İki Cephid sap arısında (Hymenoptera: Cephidae) koku reseptör protein genlerinin yüksek verimli dizileme ile tanımlanması

Öz

Böcekler, Dünya'daki karasal yaşama iyi uyum sağlamış organizmalardır. Koku reseptör ailesinin evrimi, bu olağanüstü adaptasyonun altında yatan nedenlerden biridir. Koku reseptörleri (OR'ler) çevredeki aromaları algılar ve böceğin tepki vermesine neden olur. Fitofag böceklerin konukçularından gelen koku sinyallerini algılama yeteneği çiftleşme, yumurtlama ve beslenme için çok önemlidir. Ekonomik açıdan önemli bazı bitkilerde zararlı olan Cephidae'deki koku reseptör genleri ailesi çok az anlaşılmıştır. Biyoinformatik araçlar, iki zararlı türün, Syrista parreyssi (Spinola, 1843) (Hymenoptera: Cephidae) (bir gül zararlısı) ve Pachycephus smyrnensis J.P.E.F. Stein, 1876 (Hymenoptera: Cephidae), (bir haşhaş zararlısı), koku reseptörlerini belirlemek amacıyla genomik verilerini analiz etmek için kullanılmıştır. Sivas'ta 2020 yılında toplanan P. smyrnensis tüm genom dizilemesi yeni nesil dizileme ile yapılmış ve S. parreyssii genomuna ait kısa okumalar ise önceki çalışmalardan elde edilmiştir. Analizler sonucunda P. smyrnensis'ten 67 olası koku reseptörü geni ve S. parreyssii'den 82 olası koku reseptörü geni tanımlandı ve açıklandı. Bu iki türün OR'lerinin beş ayrı kümede tekrarlayan genler olarak organize olduğu bulunmuştur. İncelenen türlerin hiçbirinde türe özgü OR genleri tespit edilmemiştir. Sonuç olarak, konakçı özgüllüğünün birden fazla OR'nin birleşik etkisi yoluyla kazanıldığı varsayılmıştır.

Anahtar Kelimeler

• Cephini
• yeni nesil dizileme
• koku almaçları
• tekrarlayan genler
• Testereli arılar

Identification of odorant receptor protein genes in two Cephid stem borers (Hymenoptera: Cephidae) by high-throughput sequencing

Abstract

Insects are well adapted organisms to the terrestrial life on Earth. The evolution of the odorant receptor family is one of the causes underpinning this remarkable adaptation. Odorant receptors (ORs) sense aromas in the environment and cause the insect to respond. The ability of phytophagous insects to detect odor signals from their hosts is crucial for mating, oviposition, and feeding. The family of odorant receptor genes in Cephidae, pest on some economically important plants, is little understood. Bioinformatic tools were used to analyze the genomic data of the two pest species, Syrista parreyssii (Spinola, 1843) (Hymenoptera: Cephidae) (a rose pest) and Pachycephus smyrnensis J.P.E.F. Stein, 1876 (Hymenoptera: Cephidae), (a poppy pest), to determine their odorant receptors. The whole genome sequencing of P. smyrnensis collected in Sivas in 2020 was performed by next generation sequencing and short reads of S. parreyssii genome were obtained from previous studies. Following bioinformatic analyses, 67 and 82 putative odorant receptor genes were identified and annotated for P. smyrnensis and S. parreyssii, respectively. The ORs of these two species were found to be organized as repetitive genes in five separate clusters. No species-specific OR genes were identified in any of the investigated species. As a result, it was hypothesized that host specificity was acquired through the combined effect of multiple ORs.

