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Year 2022, Volume: 43 Issue: 4, 577 - 583, 27.12.2022

Ertan Mahir Korkmaz

https://doi.org/10.17776/csj.1195087

Abstract

Keywords

Mitochondrial genome Rearrangement Sawflies; Tenthredinoidea Symphyta

References

  • [1] Carlucci A., Lignitto L., Feliciello A., Control of mitochondria dynamics and oxidative metabolism by cAMP, AKAPs and the proteasome, Trends Cell Biol., 18 (2008) 604–613.
  • [2] Cameron S.L., Insect mitochondrial genomics: implications for evolution and phylogeny, Annu. Rev. Entomol., 59 (2014) 95–117.
  • [3] Aydemir, M. N., Korkmaz, E. M., Comparative mitogenomics of Hymenoptera reveals evolutionary differences in structure and composition, International journal of biological macromolecules., 144 (2020) 460-472.
  • [4] Ballard J.W.O., Pichaud N., Mitochondrial DNA: more than an evolutionary bystander, Funct. Ecol., 28 (2014) 218–231.
  • [5] Boore J.L., Animal mitochondrial genomes, Nucleic Acids Res., 27 (1999) 1767–80.
  • [6] Grimaldi D., Engel M.S., Evolution of the insects., Cambridge University Press, New York, (2005).
  • [7] Klopfstein S., Vilhelmsen L., Heraty J.M., Sharkey M., Ronquist F., The hymenopteran tree of life: Evidence from protein-coding genes and objectively aligned ribosomal data, PLoS One., 8 (2013).
  • [8] Taeger A., Liston A.D., Prous M., Groll E.K., Gehroldt T., Blank S.M. ECatSym – Electronic World Catalog of Symphyta (Insecta, Hymenoptera). Program version 5.0 (19 Dec 2018), data version 40 (23 Sep 2018). – Senckenberg Deutsches Entomologisches Institut (SDEI), Müncheberg. https://sdei.de/ecatsym/ Access: 15 Oct 2022
  • [9] Cheng Y., Yan Y., Wei M., Niu G., Characterization of mitochondrial genomes of three new species: Leptocimbex praiaformis, L. clavicornis , and L. yanniae (Hymenoptera: Cimbicidae), Entomol. Res., 51 (2021) 287–304.
  • [10] Doğan Ö., Korkmaz E.M., Nearly complete mitogenome of hairy sawfly, Corynis lateralis (Brullé, 1832) (Hymenoptera: Cimbicidae): Rearrangements in the IQM and ARNS1EF gene clusters, Genetica., 145 (2017) 341–350.
  • [11] Song S.N., Tang P., Wei S.J., Chen X.X., Comparative and phylogenetic analysis of the mitochondrial genomes in basal hymenopterans, Sci. Rep., 6 (2016).
  • [12] Bagley R.K., Sousa V.C., Niemiller M.L., Linnen C.R., History, geography and host use shape genomewide patterns of genetic variation in the redheaded pine sawfly (Neodiprion lecontei), Mol. Ecol., 26 (2017) 1022–1044.
  • [13] Chen, S., Zhou, Y., Chen, Y., Gu, J., fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics., 34(17) (2018) i884-i890.
  • [14] Song, L., Florea, L., Langmead, B., Lighter: fast and memory-efficient sequencing error correction without counting, Genome biology., 15(11) (2014) 1-13.
  • [15] Kearse M., Moir R., Wilson A., Stones-Havas S., Cheung M., Sturrock S., Buxton S., Cooper A., Markowitz S., Duran C., Thierer T., Ashton B., Meintjes P., Drummond A., Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data, Bioinformatics., 28 (2012) 1647–9.
  • [16] Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., Korobeynikov, A., Using SPAdes de novo assembler, Current protocols in bioinformatics., 70(1) (2020) e102.
  • [17] Arkin AP., Cottingham RW., Henry CS., Harris NL., Stevens RL., Maslov S., Dehal P., Ware D., Perez F., Canon S., KBase: the United States department of energy systems biology knowledgebase, Nat Biotechnol., 36(7) (2018) 566–9.
  • [18] Bernt, M., Donath, A., Jühling, F., Externbrink, F., Florentz, C., Fritzsch, G., Pütz, F., Middendorf. M., Stadler, P. F., MITOS: improved de novo metazoan mitochondrial genome annotation, Molecular phylogenetics and evolution., 69(2) (2013) 313-319.
  • [19] Wyman, S. K., Jansen, R. K., Boore, J. L., Automatic annotation of organellar genomes with DOGMA, Bioinformatics., 20(17) (2004) 3252-3255.
