Comparative analysis reveals the expansion of mitochondrial DNA control region containing unusually high G-C tandem repeat arrays in Nasonia vitripennis

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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.

Introduction

Parasitoids are insects that deposit their eggs on or into other arthropods, where the young develop, eventually killing the host. Parasitoids are used extensively in biological control as an alternative to using pesticides to control agricultural pest insect population [1,2]. Nasonia (also known as jewel wasps) are parasitoids of fly pupae that are also widely used as the model system for genetics and parasitoid biology [3,4]. The Nasonia genus consists of four closely-related species: N. vitripennis, N. giraulti, N. longicornis, and N. oneida [[4], [5], [6]]. They all share a haplodiploidy system of sex determination, in which unfertilized eggs will develop into males while fertilized eggs will develop into females. Four Nasonia species are not cross-fertile due to the action of infected Wolbachia; however, they can be cross-hybridized to create F1 progenies after curing them with antibiotics [7]. Multiple studies revealed that Nasonia utilize DNA methylation, which is absent in the primary genetic model insect species, Drosophila melanogaster [[8], [9], [10], [11]].

Nasonia mitochondrial genomes experience an unusually high rate of evolution, approximately 30–40 times faster than that of the nuclear genome in Nasonia based on limited sequence data sets available at that time [12]. This finding supports the hypothesis of compensatory feedback in the nuclear genome of Nasonia, where the nuclear-encoded genes of the oxidative phosphorylation pathway underwent positive selection to compensate for the deleterious mutations in the mitochondria-encoded proteins due to rapid mutations [[12], [13], [14]]. As expected from this elevated mutation rate, nuclear-mitochondrial incompatibilities play a significant role in hybrid lethality among Nasonia species [7,[15], [16], [17]]. None of the previously-sequenced mitochondrial DNA (mtDNA) of Nasonia has been circularized. This is most likely due to its highly repetitive region, similar to Pteromalus puparum, which belongs in the same family of Pteromalidae [18]. Despite the efforts, the circularization of the mitochondrial genomes of Nasonia remained a challenge.

The mitochondrial control region, or the ‘D-loop region’ in animals, is a critical element in regulating transcription and DNA replication [19,20]. The control region in insects is generally rich in A + T content, with 85% in most insect mitochondrial genomes [21]. It varies in size and nucleotide composition even among species of the same genus [21]. For example, the size of the control region in Drosophila yakuba is 1077 bp, while the one in D. melanogaster is 4601 bp [21]. The size variation is mainly due to the tandem repeats found in the control region. Tandem repeats in the control region not only vary between and within species, but even within individuals. Length heteroplasmy can occur in individuals when the copy number of tandem repeats differs between cells and tissues [21]. The mechanism for the generation of tandem repeat units is still incompletely understood. However, it has been hypothesized that replication slippage could be the root cause of this phenomenon [[22], [23], [24], [25]].

In this work, we presented the assembly and annotation of ten mitochondrial genomes, including eight Nasonia strains from four species, the closely related species Trichomalopsis sarcophagae, and Muscidifurax raptorellus. These are then used in a comparative study of mitochondrial genome evolution in this group of insects that have rapid mitochondrial sequence evolution. All these species occur in the parasitoid family Pteromalidae. We conducted phylogenetic analyses on the protein-coding genes of six wasp species to determine their evolutionary relationship using the mitochondrial genomes and to compare rates of substitution to their nuclear genomes. We have discovered a series of unusual properties of the mitochondrial genome of N. vitripennis, which enrich the current understanding of insect mtDNA structure and evolution.

Section snippets

Sample collection and genomic DNA extraction

All ten wasp strains sequenced in this study are highly inbred and maintained at 25 °C with constant light. For Nasonia vitripennis (Nv), four strains were sequenced: LabII, a standard laboratory strain originally derived from the Netherlands; AsymCx, a Wolbachia-free strain produced from LabII by antibiotic treatment [7]; R5–11, collected in Rochester, New York and V12.1, derived from R5–11 after having lost of one Wolbachia strain [26]. In addition, we utilized a strain (R16A) with an Nv

Mitochondrial genome assembly and annotation in five jewel wasp species

By using a linked-reads technology, we assembled the mitochondrial (MT) genomes of ten strains of six related parasitoid species, including N. vitripennis (Nv), N. giraulti (Ng), N. longicornis (Nl), N. oneida (No), and the outgroup species Trichomalopsis sarcophagae (Ts) and Muscidifurax raptorellus (Mell) (Table 1). The Nv AsymCx strain mtDNA was circularized using additional information from PSR1.1 genome ONT reads (see Materials and methods). The Nv MT genome size is 22,956 bp (GenBank

Major inversion events in Nasonia-Ts MT genomes compared to other wasp species

The importance of mitochondria in cellular energy production makes it a revealing research topic in biology. As the mitochondrion has its own independent genome, an assembled MT genome may provide novel insights into the biological function, development, and evolution of mitochondrion. The Nv reference genome paper published in 2010 [9] reported two MT fragments; however, the complete MT genome assembly is still missing. In this study, we reported high-quality assemblies of MT genomes in five