Keywords

• Cephini
• next-generation sequencing
• odorant receptors
• repetitive genes
• Sawflies

Kaynakça

1. Altınayar, G., 1975. Ekin Sap Arıları (Cephus pygmeus (L.) ve Trachelus tabidus (F.) (Hymenoptera: Cephidae)’nin Konya Ilinde Biyo-Ekolojileri, Sebep Oldukları Ürün Kayıpları ve Savaş Yolları Üzerine Araştırmalar. Ankara Bölge Zirai Mücadele Araştırma Enstitüsü Yayınları, Araştırma Eserleri Serisi 36: 135 s (in Turkish).
2. Andersson, M. N., C. Löfstedt & R. D. Newcomb, 2015. Insect olfaction and the evolution of receptor tuning. Frontiers in Ecology and Evolution, 3: Article ID 53.
3. Ardila-Garcia, A. M., G. J. Umphrey & T. R. Gregory, 2010. An expansion of the genome size dataset for the insect order Hymenoptera, with a first test of parasitism and eusociality as possible constraints. Insect Molecular Biology, 19 (3): 337-346.
4. Bankevich, A., S. Nurk, D. Antipov, A. A. Gurevich, M. Dvorkin, A.S. Kulikov, V. M. Lesin, S. I. Nikolenko, S. Pham, A. D. Prjibelski, A. V. Pyshkin, A. V. Sirotkin, N. Vyahhi, G. Tesler, M. A. Alekseyev & P. A. Pevzner, 2012. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19 (5): 455-477.
5. Benson, R. B., 1951. Hymenoptera: 2. Symphyta. Section (a). Handbooks for the identification of British insects. Royal Entomological Society of London, London, Vol. VI, Part 2 (a): 50 pp.
6. Blum, M., H. Y. Chang, S. Chuguransky, T. Grego, S. Kandasaamy, A. Mitchell, G. Nuka, T. Paysan-Lafosse, M. Qureshi, S. Raj, L. Richardson, G. A. Salazar, L. Williams, P. Bork, A. Bridge, J. Gough, D. H. Haft, I. Letunic, A. Marchler-Bauer, H. Mi, D.A. Natale, M. Necci, C. A. Orengo, A. P. Pandurangan, C. Rivoire, C. J. A Sigrist, I. Sillitoe, N. Thanki, P. D. Thomas, S. C. E Tosatto, C. H. Wu, A. Bateman & R. D. Finn, 2021. The InterPro protein families and domains database: 20 years on. Nucleic Acids Research, 49 (D1): 344-354.
7. Brand, P. & S. R. Ramírez, 2017. The evolutionary dynamics of the odorant receptor gene family in corbiculate bees. Genome Biology and Evolution, 9 (8): 2023-2036.
8. Budak, M., 2012. Systematics, Biogeography and Phylogeny of Cephidae (Hymenoptera: Insecta) Species of Turkey. Cumhuriyet Üniversitesi, Fen Bilimleri Ensititüsü, (Unpublished) PhD Thesis, Sivas, 201 pp (in Turkish with abstract in English).

