The yellow mealworm, the larval stage of the darkling beetleTenebrio molitor, shows great promise as an alternative source of animal protein. Herein we present the 312 Mb draft genome assembled using 10x Genomics linked-read technology to inform research efforts and to provide resources to optimise yellow mealworm for mass production and consumption. The genome with a contig N50 of 39,478 bp contains 89% of conserved arthropod genes among the > 20,000 genes assembled (complete and partial genes). This draft assembly represents a valuable resource to understandingT. molitor biology as a means of producing alternative, sustainable protein for the growing population and in the face of changing climates.
Archak, S., Meduri, E., Kumar, P.S. and Nagaraju, J., 2007. InSatDb: a microsatellite database of fully sequenced insect genomes. Nucleic Acids Research 35: D36-D39.https://doi.org/10.1093/nar/gkl778
Barton, P.S., Gibb, H., Manning, A.D., Lindenmayer, D.B. and Cunningham, S.A., 2011. Morphological traits as predictors of diet and microhabitat use in a diverse beetle assemblage. Biological Journal of the Linnean Society 102: 301-310.https://doi.org/10.1111/j.1095-8312.2010.01580.x
Beutel, R.G. and Leschen, R.A.B., 2014. Handbook of zoology, Coleoptera. Vol. 3. Morphology and systematics (Phytophaga). Walter de Gruyter, Berlin, Germany.
'Handbook of zoology, Coleoptera', ().
Brandon, A.M., Gao, S.H., Tian, R.M., Ning, D.L., Yang, S.S., Zhou, J.Z., Wu, W.M. and Criddle, C.S., 2018. Biodegradation of polyethylene and plastic mixtures in mealworms (larvae ofTenebrio molitor) and effects on the gut microbiome. Environmental Science & Technology 52: 6526-6533.https://doi.org/10.1021/acs.est.8b02301
Choi, I.-H., Kim, J.-M., Kim, N.-J., Kim, J.-D., Park, C., Park, J.-H. and Chung, T.-H., 2018. Replacing fish meal by mealworm(Tenebrio molitor) on the growth performance and immunologic responses of white shrimp (Litopenaeus vannamei). Acta Scientiarum 40: e39077.https://doi.org/10.4025/actascianimsci.v40i1.39077
Del Angel, V.D., Hjerd, E., Sterck, L. and 2018. Ten steps to get started in genome assembly and annotation. F1000Research 148.https://doi.org/10.12688/f1000research.13598.1
English, A.C., Richards, S., Han, Y., Wang, M., Vee, V., Qu, J.X., Qin, X., Muzny, D.M., Reid, J.G., Worley, K.C. and Gibbs, R.A., 2012. Mind the gap: upgrading genomes with pacific biosciences RS long-read sequencing technology. PLoS ONE 7: e47768.https://doi.org/10.1371/journal.pone.0047768
Food and Agriculture Organisation (FAO), 2017. Insects for food and feed. FAO, Rome, Italy. Available at:http://www.fao.org/edible-insects/en/
Gilchrist, A.S., Cameron, E.C., Sved, J.A. and Meats, A.W., 2012. Genetic consequences of domestication and mass rearing of pest fruit flyBactrocera tryoni (Diptera: Tephritidae). Journal of Economic Entomology 105: 1051-1056.https://doi.org/10.1603/Ec11421
Gregory, T.R., Nicol, J.A., Tamm, H., Kullman, B., Kullman, K., Leitch, I.J., Murray, B.G., Kapraun, D.F., Greilhuber, J. and Bennett, M.D., 2007. Eukaryotic genome size databases. Nucleic Acids Research 35: D332-D338.https://doi.org/10.1093/nar/gkl828
Henry, M.A., Gasco, L., Chatzifotis, S. and Piccolo, G., 2018. Does dietary insect meal affect the fish immune system? The case of mealworm,Tenebrio molitor on European sea bass, Dicentrarchus labrax. Developmental and Comparative Immunology 81: 204-209.https://doi.org/10.1016/j.dci.2017.12.002