CRediT authorship contribution statement

Zi Jie Lin: Methodology, Software, Validation, Data Curation, Writing - Original Draft, Writing - Review & Editing, Visualization. Xiaozhu Wang: Software, Investigation, Writing - Original Draft. Jinbin Wang: Investigation. Yongjun Tan: Methodology, Software, Formal analysis, Data Curation, Writing - Review & Editing. Xueming Tang: Resources, Supervision. John H. Werren: Conceptualization, Resources, Writing- Reviewing and Editing. Dapeng Zhang: Methodology, Software, Formal analysis, Data

Acknowledgments

This project is supported by an Auburn University Intramural Grant Program Award to X.W. (AUIGP 180271) and the USDA National Institute of Food and Agriculture Hatch project 1018100. X.W. is supported by National Science Foundation EPSCoR RII Track-4 Research Fellowship (NSF OIA 1928770), an Alabama Agricultural Experiment Station (AAES) ARES Agriculture Research Enhancement, Exploration and Development (AgR-SEED) award, and a laboratory start-up fund from Auburn University College Veterinary

References (76)

  • G. Dover

    Molecular drive

    Trends Genet.

    (2002)
  • D.E. Axelrod et al.

    Gene amplification by unequal sister chromatid exchange: probabilistic modeling and analysis of drug resistance data

    J. Theor. Biol.

    (1994)
  • H. Fan et al.

    A brief review of short tandem repeat mutation

    Genomics Proteom. Bioinforma.

    (2007)
  • A. Kapranas et al.

    Encyrtid parasitoids of soft scale insects: biology, behavior, and their use in biological control

    Annu. Rev. Entomol.

    (2015)
  • J.A. Lynch

    The expanding genetic toolbox of the wasp Nasonia vitripennis and its relatives

    Genetics

    (2015)
  • J.H. Werren et al.

    The parasitoid wasp Nasonia: an emerging model system with haploid male genetics

    Cold Spring Harb Protoc

    (2009)
  • R. Raychoudhury et al.

    Behavioral and genetic characteristics of a new species of Nasonia

    Heredity

    (2010)
  • J.A.J. Breeuwer et al.

    Hybrid breakdown between two haplodiploid species: the role of nuclear and cytoplasmic genes

    Evolution

    (1995)
  • X. Wang et al.

    Genetic and epigenetic architecture of sex-biased expression in the jewel wasps Nasonia vitripennis and giraulti

    Proc. Natl. Acad. Sci. U.S.A.

    (2015)
  • L. Viljakainen et al.

    Transfers of mitochondrial DNA to the nuclear genome in the wasp Nasonia vitripennis

    Insect Mol. Biol.

    (2010)
  • X. Wang et al.

    Function and evolution of DNA methylation in Nasonia vitripennis

    PLoS Genet.

    (2013)
  • X. Wang et al.

    Allele-specific transcriptome and methylome analysis reveals stable inheritance and Cis-regulation of DNA methylation in Nasonia

    PLoS Biol.

    (2016)
  • D.C.S.G. Oliveira et al.

    Rapidly evolving mitochondrial genome and directional selection in mitochondrial genes in the parasitic wasp Nasonia (Hymenoptera: Pteromalidae)

    Mol. Biol. Evol.

    (2008)
  • Z.C. Yan et al.

    Evolutionary rate correlation between mitochondrial-encoded and mitochondria-associated nuclear-encoded proteins in insects

    Mol. Biol. Evol.

    (2019)
  • C.K. Ellison et al.

    Hybrid breakdown and mitochondrial dysfunction in hybrids of Nasonia parasitoid wasps

    J. Evol. Biol.

    (2008)
  • J.H. Werren et al.

    Functional and evolutionary insights from the genomes of three parasitoid Nasonia species

    Science

    (2010)
  • J.D. Gibson et al.

    Genetic and developmental basis of F2 hybrid breakdown in Nasonia parasitoid wasps

    Evolution

    (2013)
  • D.A. Clayton

    Replication and transcription of vertebrate mitochondrial-DNA

    Annu. Rev. Cell Biol.

    (1991)
  • R.E. Broughton et al.

    Length variation in mitochondrial-DNA of the minnow Cyprinella-Spiloptera

    Genetics

    (1994)
  • N.E. Buroker et al.

    Length heteroplasmy of sturgeon mitochondrial-DNA - an illegitimate elongation model

    Genetics

    (1990)
  • K. Hayasaka et al.

    Heteroplasmy and polymorphism in the major noncoding region of mitochondrial-DNA in Japanese monkeys - association with tandemly repeated sequences

    Mol. Biol. Evol.

    (1991)
  • D.M. Rand et al.

    Molecular population-genetics of Mtdna size variation in crickets

    Genetics

    (1989)
  • M.J. Perrot-Minnot et al.

    Single and double infections with Wolbachia in the parasitic wasp Nasonia vitripennis: effects on compatibility

    Genetics

    (1996)
  • X. Wang et al.

    Genome report: whole genome sequence and annotation of the parasitoid Jewel wasp Nasonia giraulti laboratory strain RV2X[u]

    G3 (Bethesda)

    (2020)
  • X. Wang et al.

    Genome assembly of the A-group Wolbachia in Nasonia oneida using linked-reads technology

    Genome Biol. Evol.

    (2019)
  • S. Andrews

    FastQC: A Quality Control Tool for High Throughput Sequence Data

    (2010)
  • N.I. Weisenfeld et al.

    Direct determination of diploid genome sequences

    Genome Res.

    (2017)
  • W.J. Kent

    BLAT - the BLAST-like alignment tool

    Genome Res.

    (2002)
  • View full text