9. Budak, M., E.M. Korkmaz & H.H. Basibuyuk, 2011. A molecular phylogeny of the Cephinae (Hymenoptera, Cephidae) based on mtDNA COI gene: a test of traditional classification. ZooKeys, 130: 363-378.
10. Capella-Gutiérrez, S., J. M. Silla-Martínez & T. Gabaldón, 2009. trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25 (15): 1972-1973.
11. Chak, S. T. C., S. E. Harris, K. M. Hultgren, N. W. Jeffery & D. R. Rubenstein, 2021. Eusociality in snapping shrimps is associated with larger genomes and an accumulation of transposable elements. Proceedings of the National Academy of Sciences of the United States of America, 118 (24): e2025051118.
12. Chen, S., Y. Zhou, Y. Chen & J. Gu, 2018. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34 (17): i884-i890.
13. Claros, M. G., R. Bautista, D. Guerrero-Fernández, H. Benzerki, P. Seoane & N. Fernández-Pozo, 2012. Why assembling plant genome sequences is so challenging. Biology, 1 (2): 439-459.
14. Clyne, P. J., G. C. Warr, M. R. Freeman, D. Lessing, J. Kim & J. R. Carlson, 1999. A novel family of divergent deven-transmembrane proteins: candidate odorant receptors in Drosophila. Neuron, 22 (2): 327-338.
15. Demirözer, O., I. Karaca & Y. Karsavuran, 2011. Population fluctuations of some important pests and natural enemies found in oil-bearing rose (Rosa damascena Miller) production areas in Isparta province (Turkey). Turkish Journal of Entomology, 35 (4): 539-558.
16. Eyun, S., H. Y. Soh, M. Posavi, J. B. Munro, D. S. T. Hughes, S. C. Murali, J. Qu, S. Dugan, S.L. Lee, H. Chao, H. Dinh, Y. Han, H. Doddapaneni, K. C. Worley, D. M. Muzny, E. Park, J. C. Silva, R. A. Gibbs, S. Richards & C. E. Lee, 2017. Evolutionary history of chemosensory-related gene families across the Arthropoda. Molecular Biology and Evolution, 34 (8): 1838-1862.
17. Galizia, C. G., 2014. Olfactory coding in the insect brain: data and conjectures. European Journal of Neuroscience, 39 (11): 1784-1795.
18. Ganley, A. R. D. & T. Kobayashi, 2007. Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data. Genome Research, 17 (2): 184-191. Gauld, I. D. & B. Bolton, 1988. The Hymenoptera. British Museum (Natural History) & Oxford University Press, London, 332 pp.
19. Giray, H., 1985. A list of pests of popy (Papaver somniferum L.) in Turkey, with notes on the types of damage of the important species. Türkiye Bitki Koruma Dergisi (Turkish Journal of Entomology), 9 (2): 109-124 (in Turkish with abstract in English).
20. Gregory, T. R., 2004. Insertion-deletion biases and the evolution of genome size. Gene, 324 (1): 15-34.
21. Gress, J. C., H. M. Robertson, D.K. Weaver, M. Dlakić & K. W. Wanner, 2013. Odorant receptors of a primitive hymenopteran pest, the wheat stem sawfly. Insect Molecular Biology, 22 (6): 659-667.
22. Hallem, E. A. & J. R. Carlson, 2004. Coding of odors by a receptor repertoire. Cell, 125 (1): 143-160.
23. Hallem, E. A., M. G. Ho & J. R. Carlson, 2004. The molecular basis of odor coding in the Drosophila antenna. Cell, 117 (7): 965-979.
24. Hansson, B. S. & M. C. Stensmyr, 2011. Evolution of Insect Olfaction. Neuron, 72 (5): 698-711.
25. Haverkamp, A., B. S. Hansson & M. Knaden, 2018. Combinatorial codes and labeled lines: How insects use olfactory cues to find and judge food, mates, and oviposition sites in complex environments. Frontiers in Physiology, 9: Article ID 49.
26. Johnston, J. S., L. D. Ross, L. Beani, D. P. Hughes & J. Kathirithamby, 2004. Tiny genomes and endoreduplication in Strepsiptera. Insect Molecular Biology, 13 (6): 581-585.