Huddleston, J., Ranade, S., Malig, M., Antonacci, F., Chaisson, M., Hon, L., Sudmant, P.H., Graves, T.A., Alkan, C., Dennis, M.Y., Wilson, R.K., Turner, S.W., Korlach, J. and Eichler, E.E., 2014. Reconstructing complex regions of genomes using long-read sequencing technology. Genome Research 24: 688-696.https://doi.org/10.1101/gr.168450.113
Johnston, P.R., Makarova, O. and Rolff, J., 2014. Inducible defenses stay up late: temporal patterns of immune gene expression inTenebrio molitor. G3-Genes Genomes Genetics 4: 947-955.https://doi.org/10.1534/g3.113.008516
Jones, S.J., Haulena, M., Taylor, G.A., Chan, S., Bilobram, S., Warren, R.L., Hammond, S.A., Mungall, K.L., Choo, C., Kirk, H., Pandoh, P., Ally, A., Dhalla, N., Tam, A.K.Y., Troussard, A., Paulino, D., Coope, R.J.N., Mungall, A.J., Moore, R., Zhao, Y.J., Birol, I., Ma, Y., Marra, M. and Jones, S.J.M., 2017. The genome of the Northern Sea otter (Enhydra lutris kenyoni). Genes 8: 379.https://doi.org/10.3390/genes8120379
Juan, C. and Petitpierre, E., 1991. Evolution of genome size in darkling beetles (Tenebrionidae, Coleoptera). Genome 34: 169-173.https://doi.org/10.1139/g91-026
Jung, J., Heo, A., Park, Y.W., Kim, Y.J., Koh, H. and Park, W., 2014. Gut microbiota ofTenebrio molitor and their response to environmental change. Journal of Microbiology and Biotechnology 24: 888-897.https://doi.org/10.4014/jmb.1405.05016
Kergoat, G.J., Bouchard, P., Clamens, A.L., Abbate, J.L., Jourdan, H., Jabbour-Zahab, R., Genson, G., Soldati, L. and Condamine, F.L., 2014. Cretaceous environmental changes led to high extinction rates in a hyperdiverse beetle family. BMC Evolutionary Biology 14: 220.https://doi.org/10.1186/s12862-014-0220-1
Liu, L.N. and Wang, C.Y., 2014. Complete mitochondrial genome of yellow meal worm(Tenebrio molitor). Zoological Research 35: 537-545.
'Complete mitochondrial genome of yellow meal worm(Tenebrio molitor) ' () 35 Zoological Research : 537 -545.
Liu, S., Shi, X.X., Jiang, Y.D., Zhu, Z.J., Qian, P., Zhang, M.J., Yu, H., Zhu, Q.Z., Gong, Z.J. and Zhu, Z.R., 2015. De novo analysis of theTenebrio molitor (Coleoptera: Tenebrionidae) transcriptome and identification of putative glutathione S-transferase genes. Applied Entomology and Zoology 50: 63-71.https://doi.org/10.1007/s13355-014-0305-8
Marcais, G. and Kingsford, C., 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27: 764-770.https://doi.org/10.1093/bioinformatics/btr011
McKenna, D.D., 2018. Beetle genomes in the 21st century: prospects, progress and priorities. Current Opinion in Insect Science 25: 76-82.https://doi.org/10.1016/j.cois.2017.12.002
Mckenna, D.D., Wild, A.L., Kanda, K., Bellamy, C.L., Beutel, R.G., Caterino, M.S., Farnum, C.W., Hawks, D.C., Ivie, M.A., Jameson, M.L., Leschen, R.A.B., Marvaldi, A.E., Mchugh, J.V., Newton, A.F., Robertson, J.A., Thayer, M.K., Whiting, M.F., Lawrence, J.F., Slipinski, A., Maddison, D.R. and Farrell, B.D., 2015. The beetle tree of life reveals that Coleoptera survived end-Permian mass extinction to diversify during the Cretaceous terrestrial revolution. Systematic Entomology 40: 835-880.https://doi.org/10.1111/syen.12132
Mikheenko, A., Prjibelski, A., Saveliev, V., Antipov, D. and Gurevich, A., 2018. Versatile genome assembly evaluation with QUAST-LG. Bioinformatics 34: 142-150.https://doi.org/10.1093/bioinformatics/bty266
Morales-Ramos, J.A., Kelstrup, H.C., Rojas, M.G. and Emery, V., 2019. Body mass increase induced by eight years of artificial selection in the yellow mealworm (Coleoptera: Tenebrionidae) and life history trade-offs. Journal of Insect Science 19: 4.https://doi.org/10.1093/jisesa/iey110
