Skip to main content
SpringerLink
Log in

De novo assembly and comparative analysis of the complete mitochondrial genome sequence of the pistachio psyllid, Agonoscena pistaciae (Hemiptera: Aphalaridae)

  • Original Research Article
  • Published:
International Journal of Tropical Insect Science Aims and scope Submit manuscript

Abstract

The pistachio psyllid, Agonoscena pistaciae, is one of the most deleterious pests of pistachio trees. Deciphering genetic diversity and population structure is a prerequisite for developing efficacious suppression protocols and successful management strategies for any insect pest including A. pistaciae. Mitochondrial genome sequencing furnishes valuable information about insect evolution and diversity within and among populations. Here, we assembled the first complete mitochondrial genome of the pistachio psyllid high-throughput next generation sequencing. The circular mitochondrial genome of A. pistaciae was 15,346 bp in length encoding 37 genes, including 13 protein-coding genes (PCGs), 2 rRNA genes and 22 tRNA genes, with a long non-coding region (putative control regions). The A. pistaciae mitogenome was in same typical set and arrangement as that of the ancestral insect. The mitochondrial genome of A. pistaciae was compared to all 6 publically available mitogenomes of other Psylloidea species. The conservation of the gene arrangements and identical gene ordering among all psyllid species could suggest a structurally common ancestral mitogenome shared across Psylloidea. Phylogenetic analysis based on the 13 PCGs conformed the existing morphological based taxonomy and showed the clustering of the two Aphalaridae. Whole mitochondrial genome of A. pistaciae could be utilized in subsequent population genetic studies of the species and also add to a deeper understanding of the phylogenetic research links within the subfamily Psylloidea.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

Data availability

All sequence data are available through GenBank Agonoscena Mitochondrial genome (PRJNA637689), the annotated mitochondrial genome (MT576697) and the illumine short reads (SRA) (SRR 11942466 & SRR 11942467) accession numbers.

References

  • Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF (2013) MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–319

    Article  Google Scholar 

  • Bouckaert R, Heled J, Kuhnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 10:e1003537

    Article  Google Scholar 

  • Burckhardt D, Ouvrard DA (2012) Revised classification of the jumping plant-lice (Hemiptera: Psylloidea). Zootaxa 3509:1–34

    Article  Google Scholar 

  • Camerson SL (2014) Insect mitochondrial genomics: implications for evolution and phylogeny. Annu Rev Entomol 59:95–117

    Article  Google Scholar 

  • Cantacessi C, Jex AR, Hall RS, Young ND, Campbell BE, Joachim A, Nolan MJ, Abubucker S, Sternberg PW, Ranganathan S, Mitreva M, Gasser RBA (2010) Practical, bioinformatic workflow system for large data sets generated by next-generation sequencing. Nucleic Acids Res 38(17):e171

    Article  Google Scholar 

  • Chen J, Liang G (2016) The complete mitochondrial genome sequence of Bactericera cockerelli and comparison with three other Psylloidea species. PLoS One 11(5):e0155318. https://doi.org/10.1371/journal.pone.0155318

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen S, Zhou Y, Chen Y, Gu J (2018) Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34(17):i884–i890

    Article  Google Scholar 

  • Cho G, Burckhardt D, Lee S (2017) On the taxonomy of Korean jumping plant-lice (Hemiptera: Psylloidea). Zootaxa 4238(4):531–561

    Article  Google Scholar 

  • Darling AE, Mau B, Perna NT (2010) Progressive mauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5:e11147. https://doi.org/10.1371/journal.pone.0011147

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Heled J, Drummond AJ (2010) Bayesian inference of species trees from multilocus data. Mol Biol Evol 27:570–580

    Article  CAS  Google Scholar 

  • Herd KE, Barker SC, Shao R (2015) The mitochondrial genome of the chimpanzee louse, Pediculus schaeffi: insights into the process of mitochondrial genome fragmentation in the blood-sucking lice of great apes. BMC Genomics 16(1):661

    Article  Google Scholar 

  • Jeyaprakash A, Hoy MA (2009) First divergence time estimate of spiders, scorpions, mites and ticks (subphylum: Chelicerata) inferred from mitochondrial phylogeny. Exp Appl Acarol 47(1):1–18

