Red flour beetle (Tribolium castaneum)

Female beetles are polyandrous, mating with multiple males to ensure higher fertilization rates. Read more about red flour beetles on Wikipedia's website.

Red Flour Beetle (Tribolium castaneum) by Udo Schmidt [CC BY-SA 2.0], via flickr.com

Chromosome-length genome assembly

Download the Tcas5.2_HiC.fasta.gz file containing the chromosome-length (2n=20) assembly of the red flour beetle genome. All modifications with respect to the draft (see below) are annotated in the Tcas5.2_HiC.assembly file. Some basic stats associated with the new reference, Tcas5.2_HiC, are listed below. The full data release can be explored here.

Draft

The chromosome-length genome assembly is based on the draft assembly Tcas5.2 (GCF_000002335.3), credited below.

Herndon, N., Shelton, J., Gerischer, L., Ioannidis, P., Ninova, M., Donitz, J., Waterhouse, R.M., Liang, C., Damm, C., Siemanowski, J., Kitzmann, P., Ulrich, J., Dippel, S., Oberhofer, G., Hu, Y., Schwirz, J., Schacht, M., Lehmann, S., Montino, A., Posnien, N., Gurska, D., Horn, T., Seibert, J., Vargas Jentzsch, I.M., Panfilio, K.A., Li, J., Wimmer, E.A., Stappert, D., Roth, S., Schroder, R., Park, Y., Schoppmeier, M., Chung, H.-R., Klingler, M., Kittelmann, S., Friedrich, M., Chen, R., Altincicek, B., Vilcinskas, A., Zdobnov, E., Griffiths-Jones, S., Ronshaugen, M., Stanke, M., Brown, S.J., Bucher, G., 2020. Enhanced genome assembly and a new official gene set for Tribolium castaneum. BMC Genomics 21, 47. https://doi.org/10.1186/s12864-019-6394-6; Tribolium Genome Sequencing Consortium, Richards, S., Gibbs, R.A., Weinstock, G.M., Brown, S.J., Denell, R., Beeman, R.W., Gibbs, R., Beeman, R.W., Brown, S.J., Bucher, G., Friedrich, M., Grimmelikhuijzen, C.J.P., Klingler, M., Lorenzen, M., Richards, S., Roth, S., Schroder, R., Tautz, D., Zdobnov, E.M., Muzny, D., Gibbs, R.A., Weinstock, G.M., 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., Richards, S., Ruiz, S.-J., Santibanez, J., Savard, J., Scherer, S.E., Schneider, B., Sodergren, E., Tautz, D., Vattahil, S., Villasana, D., White, C.S., Wright, R., Park, Y., Beeman, R.W., Lord, J., Oppert, B., Lorenzen, M., Brown, S., Wang, L., Savard, J., Tautz, D., Richards, S., Weinstock, G., Gibbs, R.A., Liu, Y., Worley, K., Weinstock, G., Elsik, C.G., Reese, J.T., Elhaik, E., Landan, G., Graur, D., Arensburger, P., Atkinson, P., Beeman, R.W., Beidler, J., Brown, S.J., Demuth, J.P., Drury, D.W., Du, Y.-Z., Fujiwara, H., Lorenzen, M., Maselli, V., Osanai, M., Park, Y., Robertson, H.M., Tu, Z., Wang, J., Wang, S., Richards, S., 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., Zdobnov, E.M., Wyder, S., Kriventseva, E.V., Kadowaki, T., Bork, P., Aranda, M., Bao, R., Beermann, A., Berns, N., Bolognesi, R., Bonneton, F., Bopp, D., Brown, S.J., Bucher, G., Butts, T., Chaumot, A., Denell, R.E., Ferrier, D.E.K., Friedrich, M., Gordon, C.M., Jindra, M., Klingler, M., Lan, Q., Lattorff, H.M.G., Laudet, V., von Levetsow, C., Liu, Z., Lutz, R., Lynch, J.A., da Fonseca, R.N., Posnien, N., Reuter, R., Roth, S., Savard, J., Schinko, J.B., Schmitt, C., Schoppmeier, M., Schroder, R., Shippy, T.D., Simonnet, F., Marques-Souza, H., Tautz, D., Tomoyasu, Y., Trauner, J., Van der Zee, M., Vervoort, M., Wittkopp, N., Wimmer, E.A., Yang, X., Jones, A.K., Sattelle, D.B., Ebert, P.R., Nelson, D., Scott, J.G., Beeman, R.W., Muthukrishnan, S., Kramer, K.J., Arakane, Y., Beeman, R.W., Zhu, Q., Hogenkamp, D., Dixit, R., Oppert, B., Jiang, H., Zou, Z., Marshall, J., Elpidina, E., Vinokurov, K., Oppert, C., Zou, Z., Evans, J., Lu, Z., Zhao, P., Sumathipala, N., Altincicek, B., Vilcinskas, A., Williams, M., Hultmark, D., Hetru, C., Jiang, H., Grimmelikhuijzen, C.J.P., Hauser, F., Cazzamali, G., Williamson, M., Park, Y., Li, B., Tanaka, Y., Predel, R., Neupert, S., Schachtner, J., Verleyen, P., Raible, F., Bork, P., Friedrich, M., Walden, K.K.O., Robertson, H.M., Angeli, S., Foret, S., Bucher, G., Schuetz, S., Maleszka, R., Wimmer, E.A., Beeman, R.W., Lorenzen, M., Tomoyasu, Y., Miller, S.C., Grossmann, D., Bucher, G., 2008. The genome of the model beetle and pest Tribolium castaneum. Nature 452, 949-955. https://doi.org/10.1038/nature06784.