  • [20] Tamura K., Stecher G., Peterson D., Filipski A., Kumar S., MEGA6: Molecular evolutionary genetics analysis version 6.0, Mol. Biol. Evol., 30 (2013) 2725–2729.
  • [21] Perna N.T., Kocher T.D., Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes, J. Mol. Evol., 41 (1995) 353–358.
  • [22] Katoh K., Standley D.M., MAFFT multiple sequence alignment software version 7: Improvements in performance and usability, Mol. Biol. Evol., 30 (2013) 772–780.
  • [23] Vaidya G., Lohman D.J., Meier R., SequenceMatrix: Concatenation software for the fast assembly of multi-gene datasets with character set and codon information, Cladistics., 27 (2011) 171–180.
  • [24] Lanfear R., Calcott B., Ho S.Y.W., Guindon S., PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses, Mol. Biol. Evol., 29 (2012) 1695–1701.
  • [25] R Core Team, R: A language and environment for statistical computing, Vienna, Austria, 2020.
  • [26] Swofford D.L., PAUP. Phylogenetic analysis using parsimony (and other methods), version 4, Sinauer Assoc., Sunderland, Massachusetts. (2002) 294–307.
  • [27] Minh B.Q., Schmidt H.A., Chernomor O., Schrempf D., Woodhams M.D., von Haeseler A., Lanfear R., IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era, Mol. Biol. Evol., 37 (2020) 1530–1534.
  • [28] Ronquist F., Teslenko M., Van Der Mark P., Ayres D.L., Darling A., Höhna S., Larget B., Liu L., Suchard M.A., Huelsenbeck J.P., Mrbayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space, Syst. Biol., 61 (2012) 539–542.
  • [29] Rambaut A., Suchard M.A., Xie D., Drummond A.J., Tracer v1.6., (2014).
  • [30] Rambaut A., FigTree v1.4.2, a graphical viewer of phylogenetic trees, Available from left angle bracket. http://tree.bio.ed.ac.uk/software/figtree/ (2014).
  • [31] Dowton M., Cameron S.L., Dowavic J.I., Austin A.D., Whiting M.F., Characterization of 67 mitochondrial tRNA gene rearrangements in the Hymenoptera suggests that mitochondrial tRNA gene position is selectively neutral, Mol. Biol. Evol., 26 (2009) 1607–17.
  • [32] Castro L.R., Dowton M., The position of the Hymenoptera within the Holometabola as inferred from the mitochondrial genome of Perga condei (Hymenoptera: Symphyta: Pergidae), Mol. Phylogenet. Evol., 34 (2005) 469–79.
  • [33] Niu G., Jiang S., Doğan Ö., Korkmaz E.M., Budak M., Wu D., Wei M., Mitochondrial phylogenomics of Tenthredinidae (Hymenoptera:Tenthredinoidea) supports the monophyly of Megabelesesinae as a subfamily, Insects., 12 (2021) 495.
  • [34] Wu R., Wei M., Liu M., Niu G., Advancement in sequencing the mitochondrial genome of Birmella discoidalisa Wei, 1994 (Hymenoptera: Tenthredinidae) and the phylogenetic classification of Fenusini, Mitochondrial DNA Part B., 4 (2019) 4100–4101.
  • [35] Wei S.J., Shi M., He J., Sharkey M., Chen X., The complete mitochondrial genome of Diadegma semiclausum (Hymenoptera: Ichneumonidae) indicates extensive independent evolutionary events, Genome., 52 (2009) 308–319.
  • [36] Wei S.J., Shi M., Sharkey M.J., van Achterberg C., Chen X., Comparative mitogenomics of Braconidae (Insecta: Hymenoptera) and the phylogenetic utility of mitochondrial genomes with special reference to Holometabolous insects, BMC Genomics., 11 (2010) 371.
  • [37] Crozier R.H., Crozier Y.C., The mitochondrial genome of the honeybee Apis mellifera: Complete sequence and genome organization, Genetics., 133 (1993) 97–117.
  • [38] Ojala D., Montoya J., Attardi G., tRNA punctuation model of RNA processing in human mitochondria, Nature, 290 (1981) 470–474.
  • [39] Malm T., Nyman T., Phylogeny of the symphytan grade of Hymenoptera: New pieces into the old jigsaw(fly) puzzle, Cladistics., 31 (2015) 1–17.
  • [40] Niu G., Budak M., Korkmaz E.M., Doğan Ö., Nel A., Wan S., Cai C., Jouault C., Li M., Wei M., Phylogenomic analyses of the Tenthredinoidea support the familial rank of Athaliidae (Insecta, Tenthredinoidea), Insects., 13 (2022) 858

