoing evolutionary process. With the increasing number of eukaryotic genomes available, genome-wide distributions of numts are often surveyed. However, inconsistencies in genome quality can reduce the accuracy of numt estimates, and methods used for identification can be complicated by the diverse sizes and ages of numts. Numts have been previously characterized in rodent genomes and it was postulated that they might be more prevalent in a group of voles with rapidly evolving karyotypes. Here, we examine 37 rodent genomes, and an additional 26 vertebrate genomes, while also considering numt detection methods. We identify numts using DNA:DNA and protein:translated-DNA similarity searches and compare numt distributions among rodent and vertebrate taxa to assess whether some groups are more susceptible to transfer. A combination of protein sequence comparisons (protein:translated-DNA) and BLASTN genomic DNA searches detect 50% more numts than genomic DNA:DNA searches alone. In addition, higher-quality RefSeq genomes produce lower estimates of numts than GenBank genomes, suggesting that lower quality genome assemblies can overestimate numts abundance. Phylogenetic analysis shows that mitochondrial transfers are not associated with karyotypic diversity among rodents. Surprisingly, we did not find a strong correlation between numt counts and genome size. Estimates using DNA: DNA analyses can underestimate the amount of mitochondrial DNA that is transferred to the nucleus.
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Affiliation(s)
- Deborah A. Triant
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
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Novel Gene Rearrangements in the Mitochondrial Genomes of Cynipoid Wasps (Hymenoptera: Cynipoidea). Genes (Basel) 2022; 13:genes13050914. [PMID: 35627299 PMCID: PMC9140913 DOI: 10.3390/genes13050914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 12/04/2022] Open
Abstract
Cynipoidea is a medium-sized superfamily of Hymenoptera with diverse lifestyles. In this study, 16 mitochondrial genomes were newly sequenced, 11 of which were the first obtained mitochondrial genomes in the family Liopteridae and four subfamilies (Anacharitinae, Aspicerinae, Figitinae, and Parnipinae) of Figitidae. All of the newly sequenced mitogenomes have unique rearrangement types within Cynipoidea, whereas some gene patterns are conserved in several groups. nad5-nad4-nad4L-nad6-cytb was remotely inverted and two rRNA genes were translocated to nad3 downstream in Ibaliidae and three subfamilies (Anacharitinae, Eucoilinae, and Parnipinae within Figitidae); two rRNA genes in Aspicerinae, Figitinae, and Liopteridae were remotely inverted to the cytb-nad1 junction; rrnL-rrnS was translocated to the cytb-nad1 junction in Cynipidae. Phylogenetic inference suggested that Figitidae was a polyphyletic group, while the Ibaliidae nested deep within Cynipoidea and was a sister-group to the Figitidae. These results will improve our understanding of the gene rearrangement of the mitogenomes and the phylogenetic relationships in the Cynipoidea.