Method

3D Assembly was performed using 3D-DNA pipeline (Dudchenko et al., Science, 2017). The genome was reviewed using Juicebox Assembly Tools  (Dudchenko et al., bioRxiv, 2018). See Methods for more information.

Hi-C sample

The whole insect sample for in situ Hi-C preparation was obtained from Carolina Biological.

Hi-C Contact maps

Hi-C data was aligned to the draft reference using Juicer (Durand, Shamim et al., Cell Systems, 2016), and contact maps visualizing the alignments with respect to the draft and the new reference were built using 3D-DNA (Dudchenko et al., Science, 2017). The contact maps can be explored below via Juicebox.js interactive tool (Robinson et al., Cell Systems, 2018). (Please note that the interactive figures are scaled 1:2.) To explore the assembly in greater detail, please download the .hic and .assembly files from the data release folder and use Juicebox Assembly Tools  (Dudchenko et al., bioRxiv, 2018).

References

If you use this genome assembly in your research, please check that the conditions of use associated with the draft permit it, and acknowledge the following work.

Herndon, N., Shelton, J., Gerischer, L., Ioannidis, P., Ninova, M., Donitz, J., Waterhouse, R.M., Liang, C., Damm, C., Siemanowski, J., Kitzmann, P., Ulrich, J., Dippel, S., Oberhofer, G., Hu, Y., Schwirz, J., Schacht, M., Lehmann, S., Montino, A., Posnien, N., Gurska, D., Horn, T., Seibert, J., Vargas Jentzsch, I.M., Panfilio, K.A., Li, J., Wimmer, E.A., Stappert, D., Roth, S., Schroder, R., Park, Y., Schoppmeier, M., Chung, H.-R., Klingler, M., Kittelmann, S., Friedrich, M., Chen, R., Altincicek, B., Vilcinskas, A., Zdobnov, E., Griffiths-Jones, S., Ronshaugen, M., Stanke, M., Brown, S.J., Bucher, G., 2020. Enhanced genome assembly and a new official gene set for Tribolium castaneum. BMC Genomics 21, 47. https://doi.org/10.1186/s12864-019-6394-6; Tribolium Genome Sequencing Consortium, Richards, S., Gibbs, R.A., Weinstock, G.M., Brown, S.J., Denell, R., Beeman, R.W., Gibbs, R., Beeman, R.W., Brown, S.J., Bucher, G., Friedrich, M., Grimmelikhuijzen, C.J.P., Klingler, M., Lorenzen, M., Richards, S., Roth, S., Schroder, R., Tautz, D., Zdobnov, E.M., Muzny, D., Gibbs, R.A., Weinstock, G.M., 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., Richards, S., Ruiz, S.-J., Santibanez, J., Savard, J., Scherer, S.E., Schneider, B., Sodergren, E., Tautz, D., Vattahil, S., Villasana, D., White, C.S., Wright, R., Park, Y., Beeman, R.W., Lord, J., Oppert, B., Lorenzen, M., Brown, S., Wang, L., Savard, J., Tautz, D., Richards, S., Weinstock, G., Gibbs, R.A., Liu, Y., Worley, K., Weinstock, G., Elsik, C.G., Reese, J.T., Elhaik, E., Landan, G., Graur, D., Arensburger, P., Atkinson, P., Beeman, R.W., Beidler, J., Brown, S.J., Demuth, J.P., Drury, D.W., Du, Y.