Characterization and taxonomic utility of ITS2 in Dolerus Panzer, 1801 (Hymenoptera: Tenthredinidae)
Yıl 2022,
, 13 - 23, 01.03.2022
Mehmet Gülmez
,
Mahir Budak
,
Ertan Mahir Korkmaz
,
Sevda Hastaoğlu Örgen
,
Hasan Hüseyin Başıbüyük
Öz
The widespread use of ITS2 as a potential marker in insects has accelerated species-level phylogenetic studies. Reliable and quality data can be obtained thanks to the features such as rapid evolution and secondary structure of this marker. This paper presents the phylogenetic relationship among 36 individuals of Dolerus Panzer, 1801 (Hymenoptera: Tenthredinidae) collected between 2002 and 2018 to obtain the first data on ITS2 secondary structure. Aligned of ITS2 data were analyzed by application of maximum likelihood method to reveal phylogenetic relationship among the specimens. Also, the structural properties, length variation and presence of compensatory base changes make the ITS2 useful marker in determination of species boundaries of closely related species. Four species (Dolerus triplicatus (Klug, 1818), Dolerus germanicus (Fabricius, 1775), Dolerus puncticollis Thomson, 1871 and Dolerus nigratus (Müller, 1776) and two putative species (Dolerus spp. 1 and 2) were determined from 36 individuals belonging to Dolerus.
Destekleyen Kurum
TÜBİTAK (The Scientific and Technological Research Council of Turkey)
Teşekkür
This study was financially supported by the TÜBITAK (The Scientific and Technological Research Council of Turkey) via a research project with grant number 113Z753. The members of Cumhuriyet University Evolutionary Bioinformatics Research Group (EBRG) are thanked for their contributions in bioinformatic work. Mehmet Gülmez is supported by the Council of Higher Education (CoHE) of Turkey with 100/2000 PhD Scholarship.
Kaynakça
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- Ankenbrand, M. J., A. Keller, M. Wolf, J. Schultz & F. Förster, 2015. ITS2 database V: twice as much. Molecular Biology & Evolution, 32 (11): 3030-3032.
- Barker, A. M., 1998. The identification of larvae of eight graminivorous species of the sawfly genus Dolerus Panzer 1801 (Hymenoptera: Tenthredinidae) regularly found in grass and cereal fields in southern England. Journal of Natural History, 32 (8): 1181-1215.
- Barker, A. M., N. J., Brown & C. J. M. Reynolds 1999. Do host-plant requirements and mortality from soil cultivation determine the distribution of graminivorous sawflies on farmland? Journal of Applied Ecology, 36 (2): 271-282.
- Budak, M., M. Güler, E. M. Korkmaz, S. H. Örgen & H. H. Başıbüyük, 2016. The characterisation and taxonomic utility of ITS2 in Tenthredopsis Costa, 1859 (Tenthredinidae: Hymenoptera) with some new records from Turkey. Biochemical Systematics & Ecology, 66: 76-85.
- Caisová L., B. Marin & M. Melkonian, 2011. A close-up view on ITS2 evolution and speciation-a case study in the Ulvophyceae (Chlorophyta, Viridiplantae). BMC Evolutionary Biology, 11 (1): 1-24.
- Caisová, L., B. Marin & M. A. Melkonian, 2013. A consensus secondary structure of ITS2 in the Chlorophyta identified by phylogenetic reconstruction. Protist, 164 (4): 482-496.
- Caisová, L. & M. Melkonian, 2014. Evolution of helix formation in the ribosomal internal transcribed spacer 2 (ITS2) and its significance for RNA secondary structures. Journal of Molecular Evolution, 78 (6): 324-337.
- Çalmaşur, Ö. & H. Özbek, 2004a. A contribution to the knowledge of the Tenthredinidae (Symphyta, Hymenoptera) Fauna of Turkey Part I: The Subfamily Tenthredininae. Turkish Journal of Zoology, 28 (1): 37-54.
- Çalmaşur, Ö. & H. Özbek, 2004b. Contribution to the knowledge of Tenthredinidae (Symphyta, Hymenoptera) fauna of Turkey Part II: Subfamilies Blennocampinae, Dolerinae, Nematinae and Selandrinae. Turkish Journal of Zoology, 28 (1): 55-71.
- Çalmaşur, Ö., 2020. New records and some new distribution data for the Turkish Nematinae (Hymenoptera: Symphyta: Tenthredinidae) fauna. Turkish Journal of Entomology, 44 (3): 413-422.
- Coleman, A. W., 2003. ITS2 is a double-edged tool for eukaryote evolutionary comparisons. Trends in Genetics, 19 (7): 370-375.
- Coleman, A. W., 2007. Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Research, 35 (10): 3322-3329.
- Coleman, A. W., 2009. Is there a molecular key to the level of “biological species” in eukaryotes? A DNA guide. Molecular Phylogenetics & Evolution, 50 (1): 197-203.