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Yi J, Wu H, Liu J, Li J, Lu Y, Zhang Y, Cheng Y, Guo Y, Li D, An Y. Novel gene rearrangement in the mitochondrial genome of Anastatus fulloi (Hymenoptera Chalcidoidea) and phylogenetic implications for Chalcidoidea. Sci Rep 2022; 12:1351. [PMID: 35079090 PMCID: PMC8789778 DOI: 10.1038/s41598-022-05419-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/11/2022] [Indexed: 11/17/2022] Open
Abstract
The genus Anastatus comprises a large group of parasitoids, including several biological control agents in agricultural and forest systems. The taxonomy and phylogeny of these species remain controversial. In this study, the mitogenome of A. fulloi Sheng and Wang was sequenced and characterized. The nearly full-length mitogenome of A. fulloi was 15,692 bp, compromising 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and a control region (CR). The total A + T contents were 83.83%, 82.18%, 87.58%, 87.27%, and 82.13% in the whole mitogenome, 13 PCGs, 22 tRNA genes, 2 rRNA genes, and CR, respectively. The mitogenome presented negative AT skews and positive GC skews, except for the CR. Most PCGs were encoded on the heavy strand, started with ATN codons, and ended with TAA codons. Among the 3736 amino acid-encoding codons, TTA (Leu1), CGA (Arg), TCA (Ser2), and TCT (Ser2) were predominant. Most tRNAs had cloverleaf secondary structures, except trnS1, with the absence of a dihydrouridine (DHU) arm. Compared with mitogenomes of the ancestral insect and another parasitoid within Eupelmidae, large-scale rearrangements were found in the mitogenome of A. fulloi, especially inversions and inverse transpositions of tRNA genes. The gene arrangements of parasitoid mitogenomes within Chalcidoidea were variable. A novel gene arrangement was presented in the mitogenome of A. fulloi. Phylogenetic analyses based on the 13 protein-coding genes of 20 parasitoids indicated that the phylogenetic relationship of 6 superfamilies could be presented as Mymaridae + (Eupelmidae + (Encyrtidae + (Trichogrammatidae + (Pteromalidae + Eulophidae)))). This study presents the first mitogenome of the Anastatus genus and offers insights into the identification, taxonomy, and phylogeny of these parasitoids.
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Affiliation(s)
- Jiequn Yi
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Han Wu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Jianbai Liu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Jihu Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Yinglin Lu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Yifei Zhang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Yinjie Cheng
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Yi Guo
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection/Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Dunsong Li
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection/Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yuxing An
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China.
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7
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Zhao H, Chen Y, Wang Z, Chen H, Qin Y. Two Complete Mitogenomes of Chalcididae (Hymenoptera: Chalcidoidea): Genome Description and Phylogenetic Implications. INSECTS 2021; 12:insects12121049. [PMID: 34940137 PMCID: PMC8707279 DOI: 10.3390/insects12121049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/12/2021] [Accepted: 11/22/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary The Chalcididae are a moderate-sized family of the superfamily Chalcidoidea in Hymenoptera, comprising 1548 species in 87 genera worldwide. Some species are potential natural enemies of pests in agriculture and forestry. Currently, there are still some controversies about the monophyly of Chalcididae and the phylogenetic relationships between Chalcididae and other families in Chalcidoidea. Based on the fact that no mitogenomic phylogenetic analyses of all of the published mitogenomes of Chalcidoidea have been conducted and no complete mitogenome of Chalcididae species has been reported, two newly completed mitochondrial genomes of Chalcididae species (Brachymeria lasus and Haltichella nipponensis) were sequenced and analyzed. The results show that the two chalcidid mitogenomes have quite similar structures and features. In phylogenetic analyses based on 13 PCGs of mitogenomes, the basal position and monophyly of Chalcididae within Chalcidoidea were supported by all trees derived from maximum likelihood (ML) and Bayesian inference (BI) methods. Abstract The complete mitochondrial genomes of two species of Chalcididae were newly sequenced: Brachymeria lasus and Haltichella nipponensis. Both circular mitogenomes are 15,147 and 15,334 bp in total length, respectively, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs) and an A+T-rich region. The nucleotide composition indicated a strong A/T bias. All PCGs of B. lasus and H. nipponensis began with the start codon ATD, except for B. lasus, which had an abnormal initiation codon TTG in ND1. Most PCGs of the two mitogenomes are terminated by a codon of TAR, and the remaining PCGs by the incomplete stop codon T or TA (ATP6, COX3, and ND4 in both species, with an extra CYTB in B. lasus). Except for trnS1 and trnF, all tRNAs can be folded into a typical clover structure. Both mitogenomes had similar control regions, and two repeat units of 135 bp were found in H. nipponensis. Phylogenetic analyses based on two datasets (PCG123 and PCG12) covering Chalcididae and nine families of Chalcidoidea were conducted using two methods (maximum likelihood and Bayesian inference); all the results support Mymaridae as the sister group of the remaining Chalcidoidea, with Chalcididae as the next successive group. Only analyses of PCG123 generated similar topologies of Mymaridae + (Chalcididae + (Agaonidae + remaining Chalcidoidea)) and provided one relative stable clade as Eulophidae + (Torymidae + (Aphelinidae + Trichogrammatidae)). Our mitogenomic phylogenetic results share one important similarity with earlier molecular phylogenetic efforts: strong support for the monophyly of many families, but a largely unresolved or unstable “backbone” of relationships among families.