Oonincx, D.G.A.B. and De Boer, I.J.M., 2012. Environmental impact of the production of mealworms as a protein source for humans – a life cycle assessment. PLoS ONE 7: e51145.https://doi.org/10.1371/journal.pone.0051145
Oppert, B., Dowd, S.E., Bouffard, P., Li, L., Conesa, A., Lorenzen, M.D., Toutges, M., Marshall, J., Huestis, D.L., Fabrick, J., Oppert, C. and Jurat-Fuentes, J.L., 2012. Transcriptome profiling of the intoxication response ofTenebrio molitor larvae toBacillus thuringiensis Cry3Aa protoxin. PLoS ONE 7: e34624.https://doi.org/10.1371/journal.pone.0034624
Ozerov, M.Y., Ahmad, F., Gross, R., Pukk, L., Kahar, S., Kisand, V. and Vasemagi, A., 2018. Highly continuous genome assembly of Eurasian perch (Perca fluviatilis) using linked-read sequencing. G3-Genes Genomes Genetics 8: 3737-3743.https://doi.org/10.1534/g3.118.200768
Pareek, C.S., Smoczynski, R. and Tretyn, A., 2011. Sequencing technologies and genome sequencing. Journal of Applied Genetics 52: 413-435.https://doi.org/10.1007/s13353-011-0057-x
Petitpierre, E., Gatewood, J.M. and Schmid, C.W., 1988. Satellite DNA from the beetleTenebrio-Molitor. Experientia 44: 498-499.https://doi.org/10.1007/Bf01958925
Poveda, J., Jimenez-Gomez, A., Saati-Santamaria, Z., Usategui-Martin, R., Rivas, R. and Garcia-Fraile, P., 2019. Mealworm frass as a potential biofertilizer and abiotic stress tolerance-inductor in plants. Applied Soil Ecology 142: 110-122.https://doi.org/10.1016/j.apsoil.2019.04.016
Prabhakar, S., Chen, M.S., Elpidina, E.N., Vinokurov, K.S., Smith, C.M., Marshall, J. and Oppert, B., 2007. Sequence analysis and molecular characterization of larval midgut cDNA transcripts encoding peptidases from the yellow mealworm,Tenebrio molitor L. Insect Molecular Biology 16: 455-468.https://doi.org/10.1111/j.1365-2583.2007.00740.x
Richards, S., Gibbs, R.A., Weinstock, G.M., Brown, S.J., Denell, R., Beeman, R.W., Gibbs, R., Bucher, G., Friedrich, M., Grimmelikhuijzen, C.J.P., Klingler, M., Lorenzen, M.D., Roth, S., Schroder, R., Tautz, D., Zdobnov, E.M., Muzny, D., Attaway, T., Bell, S., Buhay, C.J., Chandrabose, M.N., Chavez, D., Clerk-Blankenburg, K.P., Cree, A., Dao, M., Davis, C., Chacko, J., Dinh, H., Dugan-Rocha, S., Fowler, G., Garner, T.T., Garnes, J., Gnirke, A., Hawes, A., Hernandez, J., Hines, S., Holder, M., Hume, J., Jhangiani, S.N., Joshi, V., Khan, Z.M., Jackson, L., Kovar, C., Kowis, A., Lee, S., Lewis, L.R., Margolis, J., Morgan, M., Nazareth, L.V., Nguyen, N., Okwuonu, G., Parker, D., Ruiz, S.J., Santibanez, J., Savard, J., Scherer, S.E., Schneider, B., Sodergren, E., Vattahil, S., Villasana, D., White, C.S., Wright, R., Park, Y., Lord, J., Oppert, B., Brown, S., Wang, L.J., Savard, J., Liu, Y., Worley, K., Elsik, C.G., Reese, J.T., Elhaik, E., Landan, G., Graur, D., Arensburger, P., Atkinson, P., Beidler, J., Demuth, J.P., Drury, D.W., Du, Y.Z., Fujiwara, H., Maselli, V., Osanai, M., Robertson, H.M., Tu, Z., Wang, J.J., Wang, S.Z., Song, H., Zhang, L., Sodergren, E., Werner, D., Stanke, M., Morgenstern, B., Solovyev, V., Kosarev, P., Brown, G., Chen, H.C., Ermolaeva, O., Hlavina, W., Kapustin, Y., Kiryutin, B., Kitts, P., Maglott, D., Pruitt, K., Sapojnikov, V., Souvorov, A., Mackey, A.J., Waterhouse, R.M., Wyder, S., Zdobnov, E.M., Kriventseva, E.V., Kadowaki, T., Bork, P., Aranda, M., Bao, R.Y., Beermann, A., Berns, N., Bolognesi, R., Bonneton, F., Bopp, D., Butts, T., Chaumot, A., Denell, R.E., Ferrier, D.E.K., Gordon, C.M., Jindra, M., Klingler, M., Lan, Q., Lattorff, H.M.G., Laudet, V., Von