27. Jones P., D. Binns, H. Y. Chang, M. Fraser, W. Li, C. McAnulla, H. McWilliam, J. Maslen, A. Mitchell, G. Nuka, S. Pesseat, A. F. Quinn, A. Sangrador-Vegas, M. Scheremetjew, S. Yong, R. Lopez & S. Hunter, 2014. InterProScan 5: genome-scale protein function classification. Bioinformatics, 30 (9): 1236-1240.
28. Karner, T., I. Kellner, A. Schultze, H. Breer & J. Krieger, 2015. Co-expression of six tightly clustered odorant receptor genes in the antenna of the malaria mosquito Anopheles gambiae. Frontiers in Ecology and Evolution, 3: Article ID 26.
29. Katoh, K. & D. M. Standley, 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution, 30 (4): 772-780. Keller, A. & L. B. Vosshall, 2016. Olfactory perception of chemically diverse molecules. BMC Neuroscience, 17: Article ID 55.
30. Kirkness, E. F., ,J. B. Haas, W. Sun, H. R. Braig, M. A. Perotti, J. M. Clark, S. H. Lee, H. M. Robertson, R. C. Kennedy, E. Elhaik, D. Gerlach, E. V. Kriventseva, C. G. Elsik, D. Graur, C. A. Hill, J. A. Veenstra, ... & B. R. Pittendrigh, 2010. Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle. Proceedings of the National Academy of Sciences, 107 (27): 12168-12173.
31. Leal, W. S., 2013. Odorant reception in insects: Roles of receptors, binding proteins, and degrading enzymes. Annual Review of Entomology, 58 (1): 373-391.
32. Li, H., R. Guan, H. Guo & X. Miao, 2015. New insights into an RNAi approach for plant defence against piercing-sucking and stem-borer insect pests. Plant, Cell & Environment, 38 (11): 2277-2285.
33. Marçais, G. & C. Kingsford, 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics. 27 (6): 764-770.
34. Manni, M., M. R. Berkeley, M. Seppey & E. M. Zdobnov, 2021. BUSCO: assessing genomic data quality and beyond. Current Protocols, 1 (12): e323.
35. McKenzie, S. K. & D. J. C. Kronauer, 2018. The genomic architecture and molecular evolution of ant odorant receptors. Genome Research, 28 (11): 1757-1765.
36. Miller, S. A., D. D. Dykes & H. F. Polesky, 1988. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Research, 16 (3): Article ID 1215.
37. Missbach, C., H. K. M. Dweck, H. Vogel, A. Vilcinskas, M. C. Stensmyr, B. S. Hansson & E. Grosse-Wilde, 2014. Evolution of insect olfactory receptors. eLife, 3: e02115.
38. Niu, G., M. Budak, E. M. Korkmaz, Ö. Doğan, A. Nel, S. Wan, C. Cai, C. Jouault, M. Li & M. Wei, 2022. Phylogenomic analyses of the Tenthredinoidea support the familial rank of Athaliidae (Insecta, Tenthredinoidea). Insects, 13 (10): Article ID 858.
39. Ray, A., W. G. van Naters, T. Shiraiwa & J. R. Carlson, 2007. Mechanisms of odor receptor gene choice in Drosophila. Neuron, 53 (3): 353-369.
40. Rimal, S. & Y. Lee, 2018. The multidimensional ionotropic receptors of Drosophila melanogaster. Insect Molecular Biology, 27 (1): 1-7.
41. Robertson, H. M., 2015. The insect chemoreceptor superfamily is ancient in animals. Chemical Senses, 40: 609-614.
42. Robertson, H. M., C. G. Warr & J. R. Carlson, 2003. Molecular evolution of the insect chemoreceptor gene superfamily in Drosophila melanogaster. Proceedings of the National Academy of Sciences, 100 (2): 14537-14542.
43. Robertson, H. M., R. M. Waterhouse, K. K. O. Walden, L. Ruzzante, M. J. M. F. Reijnders, B. S. Coates, F. Legeai, J. C. Gress, S. Biyiklioglu, D. K. Weaver, K. W. Wanner & H. Budak, 2018. Genome sequence of the wheat stem sawfly, Cephus cinctus, representing an early-branching lineage of the Hymenoptera, illuminates evolution of hymenopteran chemoreceptors. Genome Biology and Evolution, 10 (11): 2997-3011.
44. Saari, T. W., A. L Schroeder, G. T. Ankley & D. L. Villeneuve, 2017. First‐generation annotations for the fathead minnow (Pimephales promelas) genome. Environmental Toxicology and Chemistry, 36 (12): 3436-3442.