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Affiliation(s)
- Huifeng Zhao
- Hebei Key Laboratory of Animal Diversity, College of Life Science, Langfang Normal University, Langfang 065000, China; (H.Z.); (Y.C.); (H.C.)
| | - Ye Chen
- Hebei Key Laboratory of Animal Diversity, College of Life Science, Langfang Normal University, Langfang 065000, China; (H.Z.); (Y.C.); (H.C.)
| | - Zitong Wang
- School of Forestry, Northeast Forestry University, Harbin 150040, China;
| | - Haifeng Chen
- Hebei Key Laboratory of Animal Diversity, College of Life Science, Langfang Normal University, Langfang 065000, China; (H.Z.); (Y.C.); (H.C.)
| | - Yaoguang Qin
- Hebei Key Laboratory of Animal Diversity, College of Life Science, Langfang Normal University, Langfang 065000, China; (H.Z.); (Y.C.); (H.C.)
- Correspondence:
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Zhang G, Geng D, Guo Q, Liu W, Li S, Gao W, Wang Y, Zhang M, Wang Y, Bu Y, Niu H. Genomic landscape of mitochondrial DNA insertions in 23 bat genomes: characteristics, loci, phylogeny, and polymorphism. Integr Zool 2021; 17:890-903. [PMID: 34496458 DOI: 10.1111/1749-4877.12582] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The transfer of mitochondrial DNA to the nuclear genome gives rise to the nuclear DNA sequences of mitochondrial origin (NUMTs), considered as a driving force in genome evolution. In this study, NUMTs in 23 bat genomes were investigated and compared systematically. The results showed that NUMTs existed in 22 genomes except for Noctilio leporinus, suggesting that mitochondrial fragment insertion in the nuclear genome was a common event in bat genomes. However, remarkable variations in NUMTs number, cumulative length, and proportion in the nuclear genome were discovered across bat species. Further orthologous NUMT loci analysis of the Phyllostomidae family indicated that the NUMTs insertion events in bat genomes were homoplasy-free. The NUMTs were mainly inserted into the intergenic regions, particularly, co-localized with repetitive sequences (especially transposable elements). However, several NUMTs were inserted into genes, some of which were in the exon region of functional genes. One NUMT in the genome of Pteropus alecto surprisingly matched with cDNA of ATP8B3 that provided evidence of NUMTs with coding function. Phylogenic analysis on NUMTs originating from COXI and COXII loci highlighted 2 clusters of Yinpterochiroptera and Yangochiroptera for Chiroptera. Seven NUMTs from Rhinolophus ferrumequinum were amplified, and the sequencing results confirmed the reliability of the NUMT analysis. One of them was polymorphic for the presence or absence of the NUMT insertion, and each genotype of NUMT loci showed a distinct regional distribution pattern. The information obtained in this study provides novel insights into the NUMT organization and features in bat genomes and establishes a basis for further studying of the evolution of bat species.
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Affiliation(s)
- Guojun Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, China.,School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Deqi Geng
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Qiulin Guo
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Wei Liu
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Shufen Li
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Wujun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yongfei Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Min Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yilin Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yanzhen Bu
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Hongxing Niu
- College of Life Sciences, Henan Normal University, Xinxiang, China
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Huang Z, Dai H, Lin Q, Zhang B. The mitochondrial genome of parasitic wasp: Anisopteromalus calandrae (Howard, 1881) (Hymenoptera: Pteromalidae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2048-2049. [PMID: 34212093 PMCID: PMC8218845 DOI: 10.1080/23802359.2021.1942257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The parasitic wasp Anisopteromalus calandrae is a natural enemy of numbers store product pests. The mitochondrial genome (mitogenome) of A. calandrae was obtained by second-generation sequencing. The assembled mitogenome of A. calandrae is 15,954 bp long (GenBank accession: MW817149) and contains 37 typical animal mitochondrial genes. The order of the mitochondrial genes is identical to that of another species of Chalcidoidae (Pteromalus puparum). All protein-coding genes start with ATN codons, and end with TAA, except NAD4 and NAD5 with T.