Levetsow, C., Liu, Z.Y., Lutz, R., Lynch, J.A., Da Fonseca, R.N., Posnien, N., Reuter, R., Roth, S., Schinko, J.B., Schmitt, C., Schoppmeier, M., Shippy, T.D., Simonnet, F., Marques-Souza, H., Tomoyasu, Y., Trauner, J., Van der Zee, M., Vervoort, M., Wittkopp, N., Wimmer, E.A., Yang, X.Y., Jones, A.K., Sattelle, D.B., Ebert, P.R., Nelson, D., Scott, J.G., Muthukrishnan, S., Kramer, K.J., Arakane, Y., Zhu, Q.S., Hogenkamp, D., Dixit, R., Jiang, H.B., Zou, Z., Marshall, J., Elpidina, E., Vinokurov, K., Oppert, C., Evans, J., Lu, Z.Q., Zhao, P.C., Sumathipala, N., Altincicek, B., Vilcinskas, A., Williams, M., Hultmark, D., Hetru, C., Hauser, F., Cazzamali, G., Williamson, M., Li, B., Tanaka, Y., Predel, R., Neupert, S., Schachtner, J., Verleyen, P., Raible, F., Walden, K.K.O., Robertson, H.M., Angeli, S., Foret, S., Schuetz, S., Maleszka, R., Miller, S.C., Grossmann, D. and Tribolium Genome Sequencing Consortium, 2008. The genome of the model beetle and pestTribolium castaneum. Nature 452: 949-955.https://doi.org/10.1038/nature06784
Simao, F.A., Waterhouse, R.M., Ioannidis, P., Kriventseva, E.V. and Zdobnov, E.M., 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31: 3210-3212.https://doi.org/10.1093/bioinformatics/btv351
Smit, A.F.A., Hubley, R. and Green, P., 2013. RepeatMasker Open-4.0. Available at:http://www.repeatmasker.org
Stanke, M. and Waack, S., 2003. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19: Ii215-Ii225.https://doi.org/10.1093/bioinformatics/btg1080
Van Broekhoven, S., Mota Gutierrez, J., De Rijk, T.C., De Nijs, W.C.M. and Van Loon, J.J.A., 2017. Degradation and excretion of theFusarium toxin deoxynivalenol by an edible insect, the Yellow mealworm (Tenebrio molitor L.). World Mycotoxin Journal 10: 169-169.
'Degradation and excretion of theFusarium toxin deoxynivalenol by an edible insect, the Yellow mealworm (Tenebrio molitor L.) ' () 10 World Mycotoxin Journal : 169 -169.
Veldkamp, T. and Bosch, G., 2015. Insects: a protein-rich feed ingredient in pig and poultry diets Animal Frontiers 5: 45-50.
'Insects: a protein-rich feed ingredient in pig and poultry diets Animal Frontiers ' () 5 : 45 -50.
Vurture, G.W., Sedlazeck, F.J., Nattestad, M., Underwood, C.J., Fang, H., Gurtowski, J. and Schatz, M.C., 2017. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33: 2202-2204.https://doi.org/10.1093/bioinformatics/btx153
Wang, W., Yan, H.J., Chen, S.Y., Li, Z.Z., Yi, J., Niu, L.L., Deng, J.P., Chen, W.G., Pu, Y., Jia, X.B., Qu, Y., Chen, A., Zhong, Y., Yu, X.M., Pang, S., Huang, W.L., Han, Y., Liu, G.J. and Yu, J.Q., 2019. The sequence and de novo assembly of hog deer genome. Scientific Data 6: 180305.https://doi.org/10.1038/sdata.2018.305
Waterhouse, R.M., Seppey, M., Simao, F.A., Manni, M., Ioannidis, P., Klioutchnikov, G., Kriventseva, E.V. and Zdobnov, E.M., 2018. BUSCO applications from quality assessments to gene prediction and phylogenomics. Molecular Biology and Evolution 35: 543-548.https://doi.org/10.1093/molbev/msx319
Weisenfeld, N.I., Kumar, V., Shah, P., Church, D.M. and Jaffe, D.B., 2017. Direct determination of diploid genome sequences. Genome Research 27: 757-767.https://doi.org/10.1101/gr.214874.116
Wickham, H., 2016. ggplot2: elegant graphics for data analysis. Springer International Publishing, New York, NY, USA.
