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Exploring bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera)

  • 1.

    Douglas, A. E. Multiorganismal insects: Diversity and function of resident microorganisms. Annu. Rev. Entomol. 60, 17–34 (2015).

    CAS 
    PubMed 

    Google Scholar 

  • 2.

    Dillon, R. J. & Dillon, V. M. THE gut bacteria of insects: Nonpathogenic interactions. Annu. Rev. Entomol. 49, 71–92 (2004).

    CAS 
    PubMed 

    Google Scholar 

  • 3.

    Duplouy, A., Hursts, G. D. D., O’neill, S. L. & Charlat, S. Rapid spread of male-killing Wolbachia in the butterfly Hypolimnas bolina. J. Evol. Biol. 23, 231–235 (2010).

    CAS 
    PubMed 

    Google Scholar 

  • 4.

    Altizer, S. M., Oberhauser, K. S. & Brower, L. P. Associations between host migration and the prevalence of a protozoan parasite in natural populations of adult monarch butterflies. Ecol. Entomol. 25, 125–139 (2000).

    Google Scholar 

  • 5.

    Jiggins, X., Hurst, X., Dolman, X. & Majerus, X. High-prevalence male-killing Wolbachia in the butterfly Acraea encedana. J. Evol. Biol. 13, 495–501 (2000).

    Google Scholar 

  • 6.

    Xu, P., Liu, Y., Graham, R. I., Wilson, K. & Wu, K. Densovirus is a mutualistic symbiont of a global crop pest (Helicoverpa armigera) and protects against a baculovirus and Bt Biopesticide. PLoS Pathog. 10, e1004490 (2014).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 7.

    Bapatla, K. G., Singh, A., Yeddula, S. & Patil, R. H. Annotation of gut bacterial taxonomic and functional diversity in Spodoptera litura and Spilosoma obliqua. J. Basic Microbiol. 58, 217–226 (2018).

    CAS 
    PubMed 

    Google Scholar 

  • 8.

    Chen, F. et al. Effects of Wolbachia on mitochondrial DNA variation in populations of Athetis lepigone (Lepidoptera: Noctuidae) in China. Mitochondrial DNA Part A 28, 826–834 (2017).

    CAS 

    Google Scholar 

  • 9.

    van Nieukerken, E. J. et al. Order Lepidoptera Linnaeus, 1758. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa 1758, 212–221 (2011).

    Google Scholar 

  • 10.

    Duplouy, A. & Hornett, E. A. Uncovering the hidden players in Lepidoptera biology: The heritable microbial endosymbionts. PeerJ 6, e4629 (2018).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 11.

    Werren, J. H., Windsor, D. & Guo, L. Distribution of Wolbachia among neotropical arthropods. Proc. R. Soc. Lond. Ser. B Biol. Sci. 262, 197–204 (1995).

    ADS 

    Google Scholar 

  • 12.

    Salunke, B. K. et al. Determination of Wolbachia diversity in butterflies from Western Ghats, India, by a multigene approach. Appl. Environ. Microbiol. 78, 4458–4467 (2012).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 13.

    Duplouy, A. & Brattström, O. Wolbachia in the genus Bicyclus: A forgotten player. Microb. Ecol. 75, 255–263 (2018).

    PubMed 

    Google Scholar 

  • 14.

    Jiggins, F. M., Bentley, J. K., Majerus, M. E. & Hurst, G. D. How many species are infected with Wolbachia ? Cryptic sex ratio distorters revealed to be common by intensive sampling. Proc. R. Soc. Lond. Ser. B Biol. Sci. 268, 1123–1126 (2001).

    CAS 

    Google Scholar 

  • 15.

    Tagami, Y. & Miura, K. Distribution and prevalence of Wolbachia in Japanese populations of Lepidoptera. Insect Mol. Biol. 13, 359–364 (2004).

    CAS 
    PubMed 

    Google Scholar 

  • 16.

    Ilinsky, Y. & Kosterin, O. E. Molecular diversity of Wolbachia in Lepidoptera: Prevalent allelic content and high recombination of MLST genes. Mol. Phylogenet. Evol. 109, 164–179 (2017).

    CAS 
    PubMed 

    Google Scholar 

  • 17.

    Sazama, E. J., Ouellette, S. P. & Wesner, J. S. Bacterial endosymbionts are common among, but not necessarily within, insect species. Environ. Entomol. 48, 127–133 (2019).

    PubMed 

    Google Scholar 

  • 18.

    Zaspel, J. M. Systematics, biology, and behavior of fruit-piercing and blood-feeding moths in the subfamily calpinae (lepidoptera: noctuidae). (2008).

  • 19.

    Mason, C. J. & Raffa, K. F. Acquisition and structuring of midgut bacterial communities in gypsy moth (Lepidoptera: Erebidae) larvae. Environ. Entomol. 43, 25 (2014).