- Coleman, A. W., 2015. Nuclear rRNA transcript processing versus internal transcribed spacer secondary structure. Trends in Genetics, 31 (3): 157-163.
- Darty, K., A. Denise & Y. Ponty, 2009. VARNA: interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25 (15): 1974-1975.
- Dover, G., 1982. Molecular drive: a cohesive mode of species evolution. Nature, 299: 111-117.
- Fagan-Jeffries, E. P., S. J. B. Cooper, T. M. Bradford & A. D. Austin, 2019. Intragenomic internal transcribed spacer 2 variation in a genus of parasitoid wasps (Hymenoptera: Braconidae): implications for accurate species delimitation and phylogenetic analysis, Insect Molecular Biology, 28 (4): 485-498.
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- Jørgensen, A., J. R. Stothard, H. Madsen, A. Nalugwa, S. Nyakaana & D. Rollinson, 2013. The ITS2 of the genus Bulinus: novel secondary structure among freshwater snails and potential new taxonomic markers. Acta Tropica, 128 (2): 218-225.
- Katılmış, Y. & S. Kıyak, 2015. A little-known species Pontania proxima (Serville, 1823) (Hymenoptera: Symphyta: Tenthredinidae) from Turkey. Munis Entomology & Zoology, 10 (1): 196-198.
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- Larkin, M., G. Blackshields, N. Brown, R. Chenna, P. McGettigan, H. McWilliam, F. Valentin, I. Wallace, A. Wilm, R. Lopez, J. Thompson, T. Gibson & D. Higgins, 2007. ClustalW and ClustalX version2. Bioinformatics, 23 (21): 2947-2948.
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- Pawłowska, J., G. Walther, M. Wilk, S. de Hoog & M. Wrzosek, 2013. The use of compensatory base change analysis of ITS2 as a tool in the phylogeny of Mucorales, illustrated by the Mucor circinelloides complex. Organisms Diversity & Evolution, 13 (4): 497-502.
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Dolerus Panzer, 1801 (Hymenoptera: Tenthredinidae) cinsinde ITS2'nin karakterizasyonu ve taksonomik kullanımı
Yıl 2022,
, 13 - 23, 01.03.2022
Mehmet Gülmez
,
Mahir Budak
,
Ertan Mahir Korkmaz
,
Sevda Hastaoğlu Örgen
,
Hasan Hüseyin Başıbüyük
Öz
Böceklerde ITS2'nin moleküler belirteç olarak kullanılmasının yaygınlaşması, tür düzeyindeki filogeni çalışmalarına hız kazandırmıştır. Bu belirtecin hem hızlı evrime sahip olması hem de ikincil yapı oluşturması gibi özellikler sayesinde güvenilir ve kaliteli veriler elde edilebilir. Bu makalede, Dolerus Panzer, 1801 cinsine ait 2002-2018 yılları arasında toplanmış olan 36 bireyin (Hymenoptera: Tenthredinidae) aralarındaki filogenetik ilişkiyi ve ITS2 ikincil yapı özelliklerine ilişkin ilk verileri sunuyoruz. ITS2'nin hizalanmış verileri, örnekler arasındaki ilişkiyi görmek için maksimum likelihood yöntemi uygulanarak analiz edildi. Aynı zamanda ITS2'nin yapısal özellikleri, uzunluk polimorfizmi ve CBC'lerin olması, yakından ilişkili türlerin tür sınırlarının belirlenmesinde faydalıdır, Dolerus cinsine ait 36 bireyden, 4 tür (Dolerus triplicatus (Klug, 1818), Dolerus germanicus (Fabricus, 1775), Dolerus puncticollis Thomson, 1871 ve Dolerus nigratus (Müller, 1776) ve 2 olası tür (Dolerus spp. 1 ve 2) belirlenmiştir.
Kaynakça
- Aljanabi, S. M. & I. Martinez, 1997. Universal and rapid salt-extraction of high-quality genomic DNA for PCR-based techniques. Nucleic Acids Research, 25 (22): 4692-4693.
- Ankenbrand, M. J., A. Keller, M. Wolf, J. Schultz & F. Förster, 2015. ITS2 database V: twice as much. Molecular Biology & Evolution, 32 (11): 3030-3032.
- Barker, A. M., 1998. The identification of larvae of eight graminivorous species of the sawfly genus Dolerus Panzer 1801 (Hymenoptera: Tenthredinidae) regularly found in grass and cereal fields in southern England. Journal of Natural History, 32 (8): 1181-1215.
- Barker, A. M., N. J., Brown & C. J. M. Reynolds 1999. Do host-plant requirements and mortality from soil cultivation determine the distribution of graminivorous sawflies on farmland? Journal of Applied Ecology, 36 (2): 271-282.