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Affiliation(s)
- Zhengyu Huang
- National Engineering Laboratory for Rice and By-product Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - Haiyan Dai
- National Engineering Laboratory for Rice and By-product Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - Qinlu Lin
- National Engineering Laboratory for Rice and By-product Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - Bin Zhang
- Department of Anatomy and Neurobiology, Biology Postdoctoral Workstation, School of Basic Medical Sciences, Central South University, Changsha, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Shanghai Clinical Research Center Co., Ltd., Shanghai, China.,Shanghai Engineering Research Center of Biobank, Shanghai, China
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10
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Lin ZJ, Wang X, Wang J, Tan Y, Tang X, Werren JH, Zhang D, Wang X. Comparative analysis reveals the expansion of mitochondrial DNA control region containing unusually high G-C tandem repeat arrays in Nasonia vitripennis. Int J Biol Macromol 2020; 166:1246-1257. [PMID: 33159940 DOI: 10.1016/j.ijbiomac.2020.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/01/2020] [Accepted: 11/02/2020] [Indexed: 11/25/2022]
Abstract
Insect mitochondrial DNA (mtDNA) ranges from 14 to 19 kbp, and the size difference is attributed to the AT-rich control region. Jewel wasps have a parasitoid lifestyle, which may affect mitochondria function and evolution. We sequenced, assembled, and annotated mitochondrial genomes in Nasonia and outgroup species. Gene composition and order are conserved within Nasonia, but they differ from other parasitoids by two large inversion events that were not reported before. We observed a much higher substitution rate relative to the nuclear genome and mitochondrial introgression between N. giraulti and N. oneida, which is consistent with previous studies. Most strikingly, N. vitripennis mtDNA has an extremely long control region (7665 bp), containing twenty-nine 217 bp tandem repeats and can fold into a super-cruciform structure. In contrast to tandem repeats commonly found in other mitochondria, these high-copy repeats are highly conserved (98.7% sequence identity), much longer in length (approximately 8 Kb), extremely GC-rich (50.7%), and CpG-rich (percent CpG 19.4% vs. 1.1% in coding region), resulting in a 23 kbp mtDNA beyond the typical size range in insects. These N. vitripennis-specific mitochondrial repeats are not related to any known sequences in insect mitochondria. Their evolutionary origin and functional consequences warrant further investigations.
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Affiliation(s)
- Zi Jie Lin
- Department of Chemistry, Columbus State University, Columbus, GA 31909, United States of America
| | - Xiaozhu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, United States of America
| | - Jinbin Wang
- Institute of Biotechnology Research, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Yongjun Tan
- Department of Biology, College of Arts & Sciences, Saint Louis University, St. Louis, MO 63103, United States of America
| | - Xueming Tang
- Institute of Biotechnology Research, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY 14627, United States of America
| | - Dapeng Zhang
- Department of Biology, College of Arts & Sciences, Saint Louis University, St. Louis, MO 63103, United States of America
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, United States of America; HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States of America; Alabama Agricultural Experiment Station, Auburn University, Auburn, AL 36849, United States of America; Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, United States of America.