'ggplot2: elegant graphics for data analysis', ().
Zhang, Z.Q., Hooper, J.N.A., Van Soest, R.W.M., Pisera, A., Crowther, A.L., Tyler, S., Schilling, S., Eschmeyer, W.N., Fong, J.D., Blackburn, D.C., Wake, D.B., Wilson, D.E., Reeder, D.M., Fritz, U., Hodda, M., Guidetti, R., Bertolani, R., Mayer, G., Oliveira, I.D., Zhang, Z.Q., Adrain, J.M., Bamber, R.N., Kury, A.B., Prendini, L., Harvey, M.S., Beaulieu, F., Dowling, A.P.G., Klompen, H., De Moraes, G.J., Walter, D.E., Zhang, Z.Q., Fan, Q.H., Pesic, V., Smit, H., Bochkov, A.V., Khaustov, A.A., Baker, A., Wohltmann, A., Wen, T.H., Amrine, J.W., Beron, P., Lin, J.Z., Gabrys, G., Husband, R., Bolton, S., Uusitalo, M., Zhang, Z.Q., Schatz, H., Behan-Pelletier, V.M., OConnor, B.M., Norton, R.A., Dunlop, J.A., Penney, D., Minelli, A., Shear, W., Ahyong, S.T., Lowry, J.K., Alonso, M., Bamber, R.N., Boxshall, G.A., Castro, P., Gerken, S., Karaman, G.S., Goy, J.W., Jones, D.S., Meland, K., Rogers, D.C., Svavarsson, J., Janssens, F., Christiansen, K.A., Ingrisch, S., Brock, P.D., Marshall, J., Beccaloni, G.W., Eggleton, P., Mound, L.A., Slipinski, S.A., Leschen, R.A.B., Lawrence, J.F., Holzenthal, R.W., Morse, J.C., Kjer, K.M., Van Nieukerken, E.J., Kaila, L., Kitching, I.J., Kristensen, N.P., Lees, D.C., Minet, J., Mitter, C., Mutanen, M., Regier, J.C., Simonsen, T.J., Wahlberg, N., Yen, S.H., Zahiri, R., Adamski, D., Baixeras, J., Bartsch, D., Bengtsson, B.A., Brown, J.W., Bucheli, S.R., Davis, D.R., De Prins, J., De Prins, W., Epstein, M.E., Gentili-Poole, P., Gielis, C., Hattenschwiler, P., Hausmann, A., Holloway, J.D., Kallies, A., Karsholt, O., Kawahara, A.Y., Koster, S., Kozlov, M.V., Lafontaine, J.D., Lamas, G., Landry, J.F., Lee, S., Nuss, M., Park, K.T., Penz, C., Rota, J., Schintlmeister, A., Schmidt, B.C., Sohn, J.C., Solis, M.A., Tarmann, G.M., Warren, A.D., Weller, S., Yakovlev, R.V., Zolotuhin, V.V., Zwick, A., Pape, T., Blagoderov, V., Mostovski, M.B., Emig, C.C., Segers, H., Monks, S. and Richardson, D.J., 2011. Animal biodiversity: an outline of higher-level classification and taxonomic richness. Zootaxa: 7-237.https://doi.org/10.11646/zootaxa.3148.1.3
Zhu, J.Y., Yang, P., Zhang, Z., Wu, G.X. and Yang, B., 2013. Transcriptomic immune response ofTenebrio molitor pupae to parasitization by Scleroderma guani. PLoS ONE 8: e54411.https://doi.org/10.1371/journal.pone.0054411
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The yellow mealworm, the larval stage of the darkling beetleTenebrio molitor, shows great promise as an alternative source of animal protein. Herein we present the 312 Mb draft genome assembled using 10x Genomics linked-read technology to inform research efforts and to provide resources to optimise yellow mealworm for mass production and consumption. The genome with a contig N50 of 39,478 bp contains 89% of conserved arthropod genes among the > 20,000 genes assembled (complete and partial genes). This draft assembly represents a valuable resource to understandingT. molitor biology as a means of producing alternative, sustainable protein for the growing population and in the face of changing climates.
All Time | Past 365 days | Past 30 Days | |
---|---|---|---|
Abstract Views | 0 | 0 | 0 |
Full Text Views | 552 | 328 | 47 |
PDF Views & Downloads | 563 | 338 | 57 |