- Budak, M., M. Güler, E. M. Korkmaz, S. H. Örgen & H. H. Başıbüyük, 2016. The characterisation and taxonomic utility of ITS2 in Tenthredopsis Costa, 1859 (Tenthredinidae: Hymenoptera) with some new records from Turkey. Biochemical Systematics & Ecology, 66: 76-85.
- Caisová L., B. Marin & M. Melkonian, 2011. A close-up view on ITS2 evolution and speciation-a case study in the Ulvophyceae (Chlorophyta, Viridiplantae). BMC Evolutionary Biology, 11 (1): 1-24.
- Caisová, L., B. Marin & M. A. Melkonian, 2013. A consensus secondary structure of ITS2 in the Chlorophyta identified by phylogenetic reconstruction. Protist, 164 (4): 482-496.
- Caisová, L. & M. Melkonian, 2014. Evolution of helix formation in the ribosomal internal transcribed spacer 2 (ITS2) and its significance for RNA secondary structures. Journal of Molecular Evolution, 78 (6): 324-337.
- Çalmaşur, Ö. & H. Özbek, 2004a. A contribution to the knowledge of the Tenthredinidae (Symphyta, Hymenoptera) Fauna of Turkey Part I: The Subfamily Tenthredininae. Turkish Journal of Zoology, 28 (1): 37-54.
- Çalmaşur, Ö. & H. Özbek, 2004b. Contribution to the knowledge of Tenthredinidae (Symphyta, Hymenoptera) fauna of Turkey Part II: Subfamilies Blennocampinae, Dolerinae, Nematinae and Selandrinae. Turkish Journal of Zoology, 28 (1): 55-71.
- Çalmaşur, Ö., 2020. New records and some new distribution data for the Turkish Nematinae (Hymenoptera: Symphyta: Tenthredinidae) fauna. Turkish Journal of Entomology, 44 (3): 413-422.
- Coleman, A. W., 2003. ITS2 is a double-edged tool for eukaryote evolutionary comparisons. Trends in Genetics, 19 (7): 370-375.
- Coleman, A. W., 2007. Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Research, 35 (10): 3322-3329.
- Coleman, A. W., 2009. Is there a molecular key to the level of “biological species” in eukaryotes? A DNA guide. Molecular Phylogenetics & Evolution, 50 (1): 197-203.
- Coleman, A. W., 2015. Nuclear rRNA transcript processing versus internal transcribed spacer secondary structure. Trends in Genetics, 31 (3): 157-163.
- Darty, K., A. Denise & Y. Ponty, 2009. VARNA: interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25 (15): 1974-1975.
- Dover, G., 1982. Molecular drive: a cohesive mode of species evolution. Nature, 299: 111-117.
- Fagan-Jeffries, E. P., S. J. B. Cooper, T. M. Bradford & A. D. Austin, 2019. Intragenomic internal transcribed spacer 2 variation in a genus of parasitoid wasps (Hymenoptera: Braconidae): implications for accurate species delimitation and phylogenetic analysis, Insect Molecular Biology, 28 (4): 485-498.
- Goulet, H., 1986. The genera and species of the Nearctic Dolerini (Symphyta: Tenthredinidae: Selandriinae): classification and phylogeny. The Memoirs of the Entomological Society of Canada, 118 (S135): 5-208.
- Gutell, R. R., N. Larsen & C. R. Woese, 1994. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiological Reviews, 58 (1): 10-26.
- Haris, A., 1995. Further data on the food-choice of wheat-sawflies (Dolerus spp., Hymenoptera, Tenthredinidae). Acta Phytopathologica et Entomologica Hungarica, 30 (1): 255-264.
- Haris, A., 2000. Study on the Palaearctic Dolerus Panzer, 1801 species (Hymenoptera: Tenthredinidae). Folia Entomologica Hungarica, 61 (1): 95-148.
- Heidemaa, M., 2004. Systematic Studies on Sawflies of the Genera Dolerus, Empria and Caliroa (Hymenoptera: Tenthredinidae). University of Tartu, Institute of Zoology and Hydrobiology, Faculty of Biology and Geography, (Unpublished) Phd Thesis, Estonia, 162 pp.
- Hong, J. H., C. S. Oh, M. Seo & D. H. Shin, 2019. Analysis of COI and ITS2 Regions of DNA Obtained from Paragonimus westermani Eggs in Ancient Coprolites on Joseon Dynasty Mummies. Memorias do Instituto Oswaldo Cruz, 114 pp.
- Ji, Y. J., D. X. Zhang & L. J. He, 2003. Evolutionary conservation and versatility of a new set of primers for amplifying the ribosomal internal transcribed spacer regions in insects and other invertebrates. Molecular Ecology Notes, 3 (4): 581-585.