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Tracking the Distribution and Burst of Nuclear Mitochondrial DNA Sequences (NUMTs) in Fig Wasp Genomes. INSECTS 2020; 11:insects11100680. [PMID: 33036463 PMCID: PMC7600805 DOI: 10.3390/insects11100680] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/29/2020] [Accepted: 10/06/2020] [Indexed: 11/17/2022]
Abstract
Simple Summary Nuclear mitochondrial DNA sequences (NUMTs), which result from the insertion of exogenous mtDNA into the nuclear genome, are widely distributed in eukaryotes. However, how NUMTs are inserted into the nuclear genome and their post-insertion fates remain a mystery. Previous studies have suggested that Hymenoptera may be a group rich in NUMTs, which will be helpful to study the biological issues of NUMTs. We here select 11 species of fig wasps (Chalcidoidea, Hymenoptera) to analyze the distribution and evolution of NUMTs at the genomic level. The results show that the distributions of NUMTs are species- or lineage-specific. Furthermore, genomic environmental factors such as genome size, the damage-prone regions, and the mode of TE dynamics can determine the insertion and post-insertion fate of NUMTs. Especially because of TEs, the fragmentation and duplication of NUMTs, and thus their burst, are common. This is a relatively comprehensive investigation of the specific distribution of NUMTs and its influencing factors. Our study will help people to understand the evolution of exogenous fragments in the nuclear genome. Abstract Mitochondrial DNA sequences can be transferred into the nuclear genome, giving rise to nuclear mitochondrial DNA sequences (NUMTs). NUMTs have been described in numerous eukaryotes. However, the studies on the distribution of NUMTs and its influencing factors are still inadequate and even controversial. Previous studies have suggested that Hymenoptera may be a group rich in NUMTs, in which we selected 11 species of fig wasps (Chalcidoidea, Hymenoptera) to analyze the distribution and evolution of NUMTs at the genomic level. The results showed that the contents of NUMTs varied greatly in these species, and bursts of NUMTs existed in some species or lineages. Further detailed analyses showed that the large number of NUMTs might be related to the large genomes; NUMTs tended to be inserted into unstable regions of the genomes; and the inserted NUMTs might also be affected by transposable elements (TEs) in the neighbors, leading to fragmentations and duplications, followed by bursts of NUMTs. In summary, our results suggest that a variety of genomic environmental factors can determine the insertion and post-insertion fate of NUMTs, resulting in their species- or lineage-specific distribution patterns, and that studying the evolution of NUMTs can provide good evidence and theoretical basis for exploring the dynamics of exogenous DNA entering into the nuclear genome.
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Feng Z, Wu Y, Yang C, Gu X, Wilson JJ, Li H, Cai W, Yang H, Song F. Evolution of tRNA gene rearrangement in the mitochondrial genome of ichneumonoid wasps (Hymenoptera: Ichneumonoidea). Int J Biol Macromol 2020; 164:540-547. [PMID: 32693134 DOI: 10.1016/j.ijbiomac.2020.07.149] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 12/21/2022]
Abstract
Gene rearrangements in the mitochondrial genome (mt genome) are common in certain insect groups and can be an informative character for phylogenetic reconstruction. However, knowledge of the mechanism and biases of gene rearrangement in insect mt genomes is still limited. With an accelerated rate of gene rearrangements, Hymenoptera is an important group for mt genome rearrangements diversity and for understanding the gene rearrangement evolution in mt genomes. Here, we sequenced the complete mt genome of Aphidius gifuensis and analyzed the evolution of tRNA gene rearrangements in the mt genomes of ichneumonoid wasps. Two control regions were detected in A. gifuensis and most of the tRNA rearrangement events occurred around these control regions. tRNA gene rearrangements occurred in almost all of the sequenced mt genomes of Ichneumonoidea and the gene block CR-trnI-trnQ-trnM-ND2-trnW-trnC-trnY was the main hot spot of gene rearrangement. Mapped over the backbone phylogeny of Ichneumonoidea, we found that the inversion and translocation of both trnI and trnM is likely a synapomorphic rearrangement in Braconidae. Our study also demonstrated that the gene block CR-trnI-trnQ-trnM-ND2-trnW-trnC-trnY was important for inferring the gene rearrangement dynamics in Ichneumonoidea.