    Article  CAS  Google Scholar 

  • Jiang F, Pan X, Li X, Yu Y, Zhang J, Jiang H, Dou L, Zhu S (2016) The first complete mitochondrial genome of Dacus longicornis (Diptera: Tephritidae) using next-generation sequencing and mitochondrial genome phylogeny of Dacini tribe. Sci Rep 6:36426. https://doi.org/10.1038/srep36426

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Karimi S, Hosseini R, Farahpour A, Aalami A (2014) Application of RAPD in comparison of diversity of commonpistachio psylla (Agonoscena pistaciae Burckhardt & Lauterer) populations in some northern and southern regions of Kerman province. Plant Pest Res 4(1):21–34 (In Persian)

    Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  Google Scholar 

  • Li H, Liu H, Shi A, Stys P, Zhou X, Cai W (2012) The complete mitochondrial genome and novel gene arrangement of the unique-headed bug Stenopirates sp. (Hemiptera: Enicocephalidae). PLoS One 7(1):e29419

    Article  CAS  Google Scholar 

  • Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452

    Article  CAS  Google Scholar 

  • Martoni F, Armstrong KF (2019) Acizzia errabunda sp. nov. and Ctenarytaina insularis sp.nov.: descriptions of two new species of psyllids (Hemiptera:Psylloidea) discovered on exotic host plants in New Zealand. PLoS ONE 14(4):e0214220

    Article  CAS  Google Scholar 

  • Mehrnejad MR (2002) Bionomics of the common pistachio psylla, Agonoscena pistaciae, in Iran. Acta Hortic 591:535–539

    Article  Google Scholar 

  • Mehrnejad MR (2003) Pistachio Psylla and other major Psyllids of Iran. Ministry of Jihad-e-Agriculture, Tehran

    Google Scholar 

  • Mehrnejad MR (2010) Potential biological control agents of the common pistachio psylla, Agonoscena pistaciae, a review. Entomofauna 31(21):317–340

    Google Scholar 

  • Mehrnejad MR (2014) The psyllids of pistachio trees in Iran. Acta Hortic 1028:191–194

    Article  Google Scholar 

  • Mostafavi M, Lashkari M, Iranmanesh S, Mansouri SM (2017) Variation in populations of common pistachio psyllid, Agonoscena pistaciae (Hem.: Psyllidae), with different chemical control levels: narrower wing shape in the stressed environment. J Crop Prot 6(3):353–362

    Google Scholar 

  • Nezam Kheirabadi M, Dhami MK, Fekrat L, Lashkari MR, Pramual P (2020) Genetic structure and diversity of the common pistachio psylla, Agonoscena pistaciae Burckhardt & Lauterer, (Hemiptera: Aphalaridae) in Iran. Manusript submitted for publication

  • Ouvrard D. (2020) Psyl’list— The World Psylloidea Database. http://www.hemiptera-databases.com/psyllist- searched on the 5th of May 2020

  • Perilla-Henao LM, Casteel CL (2016) Vector-borne bacterial plant pathogens: interactions with hemipteran insects and plants. Front Plant Sci 7:1163. https://doi.org/10.3389/fpls.2016.01163

    Article  PubMed  PubMed Central  Google Scholar 

  • Perna NT, Kocher TD (1995) Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol 41:353–358

    Article  CAS  Google Scholar 

  • Que S, Yu L, Xin T, Zou Z, Hu L, Xia B (2016) Complete mitochondrial genome of Cacopsylla coccinae (Hemiptera: Psyllidae). Mitochondrial DNA A DNA Mapp Seq Anal 27(5):3169–3170

    CAS  PubMed  Google Scholar 

  • Rambaut A. (2012) FigTree (version 1.4.3), http://tree.bio.ed.ac.uk/software/figtree/

  • Song F, Li H, Jiang P, Zhou X, Liu J, Sun C, Volger AP, Cai W (2016) Capturing the phylogeny of Holometabola with mitochondrial genome data and Bayesian site-heterogeneous mixture models. Genome Biol Evol 8(5):1411–1426

    Article  Google Scholar 

  • Thao ML, Baumann L, Baumann P (2004) Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha). BMC Evol Biol 4(1):25.13