45. Saina, M., H. Busengdal, C. Sinigaglia, L. Petrone, P. Oliveri, F. Rentzsch & R. Benton, 2015. A cnidarian homologue of an insect gustatory receptor functions in developmental body patterning. Nature Communications, 6 (1): 6243.
46. Sánchez-Gracia, A., F. G. Vieira & J. Rozas, 2009. Molecular evolution of the major chemosensory gene families in insects. Heredity, 103 (3): 208-216.
47. Scott, K., R. Brady Jr., A. Cravchik, P. Morozov, A. Rzhetsky, C. Zuker & R. Axel, 2001. A Chemosensory Gene Family Encoding Candidate Gustatory and Olfactory Receptors in Drosophila. Cell, 104 (5): 661-673.
48. Smith, D. R. & A. Shinohara, 2002. A new genus and new species of Cephidae (Hymenoptera) from Sulawesi Utara, Indonesia. Proceedings of the Entomological Society of Washington, 104 (3): 624-628.
49. Smith, D. R. & S. Schmidt, 2009. A new subfamily, genus, and species of Cephidae (Hymenoptera) from Australia. Zootaxa, 2034 (1): 56-60.
50. Stamatakis, A., 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30 (9): 1312-1313.
51. Stanke, M., O. Keller, İ. Gunduz, A. Hayes, S. Waack & B. Morgenstern, 2006. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Research, 34 (2): W435-W439.
52. Stanke, M., M. Diekhans, R. Baertsch & D. Haussler, 2008. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics, 24 (5): 637-644.
53. Taeger, A., A. D. Liston, M. Prous, E. K. Groll, T. Gehroldt & S. M. Blank, 2018. ECatSym: electronic world catalog of symphyta. (Web page: https://www.sdei.de/ecatsym) (Date accessed: June 2023).
54. Treangen, T. J. & S. L. Salzberg, 2011. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nature Reviews Genetics, 13 (1): 36-46.
55. Tsutsui, N. D., A. V. Suarez, J. C. Spagna & J. S. Johnston, 2008. The evolution of genome size in ants. BMC Evolutionary Biology, 8 (1): Article ID 64.
56. Venthur, H. & J. J. Zhou, 2018. Odorant receptors and odorant-binding proteins as insect pest control targets: A comparative analysis. Frontiers in Physiology, 9: Article ID 1163.
57. Vosshall, L. B., A. M. Wong & R. Axel, 2000. An olfactory sensory map in the fly brain. Cell, 102 (2): 147-159.
58. Vosshall, L. B., H. Amrein, P. S. Morozov, A. Rzhetsky & R. Axel, 1999. A spatial map of olfactory receptor expression in the Drosophila antenna. Cell, 96 (5): 725-36.
59. Waterhouse, R. M., M. Seppey, F. A. Simão, M. Manni, P. Ioannidis, G. Klioutchnikov, E. V. Kriventseva & E. M. Zdobnov, 2018. BUSCO applications from quality assessments to gene prediction and phylogenomics. Molecular Biology and Evolution, 35 (3): 543-548.
60. Wernegreen, J. J., 2012. Endosymbiosis. Current Biology, 22 (14): R555-R561.
61. Wicher, D. & F. Miazzi, 2021. Functional properties of insect olfactory receptors: ionotropic receptors and odorant receptors. Cell and Tissue Research, 383: 7-19.
62. Wicher, D., R. Schäfer, R. Bauernfeind, M. C. Stensmyr, R. Heller, S. H. Heinemann & B. S. Hansson, 2008. Drosophila odorant receptors are both ligand-gated and cyclic-nucleotide-activated cation channels. Nature, 452 (190): 1007-1011.
63. Yan, H., S. Jafari, G. Pask, X. Zhou, D. Reinberg & C. Desplan, 2020. Evolution, developmental expression and function of odorant receptors in insects. Journal of Experimental Biology, 223 (Suppl_1): jeb208215.
64. Yuvaraj, J. K., R. E. Roberts, Y. Sonntag, X. Q. Hou, E. Grosse-Wilde, A. Machara, D. Zhang, B. S. Hansson, U. Johanson, C. Löfstedt & M. N. Andersson, 2021. Putative ligand binding sites of two functionally characterized bark beetle odorant receptors. BMC Biology, 19: Article ID 16.