The Complete Mitogenome of Redheaded Pine Sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae): Duplication of trnR Gene and Rearrangement in the ARNS1EF Gene Cluster

Year 2022, Volume: 43 Issue: 4, 577 - 583, 27.12.2022

Ertan Mahir Korkmaz

https://doi.org/10.17776/csj.1195087

Abstract

Neodiprion is a genus belonging to the small sawfly family Diprionidae, feeding the plant family Pinaceae entirely. Here, the complete mitogenome of the redheaded pine sawfly Neodiprion lecontei (Hymenoptera: Diprionidae) was assembled, annotated as third party annotation from the raw genome dataset of N. lecontei and comparatively characterised. The length of N. lecontei mitogenome was 16,067 bp in size, with an AT content of 81.32%. The initiation codons of protein coding genes (PCGs) are ATN (except for nad6 (TTA-Phe), while termination codons are TAA or T−. tRNA genes favoured usual anticodons except for trnS1 which preferred an unusual anticodon GCU. Compared with the Neodiprion sertifer mitogenome, the ARNS1EF gene cluster was rearranged as RAS1RNEF and trnR gene has a duplicated copy, revealing a new event not formerly reported in Symphyta. The phylogeny confirms the position of N. lecontei within the family of Diprionidae and supports the monophyly of included genera and families in Tenthredinoidea.