    Article  Google Scholar 

  • Wang HL, Xiao N, Yang J, Wang XW, Colvin J, Liu SS (2016) The complete mitochondrial genome of Bemisia afer (Hemiptera: Aleyrodidae). Mitochondrial DNA 27(2):98–99

    Article  Google Scholar 

  • Wang N, Pierson EA, Setubal JC, Xu J, Levy JG, Zhang Y, Li J, Rangel LT, Martins J Jr (2017) The Candidatus Liberibacter-host Interface: insights into pathogenesis mechanisms and disease control. Annu Rev Phytopathol 55:451–482. https://doi.org/10.1146/annurev-phyto-080516-035513

    Article  CAS  PubMed  Google Scholar 

  • Wang AY, Peng YQ, Harder LD, Huang JF, Yang DR, Zhang DY, Liao WJ (2019) The nature of interspecific interactions and co-diversification patterns, as illustrated by the fig microcosm. New Phytol 224:1304–1315

    Article  Google Scholar 

  • Williams ST, Foster PG, Littlewood DTJ (2014) The completemitochondrial genome of a turbinid vetigastropod from MiSeq Illu-mina sequencing of genomic DNA and steps towards a resolved gas-tropod phylogeny. Gene 533:38–47

  • Wolstenholme DR (1992) Animal mitochondrial DNA: structure and evolution. Int Rev Cytol 141:173–216

    Article  CAS  Google Scholar 

  • Wu F, Cen Y, Wallis CM, Trumble JT, Prager S, Yokomi R, Zheng Z, Deng X, Wang Y, Huang XL, Qiao GX (2014) The complete mitochondrial genome of Cervaphis quercus (Insecta: Hemiptera: Aphididae: Greenideinae). Insect sci 21(3):278–290

    Article  Google Scholar 

  • Wu F, Cen Y, Deng X, Zheng Z, Chen J, Liang G (2016a) The complete mitochondrial genome sequence of Diaphorina citri (Hemiptera: Psyllidae). Mitochondrial DNA B 1(1):239–240

    Article  Google Scholar 

  • Wu F, Cen Y, Wallis CM, Trumble JT, Prager S, Yokomi R, Zheng Z, Deng X, Chen J, Liang G (2016b) The complete mitochondrial genome sequence of Bactericera cockerelli and comparison with three other Psylloidea species. PLoS One 11(5):e0155318. https://doi.org/10.1371/journal.pone.0155318

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang QL, Guo ZL, Yuan ML (2016a) The complete mitochondrial genome of Poratrioza sinica (Insecta: Hemiptera: Psyllidae). Mitochondrial DNA Part A 27(1):734–735

    Article  CAS  Google Scholar 

  • Zhang S, Luo J, Wang C, Lv L, Li C, Jiang W, Cui J, Rajput LB (2016b) Complete mitochondrial genome of Aphis gossypii glover (Hemiptera: Aphididae). Mitochondrial DNA Part A 27(2):854–855

    Article  CAS  Google Scholar 

  • Zhang Y, Feng S, Fekrat L, Jiang F, Khathutshelo M, Li Z (2019) The first two complete mitochondrial genome of Dacus bivittatus and Dacus ciliatus (Diptera: Tephritidae) by next-generation sequencing and implications for the higher phylogeny of Tephritidae. Int J Biol Macromol 140:469–476

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Plant protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran

    Lida Fekrat, Mohammad Zakiaghl & Marzieh Koohkanzade

  2. Biodiversity & Conservation, Manaaki Whenua Landcare Research, Lincoln, New Zealand

    Manpreet K. Dhami

  3. Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, China

    Yue Zhang

Authors
  1. Lida Fekrat
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mohammad Zakiaghl
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Manpreet K. Dhami
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yue Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Marzieh Koohkanzade
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Lida Fekrat.

Ethics declarations

Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

ESM 1

(DOCX 13 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Fekrat, L., Zakiaghl, M., Dhami, M.K. et al. De novo assembly and comparative analysis of the complete mitochondrial genome sequence of the pistachio psyllid, Agonoscena pistaciae (Hemiptera: Aphalaridae). Int J Trop Insect Sci 41, 1387–1396 (2021). https://doi.org/10.1007/s42690-020-00332-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s42690-020-00332-3

Keywords

Search

Navigation