-Z., Fujiwara, H., Lorenzen, M., Maselli, V., Osanai, M., Park, Y., Robertson, H.M., Tu, Z., Wang, J., Wang, S., Richards, S., 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., Zdobnov, E.M., Wyder, S., Kriventseva, E.V., Kadowaki, T., Bork, P., Aranda, M., Bao, R., Beermann, A., Berns, N., Bolognesi, R., Bonneton, F., Bopp, D., Brown, S.J., Bucher, G., Butts, T., Chaumot, A., Denell, R.E., Ferrier, D.E.K., Friedrich, M., Gordon, C.M., Jindra, M., Klingler, M., Lan, Q., Lattorff, H.M.G., Laudet, V., von Levetsow, C., Liu, Z., Lutz, R., Lynch, J.A., da Fonseca, R.N., Posnien, N., Reuter, R., Roth, S., Savard, J., Schinko, J.B., Schmitt, C., Schoppmeier, M., Schroder, R., Shippy, T.D., Simonnet, F., Marques-Souza, H., Tautz, D., Tomoyasu, Y., Trauner, J., Van der Zee, M., Vervoort, M., Wittkopp, N., Wimmer, E.A., Yang, X., Jones, A.K., Sattelle, D.B., Ebert, P.R., Nelson, D., Scott, J.G., Beeman, R.W., Muthukrishnan, S., Kramer, K.J., Arakane, Y., Beeman, R.W., Zhu, Q., Hogenkamp, D., Dixit, R., Oppert, B., Jiang, H., Zou, Z., Marshall, J., Elpidina, E., Vinokurov, K., Oppert, C., Zou, Z., Evans, J., Lu, Z., Zhao, P., Sumathipala, N., Altincicek, B., Vilcinskas, A., Williams, M., Hultmark, D., Hetru, C., Jiang, H., Grimmelikhuijzen, C.J.P., Hauser, F., Cazzamali, G., Williamson, M., Park, Y., Li, B., Tanaka, Y., Predel, R., Neupert, S., Schachtner, J., Verleyen, P., Raible, F., Bork, P., Friedrich, M., Walden, K.K.O., Robertson, H.M., Angeli, S., Foret, S., Bucher, G., Schuetz, S., Maleszka, R., Wimmer, E.A., Beeman, R.W., Lorenzen, M., Tomoyasu, Y., Miller, S.C., Grossmann, D., Bucher, G., 2008. The genome of the model beetle and pest Tribolium castaneum. Nature 452, 949-955. https://doi.org/10.1038/nature06784.

Dudchenko, O., Batra, S.S., Omer, A.D., Nyquist, S.K., Hoeger, M., Durand, N.C., Shamim, M.S., Machol, I., Lander, E.S., Aiden, A.P., Aiden, E.L., 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95. https://doi.org/10.1126/science.aal3327.

Dudchenko, O., Shamim, M.S., Batra, S., Durand, N.C., Musial, N.T., Mostofa, R., Pham, M., Hilaire, B.G.S., Yao, W., Stamenova, E., Hoeger, M., Nyquist, S.K., Korchina, V., Pletch, K., Flanagan, J.P., Tomaszewicz, A., McAloose, D., Estrada, C.P., Novak, B.J., Omer, A.D., Aiden, E.L., 2018. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. bioRxiv 254797. https://doi.org/10.1101/254797.

Disclaimer

This is a work in progress. If you notice any discrepancies in the map or have data that confirms or contradicts the suggested reference, please email us at theaidenlab@gmail.com or leave a comment on the Forum.

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© 2018-2020 by the Aiden Lab.