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Affiliation(s)
- Zengbei Feng
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yunfei Wu
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Chun Yang
- Tobacco Company, Yuxi 653100, Yunnan, China
| | - Xinghui Gu
- Tobacco Company, Yuxi 653100, Yunnan, China
| | - John James Wilson
- Vertebrate Zoology at World Museum, National Museums Liverpool, Liverpool, UK; Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Hu Li
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wanzhi Cai
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Hailin Yang
- Tobacco Company, Yuxi 653100, Yunnan, China.
| | - Fan Song
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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Novel gene rearrangement in the mitochondrial genome of Pachyneuron aphidis (Hymenoptera: Pteromalidae). Int J Biol Macromol 2020; 149:1207-1212. [PMID: 32018006 DOI: 10.1016/j.ijbiomac.2020.01.308] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/04/2020] [Accepted: 01/31/2020] [Indexed: 11/21/2022]
Abstract
Species in Hymenoptera usually show exceptionally high rates of mitochondrial molecular evolution and dramatic gene rearrangements, which has been attributed to their parasitic lifestyle. However, mitochondrial genome (mitogenome) of chalcidoid wasps is still poorly understood and the evolution of gene rearrangements is still unclear. In this study, the nearly complete mitogenome of Pachyneuron aphidis, a chalcidoid wasp mainly hyperparasitizes the Aphidius gifuensis, was sequenced using a next-generation sequencing strategy. This genome is 15,137 bp in length, including 13 PCGs, 22 tRNAs, two rRNAs and a partial control region. Alignment with other Chalcidoidea mitogenomes revealed a novel inversion in the srRNA-trnV gene cluster in P. aphidis, which is the first of its kind to be reported in Chalcidoidea. Breakpoint distances analysis showed the high value of chalcidoid wasps compare to the ancestral arrangement pattern, which reflected as extensive gene rearrangements. Despite the high frequency of gene rearrangements in these insects, analyses of gene rearrangement and phylogenetic trees showed that species from the same family and the genus tent to have similar gene orders, and the conserved gene blocks (ND3-trnG, srRNA-trnV and COIII-ATP6-ATP8-trnD-trnK-COII-trnL2-COI) can usually be identified, especially at the family level of chalcidoid wasps.
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Zhang GJ, Dong R, Lan LN, Li SF, Gao WJ, Niu HX. Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants. Int J Mol Sci 2020; 21:ijms21030707. [PMID: 31973163 PMCID: PMC7037861 DOI: 10.3390/ijms21030707] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/16/2020] [Accepted: 01/18/2020] [Indexed: 11/16/2022] Open
Abstract
The transfer of genetic material from the mitochondria and plastid to the nucleus gives rise to nuclear integrants of mitochondrial DNA (NUMTs) and nuclear integrants of plastid DNA (NUPTs). This frequently occurring DNA transfer is ongoing and has important evolutionary implications. In this review, based on previous studies and the analysis of NUMT/NUPT insertions of more than 200 sequenced plant genomes, we analyzed and summarized the general features of NUMTs/NUPTs and highlighted the genetic consequence of organellar DNA insertions. The statistics of organellar DNA integrants among various plant genomes revealed that organellar DNA-derived sequence content is positively correlated with the nuclear genome size. After integration, the nuclear organellar DNA could undergo different fates, including elimination, mutation, rearrangement, fragmentation, and proliferation. The integrated organellar DNAs play important roles in increasing genetic diversity, promoting gene and genome evolution, and are involved in sex chromosome evolution in dioecious plants. The integrating mechanisms, involving non-homologous end joining at double-strand breaks were also discussed.
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Affiliation(s)
- Guo-Jun Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China
| | - Ran Dong
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
| | - Li-Na Lan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
| | - Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
- Correspondence: (W.-J.G.); (H.-X.N.)
| | - Hong-Xing Niu
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
- Correspondence: (W.-J.G.); (H.-X.N.)
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