Keywords

Mitochondrial genome Rearrangement Sawflies; Tenthredinoidea Symphyta

References

  • [1] Carlucci A., Lignitto L., Feliciello A., Control of mitochondria dynamics and oxidative metabolism by cAMP, AKAPs and the proteasome, Trends Cell Biol., 18 (2008) 604–613.
  • [2] Cameron S.L., Insect mitochondrial genomics: implications for evolution and phylogeny, Annu. Rev. Entomol., 59 (2014) 95–117.
  • [3] Aydemir, M. N., Korkmaz, E. M., Comparative mitogenomics of Hymenoptera reveals evolutionary differences in structure and composition, International journal of biological macromolecules., 144 (2020) 460-472.
  • [4] Ballard J.W.O., Pichaud N., Mitochondrial DNA: more than an evolutionary bystander, Funct. Ecol., 28 (2014) 218–231.
  • [5] Boore J.L., Animal mitochondrial genomes, Nucleic Acids Res., 27 (1999) 1767–80.
  • [6] Grimaldi D., Engel M.S., Evolution of the insects., Cambridge University Press, New York, (2005).
  • [7] Klopfstein S., Vilhelmsen L., Heraty J.M., Sharkey M., Ronquist F., The hymenopteran tree of life: Evidence from protein-coding genes and objectively aligned ribosomal data, PLoS One., 8 (2013).
  • [8] Taeger A., Liston A.D., Prous M., Groll E.K., Gehroldt T., Blank S.M. ECatSym – Electronic World Catalog of Symphyta (Insecta, Hymenoptera). Program version 5.0 (19 Dec 2018), data version 40 (23 Sep 2018). – Senckenberg Deutsches Entomologisches Institut (SDEI), Müncheberg. https://sdei.de/ecatsym/ Access: 15 Oct 2022
  • [9] Cheng Y., Yan Y., Wei M., Niu G., Characterization of mitochondrial genomes of three new species: Leptocimbex praiaformis, L. clavicornis , and L. yanniae (Hymenoptera: Cimbicidae), Entomol. Res., 51 (2021) 287–304.
  • [10] Doğan Ö., Korkmaz E.M., Nearly complete mitogenome of hairy sawfly, Corynis lateralis (Brullé, 1832) (Hymenoptera: Cimbicidae): Rearrangements in the IQM and ARNS1EF gene clusters, Genetica., 145 (2017) 341–350.
  • [11] Song S.N., Tang P., Wei S.J., Chen X.X., Comparative and phylogenetic analysis of the mitochondrial genomes in basal hymenopterans, Sci. Rep., 6 (2016).
  • [12] Bagley R.K., Sousa V.C., Niemiller M.L., Linnen C.R., History, geography and host use shape genomewide patterns of genetic variation in the redheaded pine sawfly (Neodiprion lecontei), Mol. Ecol., 26 (2017) 1022–1044.
  • [13] Chen, S., Zhou, Y., Chen, Y., Gu, J., fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics., 34(17) (2018) i884-i890.
  • [14] Song, L., Florea, L., Langmead, B., Lighter: fast and memory-efficient sequencing error correction without counting, Genome biology., 15(11) (2014) 1-13.
  • [15] Kearse M., Moir R., Wilson A., Stones-Havas S., Cheung M., Sturrock S., Buxton S., Cooper A., Markowitz S., Duran C., Thierer T., Ashton B., Meintjes P., Drummond A., Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data, Bioinformatics., 28 (2012) 1647–9.
  • [16] Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., Korobeynikov, A., Using SPAdes de novo assembler, Current protocols in bioinformatics., 70(1) (2020) e102.
  • [17] Arkin AP., Cottingham RW., Henry CS., Harris NL., Stevens RL., Maslov S., Dehal P., Ware D., Perez F., Canon S., KBase: the United States department of energy systems biology knowledgebase, Nat Biotechnol., 36(7) (2018) 566–9.
  • [18] Bernt, M., Donath, A., Jühling, F., Externbrink, F., Florentz, C., Fritzsch, G., Pütz, F., Middendorf. M., Stadler, P. F., MITOS: improved de novo metazoan mitochondrial genome annotation, Molecular phylogenetics and evolution., 69(2) (2013) 313-319.
  • [19] Wyman, S. K., Jansen, R. K., Boore, J. L., Automatic annotation of organellar genomes with DOGMA, Bioinformatics., 20(17) (2004) 3252-3255.
  • [20] Tamura K., Stecher G., Peterson D., Filipski A., Kumar S., MEGA6: Molecular evolutionary genetics analysis version 6.0, Mol. Biol. Evol., 30 (2013) 2725–2729.
  • [21] Perna N.T., Kocher T.D., Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes, J. Mol. Evol., 41 (1995) 353–358.
  • [22] Katoh K., Standley D.M., MAFFT multiple sequence alignment software version 7: Improvements in performance and usability, Mol. Biol. Evol., 30 (2013) 772–780.