- Jørgensen, A., J. R. Stothard, H. Madsen, A. Nalugwa, S. Nyakaana & D. Rollinson, 2013. The ITS2 of the genus Bulinus: novel secondary structure among freshwater snails and potential new taxonomic markers. Acta Tropica, 128 (2): 218-225.
- Katılmış, Y. & S. Kıyak, 2015. A little-known species Pontania proxima (Serville, 1823) (Hymenoptera: Symphyta: Tenthredinidae) from Turkey. Munis Entomology & Zoology, 10 (1): 196-198.
- Kearse, M., R. Moir, A. Wilson, S. Stones-Havas, M. Cheung, S. Sturrock, S. Buxton, A. Cooper, S. Markowitz, C. Duran, T. Thierer, B. Ashton, P. Meintjes & A. Drummond, 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28 (12): 1647-1649.
- Kitthawee, S., 2003. ITS2 sequence variations among members of Diachasmimorpha longicaudata complex (Hymenoptera: Braconidae) in Thailand. Journal of Asia-Pacific Entomology, 16 (2): 173-179.
- Kumar, S., G. Stecher & K. Tamura, 2016. Molecular Biology & Evolution, 33 (7): 1870-1874.
- Larkin, M., G. Blackshields, N. Brown, R. Chenna, P. McGettigan, H. McWilliam, F. Valentin, I. Wallace, A. Wilm, R. Lopez, J. Thompson, T. Gibson & D. Higgins, 2007. ClustalW and ClustalX version2. Bioinformatics, 23 (21): 2947-2948.
- Leppänen, S. A., E. Altenhofer, A. D. Liston & T. Nyman, 2012. Phylogenetics and evolution of host-plant use in leafmining sawflies (Hymenoptera: Tenthredinidae: Heterarthrinae). Molecular Phylogenetics & Evolution, 64 (2): 331-341.
- Liao, D., 1999. Concerted evolution: Molecular mechanism and biological implications. American Journal of Human Genetics, 64 (1): 24-30.
- Malm, T. & T. Nyman, 2015. Phylogeny of the symphytan grade of Hymenoptera: new pieces into the old jigsaw (fly) puzzle. Cladistics, 31 (1): 1-17.
- Mathews, D. H., J. Sabina, M. Zuker & D. H. Turner, 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. Journal of Molecular Biology, 28 (5): 911-940.
- Müller, T., N. Philippi, T. Dandekar, J. Schultz & M. Wolf, 2007. Distinguishing species. Rna, 13 (9): 1469-1472.
- Mullineux, T. & G. Hausner, 2009. Evolution of rDNA ITS1 and ITS2 sequences and RNA secondary structures within members of the fungal genera Grosmannia and Leptographium. Fungal Genetics Biology, 46 (11): 855-867.
- Nelson, L. A., J. F. Wallman & M. Dowton, 2008. Identification of forensically important Chrysomya (Diptera: Calliphoridae) species using the second ribosomal internal transcribed spacer (ITS2). Forensic Science International, 177 (2-3): 238-247.
- Niu, G., S. Jiang, Ö. Doğan, E. M. Korkmaz, M. Budak, D. Wu & M. Wei, 2021. Mitochondrial phylogenomics of Tenthredinidae (Hymenoptera: Tenthredinoidea) supports the monophyly of Megabelesesinae as a Subfamily. Insects, 12 (6): 495: 1-19.
- Niu, G., E. M. Korkmaz, Ö. Doğan, Y. Zhang, M. N. Aydemir, M. Budak, S. Du, H. H. Başıbüyük & M. Wei, 2019. The first mitogenomes of the superfamily Pamphilioidea (Hymenoptera: Symphyta): Mitogenome architecture and phylogenetic inference. International Journal of Biological Macromolecules, 124: 185-199.
- Pawłowska, J., G. Walther, M. Wilk, S. de Hoog & M. Wrzosek, 2013. The use of compensatory base change analysis of ITS2 as a tool in the phylogeny of Mucorales, illustrated by the Mucor circinelloides complex. Organisms Diversity & Evolution, 13 (4): 497-502.
- Poczai, P., I. Varga & J. Hyvönen, 2015. Internal transcribed spacer (ITS) evolution in populations of the hyperparasitic European mistletoe pathogen fungus, Sphaeropsis visci (Botryosphaeriaceae): the utility of ITS2 secondary structures. Gene, 558 (1): 54-64.
- Ponce-Gordo, F., F. Fonseca-Salamanca & R. A. Martínez-Díaz, 2011. Genetic heterogeneity in internal transcribed spacer genes of Balantidium coli (Litostomatea, Ciliophora), Protist, 162 (5): 774-794.
- Prous, M., M. Heidemaa, S. Akihiko & V. Soon, 2011. Review of the sawfly genus Empria (Hymenoptera, Tenthredinidae) in Japan. ZooKeys, 150: 347-380.
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