    Google Scholar 

  • 20.

    Ilinsky, Y. et al. Detection of bacterial symbionts (Wolbachia, Spiroplasma)and eukaryotic pathogen (Microsporidia) in Japanese populationsof gypsy moth species (Lymantria spp.). Euroasian Entomol. J. 16, 1–5 (2017).

    Google Scholar 

  • 21.

    Boonsit, P. & Wiwatanaratanabutr, I. Infection density, diversity, and distribution of Wolbachia bacteria in moths (Order Lepidoptera): First systematic report from Thailand. J. Asia-Pac. Entomol. 24, 20 (2021).

    Google Scholar 

  • 22.

    Gavotte, L. et al. A survey of the bacteriophage WO in the endosymbiotic bacteria Wolbachia. Mol. Biol. Evol. 24, 427–435 (2006).

    PubMed 

    Google Scholar 

  • 23.

    Wang, G. H. et al. Bacteriophage WO can mediate horizontal gene transfer in endosymbiotic wolbachia genomes. Front. Microbiol. 7, 1–16 (2016).

    Google Scholar 

  • 24.

    Wang, N., Jia, S., Xu, H., Liu, Y. & Huang, D. Multiple horizontal transfers of bacteriophage WO and host wolbachia in fig wasps in a closed community. Front. Microbiol. 7, 1–10 (2016).

    Google Scholar 

  • 25.

    Tanaka, K., Furukawa, S., Nikoh, N., Sasaki, T. & Fukatsu, T. Complete WO phage sequences reveal their dynamic evolutionary trajectories and putative functional elements required for integration into the wolbachia genome. Appl. Environ. Microbiol. 75, 5676–5686 (2009).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 26.

    Kaushik, S., Sharma, K. K., Ramani, R. & Lakhanpaul, S. Detection of Wolbachia phage (WO) in Indian Lac insect [Kerria lacca (Kerr)] and its implications. Indian J. Microbiol. 59, 237–240 (2019).

    CAS 
    PubMed 

    Google Scholar 

  • 27.

    LePage, D. P. et al. Prophage WO genes recapitulate and enhance Wolbachia-induced cytoplasmic incompatibility. Nature 543, 243–247 (2017).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 28.

    Shropshire, J. D., On, J., Layton, E. M., Zhou, H. & Bordenstein, S. R. One prophage WO gene rescues cytoplasmic incompatibility in Drosophila melanogaster. Proc. Natl. Acad. Sci. 115, 4987 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 29.

    Bordenstein, S. R. & Bordenstein, S. R. Eukaryotic association module in phage WO genomes from Wolbachia. Nat. Commun. 7, 13155 (2016).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 30.

    Kent, B. N. & Bordenstein, S. R. Phage WO of Wolbachia: Lambda of the endosymbiont world. Trends Microbiol. 18, 173–181 (2010).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 31.

    Dale, C., Young, S. A., Haydon, D. T. & Welburn, S. C. The insect endosymbiont Sodalis glossinidius utilizes a type III secretion system for cell invasion. Proc. Natl. Acad. Sci. 98, 1883–1888 (2001).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 32.

    Boyd, B. M. et al. Two bacterial genera, sodalis and rickettsia, associated with the seal louse Proechinophthirus fluctus (Phthiraptera: Anoplura). Appl. Environ. Microbiol. 82, 3185–3197 (2016).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 33.

    Fukatsu, T. et al. Bacterial endosymbiont of the slender pigeon louse, Columbicola columbae, allied to endosymbionts of grain weevils and tsetse flies. Appl. Environ. Microbiol. 73, 6660–6668 (2007).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 34.

    Šochová, E., Husník, F., Nováková, E., Halajian, A. & Hypša, V. Arsenophonus and Sodalis replacements shape evolution of symbiosis in louse flies. PeerJ 5, e4099 (2017).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 35.

    Burke, G. R., Normark, B. B., Favret, C. & Moran, N. A. Evolution and diversity of facultative symbionts from the aphid subfamily lachninae. Appl. Environ. Microbiol. 75, 5328–5335 (2009).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 36.

    Santos-Garcia, D., Silva, F. J., Morin, S., Dettner, K. & Kuechler, S. M. The all-rounder sodalis: A new bacteriome-associated endosymbiont of the lygaeoid bug henestaris halophilus (Heteroptera: Henestarinae) and a critical examination of its evolution. Genome Biol. Evol. 9, 2893–2910 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 37.

    Toju, H. & Fukatsu, T. Diversity and infection prevalence of endosymbionts in natural populations of the chestnut weevil: Relevance of local climate and host plants. Mol. Ecol. 20, 853–868 (2011).

    PubMed 

    Google Scholar 

  • 38.