  • [23] Vaidya G., Lohman D.J., Meier R., SequenceMatrix: Concatenation software for the fast assembly of multi-gene datasets with character set and codon information, Cladistics., 27 (2011) 171–180.
  • [24] Lanfear R., Calcott B., Ho S.Y.W., Guindon S., PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses, Mol. Biol. Evol., 29 (2012) 1695–1701.
  • [25] R Core Team, R: A language and environment for statistical computing, Vienna, Austria, 2020.
  • [26] Swofford D.L., PAUP. Phylogenetic analysis using parsimony (and other methods), version 4, Sinauer Assoc., Sunderland, Massachusetts. (2002) 294–307.
  • [27] Minh B.Q., Schmidt H.A., Chernomor O., Schrempf D., Woodhams M.D., von Haeseler A., Lanfear R., IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era, Mol. Biol. Evol., 37 (2020) 1530–1534.
  • [28] Ronquist F., Teslenko M., Van Der Mark P., Ayres D.L., Darling A., Höhna S., Larget B., Liu L., Suchard M.A., Huelsenbeck J.P., Mrbayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space, Syst. Biol., 61 (2012) 539–542.
  • [29] Rambaut A., Suchard M.A., Xie D., Drummond A.J., Tracer v1.6., (2014).
  • [30] Rambaut A., FigTree v1.4.2, a graphical viewer of phylogenetic trees, Available from left angle bracket. http://tree.bio.ed.ac.uk/software/figtree/ (2014).
  • [31] Dowton M., Cameron S.L., Dowavic J.I., Austin A.D., Whiting M.F., Characterization of 67 mitochondrial tRNA gene rearrangements in the Hymenoptera suggests that mitochondrial tRNA gene position is selectively neutral, Mol. Biol. Evol., 26 (2009) 1607–17.
  • [32] Castro L.R., Dowton M., The position of the Hymenoptera within the Holometabola as inferred from the mitochondrial genome of Perga condei (Hymenoptera: Symphyta: Pergidae), Mol. Phylogenet. Evol., 34 (2005) 469–79.
  • [33] Niu G., Jiang S., Doğan Ö., Korkmaz E.M., Budak M., Wu D., Wei M., Mitochondrial phylogenomics of Tenthredinidae (Hymenoptera:Tenthredinoidea) supports the monophyly of Megabelesesinae as a subfamily, Insects., 12 (2021) 495.
  • [34] Wu R., Wei M., Liu M., Niu G., Advancement in sequencing the mitochondrial genome of Birmella discoidalisa Wei, 1994 (Hymenoptera: Tenthredinidae) and the phylogenetic classification of Fenusini, Mitochondrial DNA Part B., 4 (2019) 4100–4101.
  • [35] Wei S.J., Shi M., He J., Sharkey M., Chen X., The complete mitochondrial genome of Diadegma semiclausum (Hymenoptera: Ichneumonidae) indicates extensive independent evolutionary events, Genome., 52 (2009) 308–319.
  • [36] Wei S.J., Shi M., Sharkey M.J., van Achterberg C., Chen X., Comparative mitogenomics of Braconidae (Insecta: Hymenoptera) and the phylogenetic utility of mitochondrial genomes with special reference to Holometabolous insects, BMC Genomics., 11 (2010) 371.
  • [37] Crozier R.H., Crozier Y.C., The mitochondrial genome of the honeybee Apis mellifera: Complete sequence and genome organization, Genetics., 133 (1993) 97–117.
  • [38] Ojala D., Montoya J., Attardi G., tRNA punctuation model of RNA processing in human mitochondria, Nature, 290 (1981) 470–474.
  • [39] Malm T., Nyman T., Phylogeny of the symphytan grade of Hymenoptera: New pieces into the old jigsaw(fly) puzzle, Cladistics., 31 (2015) 1–17.
  • [40] Niu G., Budak M., Korkmaz E.M., Doğan Ö., Nel A., Wan S., Cai C., Jouault C., Li M., Wei M., Phylogenomic analyses of the Tenthredinoidea support the familial rank of Athaliidae (Insecta, Tenthredinoidea), Insects., 13 (2022) 858
There are 40 citations in total.

Details

Primary Language English
Subjects Structural Biology
Journal Section Natural Sciences
Authors

Ertan Mahir Korkmaz 0000-0003-0699-1354

Publication Date December 27, 2022
Submission Date October 26, 2022
Acceptance Date December 20, 2022
Published in Issue Year 2022Volume: 43 Issue: 4

Cite

APA Korkmaz, E. M. (2022). The Complete Mitogenome of Redheaded Pine Sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae): Duplication of trnR Gene and Rearrangement in the ARNS1EF Gene Cluster. Cumhuriyet Science Journal, 43(4), 577-583. https://doi.org/10.17776/csj.1195087
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