    Conord, C. et al. Long-term evolutionary stability of bacterial endosymbiosis in curculionoidea: Additional evidence of symbiont replacement in the dryophthoridae family. Mol. Biol. Evol. 25, 859–868 (2008).

    CAS 
    PubMed 

    Google Scholar 

  • 39.

    Kaiwa, N. et al. Bacterial symbionts of the giant jewel stinkbug Eucorysses grandis (Hemiptera: Scutelleridae). Zool. Sci. 28, 169–174 (2011).

    Google Scholar 

  • 40.

    Rubin, B. E. R., Sanders, J. G., Turner, K. M., Pierce, N. E. & Kocher, S. D. Social behaviour in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts. R. Soc. Open Sci. 5, 180369 (2018).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 41.

    Sameshima, S., Hasegawa, E., Kitade, O., Minaka, N. & Matsumoto, T. Phylogenetic comparison of endosymbionts with their host ants based on molecular evidence. Zool. Sci. 16, 993–1000 (1999).

    CAS 

    Google Scholar 

  • 42.

    Oishi, S., Moriyama, M., Koga, R. & Fukatsu, T. Morphogenesis and development of midgut symbiotic organ of the stinkbug Plautia stali (Hemiptera: Pentatomidae). Zool. Lett. 5, 16 (2019).

    Google Scholar 

  • 43.

    Mason, C. J. & Raffa, K. F. Acquisition and structuring of midgut bacterial communities in gypsy moth (Lepidoptera: Erebidae) larvae. Environ. Entomol. 43, 595–604 (2014).

    PubMed 

    Google Scholar 

  • 44.

    Khojandi, N., Haselkorn, T. S., Eschbach, M. N., Naser, R. A. & DiSalvo, S. Intracellular Burkholderia Symbionts induce extracellular secondary infections; driving diverse host outcomes that vary by genotype and environment. ISME J. 13, 2068–2081 (2019).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 45.

    Itoh, H. et al. Host–symbiont specificity determined by microbe–microbe competition in an insect gut. Proc. Natl. Acad. Sci. USA 116, 22673–22682 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 46.

    Ohbayashi, T., Itoh, H., Lachat, J., Kikuchi, Y. & Mergaert, P. Burkholderia gut symbionts associated with European and Japanese populations of the dock bug Coreus marginatus (Coreoidea: Coreidae). Microbes Environ. 34, 219–222 (2019).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 47.

    Itoh, H. et al. Evidence of environmental and vertical transmission of Burkholderia symbionts in the oriental chinch bug, Cavelerius saccharivorus (Heteroptera: Blissidae). Appl. Environ. Microbiol. 80, 5974–5983 (2014).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 48.

    Kikuchi, Y. et al. Symbiont-mediated insecticide resistance. Proc. Natl. Acad. Sci. USA 109, 8618–8622 (2012).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 49.

    Louis, F. et al. The bracovirus genome of the parasitoid wasp Cotesia congregata is amplified within 13 replication units, including sequences not packaged in the particles. J. Virol. 87, 9649–9660 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 50.

    Ghanavi, H. R., Twort, V., Hartman, T. J., Zahiri, R. & Wahlberg, N. The (non) accuracy of mitochondrial genomes for family level phylogenetics: The case of erebid moths (Lepidoptera; Erebidae). bioRxiv https://doi.org/10.1101/2021.07.14.452330 (2021).

    Article 

    Google Scholar 

  • 51.

    Rigaud, T. & Juchault, P. Success and failure of horizontal transfers of feminizing Wolbachia endosymbionts in woodlice. J. Evol. Biol. 8, 25 (1995).

    Google Scholar 

  • 52.

    Zahiri, R. et al. Molecular phylogenetics of Erebidae (Lepidoptera, Noctuoidea). Syst. Entomol. 37, 102–124 (2012).

    Google Scholar 

  • 53.

    Andrews, S. FastQC: A Quality Control Tool for High Throughput Sequence Data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (2010).

  • 54.

    Schmieder, R. & Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics https://doi.org/10.1093/bioinformatics/btr026 (2011).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 55.

    Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics https://doi.org/10.1093/bioinformatics/btu170 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 56.

    Wood, D. E. & Salzberg, S. L. Kraken: Ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15, R46 (2014).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 57.

    Segata, N. et al. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods 9, 811–814 (2012).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 58.

    Kikuchi, Y. & Yumoto, I. Efficient colonization of the bean bug Riptortus pedestris by an environmentally transmitted Burkholderia Symbiont. Appl. Environ. Microbiol. 79, 2088–2091 (2013).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 59.

    Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 20 (2012).

    Google Scholar 

  • 60.

    Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 20 (2009).

    CAS 

    Google Scholar 

  • 61.

    Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2009).

    MATH 

    Google Scholar 


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