References

Alioto, T.S., Buchhalter, I., Derdak, S., Hutter, B., Eldridge, M.D., Hovig, E., Heisler, L.E., Beck, T.A., Simpson, J.T., Tonon, L., Sertier, A.S., Patch, A.M., Jäger, N., Ginsbach, P., Drews, R., Paramasivam, N., Kabbe, R., Chotewutmontri, S., Diessl, N., Previti, C., Schmidt, S., Brors, B., Feuerbach, L., Heinold, M., Gröbner, S., Korshunov, A., Tarpey, P.S., Butler, A.P., Hinton, J., Jones, D., Menzies, A., Raine, K., Shepherd, R., Stebbings, L., Teague, J.W., Ribeca, P., Giner, F.C., Beltran, S., Raineri, E., Dabad, M., Heath, S.C., Gut, M., Denroche, R.E., Harding, N.J., Yamaguchi, T.N., Fujimoto, A., Nakagawa, H., Quesada, V., Valdés-Mas, R., Nakken, S., Vodák, D., Bower, L., Lynch, A.G., Anderson, C.L., Waddell, N., Pearson, J.V., Grimmond, S.M., Peto, M., Spellman, P., He, M., Kandoth, C., Lee, S., Zhang, J., Létourneau, L., Ma, S., Seth, S., Torrents, D., Xi, L., Wheeler, D.A., López-Otín, C., Campo, E., Campbell, P.J., Boutros, P.C., Puente, X.S., Gerhard, D.S., Pfister, S.M., McPherson, J.D., Hudson, T.J., Schlesner, M., Lichter, P., Eils, R., Jones, D.T.W. & Gut, I.G. (2015). A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nature Communications, 6.
Belser, C., Istace, B., Denis, E., Dubarry, M., Baurens, F.C., Falentin, C., Genete, M., Berrabah, W., Chèvre, A.M., Delourme, R., Deniot, G., Denoeud, F., Duffé, P., Engelen, S., Lemainque, A., Manzanares-Dauleux, M., Martin, G., Morice, J., Noel, B., Vekemans, X., D’Hont, A., Rousseau-Gueutin, M., Barbe, V., Cruaud, C., Wincker, P. & Aury, J.M. (2018). Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps. Nature Plants, 4, 879–887. Retrieved from http://dx.doi.org/10.1038/s41477-018-0289-4
Cibulskis, K., Lawrence, M.S., Carter, S.L., Sivachenko, A., Jaffe, D., Sougnez, C., Gabriel, S., Meyerson, M., Lander, E.S. & Getz, G. (2013). Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nature Biotechnology, 31, 213–219.
Edwards, P.B., Wanjura, W.J., Brown, W.V. & Dearn, J.M. (1990). Mosaic resistance in plants. Nature, 347, 434.
Hanlon, V.C.T., Otto, S.P. & Aitken, S.N. (2019). Somatic mutations substantially increase the per‐generation mutation rate in the conifer picea sitchensis. Evolution Letters, 3, 348–358.
Johnson, L.K., Sahasrabudhe, R., Gill, J.A., Roach, J.L., Froenicke, L., Brown, C.T. & Whitehead, A. (2020). Draft genome assemblies using sequencing reads from oxford nanopore technology and illumina platforms for four species of north american fundulus killifish. GigaScience, 9, 1–8.
Leebens-Mack, J.H., Barker, M.S., Carpenter, E.J., Deyholos, M.K., Gitzendanner, M.A., Graham, S.W., Grosse, I., Li, Z., Melkonian, M., Mirarab, S., Porsch, M., Quint, M., Rensing, S.A., Soltis, D.E., Soltis, P.S., Stevenson, D.W., Ullrich, K.K., Wickett, N.J., DeGironimo, L., Edger, P.P., Jordon-Thaden, I.E., Joya, S., Liu, T., Melkonian, B., Miles, N.W., Pokorny, L., Quigley, C., Thomas, P., Villarreal, J.C., Augustin, M.M., Barrett, M.D., Baucom, R.S., Beerling, D.J., Benstein, R.M., Biffin, E., Brockington, S.F., Burge, D.O., Burris, J.N., Burris, K.P., Burtet-Sarramegna, V., Caicedo, A.L., Cannon, S.B., Çebi, Z., Chang, Y., Chater, C., Cheeseman, J.M., Chen, T., Clarke, N.D., Clayton, H., Covshoff, S., Crandall-Stotler, B.J., Cross, H., dePamphilis, C.W., Der, J.P., Determann, R., Dickson, R.C., Stilio, V.S.D., Ellis, S., Fast, E., Feja, N., Field, K.J., Filatov, D.A., Finnegan, P.M., Floyd, S.K., Fogliani, B., García, N., Gâteblé, G., Godden, G.T., Yun) Goh, F. (Qi, Greiner, S., Harkess, A., Heaney, J.M., Helliwell, K.E., Heyduk, K., Hibberd, J.M., Hodel, R.G.J., Hollingsworth, P.M., Johnson, M.T.J., Jost, R., Joyce, B., Kapralov, M.V., Kazamia, E., Kellogg, E.A., Koch, M.A., Konrat, M.V., Könyves, K., Kutchan, T.M., Lam, V., Larsson, A., Leitch, A.R., Lentz, R., Li, F.W., Lowe, A.J., Ludwig, M., Manos, P.S., Mavrodiev, E., McCormick, M.K., McKain, M., McLellan, T., McNeal, J.R., Miller, R.E., Nelson, M.N., Peng, Y., Ralph, P., Real, D., Riggins, C.W., Ruhsam, M., Sage, R.F., Sakai, A.K., Scascitella, M., Schilling, E.E., Schlösser, E.M., Sederoff, H., Servick, S., Sessa, E.B., Shaw, A.J., Shaw, S.W., Sigel, E.M., Skema, C., Smith, A.G., Smithson, A., Stewart, C.N., Stinchcombe, J.R., Szövényi, P., Tate, J.A., Tiebel, H., Trapnell, D., Villegente, M., Wang, C.N., Weller, S.G., Wenzel, M., Weststrand, S., Westwood, J.H., Whigham, D.F., Wu, S., Wulff, A.S., Yang, Y., Zhu, D., Zhuang, C., Zuidof, J., Chase, M.W., Pires, J.C., Rothfels, C.J., Yu, J., Chen, C., Chen, L., Cheng, S., Li, J., Li, R., Li, X., Lu, H., Ou, Y., Sun, X., Tan, X., Tang, J., Tian, Z., Wang, F., Wang, J., Wei, X., Xu, X., Yan, Z., Yang, F., Zhong, X., Zhou, F., Zhu, Y., Zhang, Y., Ayyampalayam, S., Barkman, T.J., Nguyen, N. phuong, Matasci, N., Nelson, D.R., Sayyari, E., Wafula, E.K., Walls, R.L., Warnow, T., An, H., Arrigo, N., Baniaga, A.E., Galuska, S., Jorgensen, S.A., Kidder, T.I., Kong, H., Lu-Irving, P., Marx, H.E., Qi, X., Reardon, C.R., Sutherland, B.L., Tiley, G.P., Welles, S.R., Yu, R., Zhan, S., Gramzow, L., Theißen, G. & Wong, G.K.S. (2019). One thousand plant transcriptomes and the phylogenomics of green plants. Nature, 574, 679–685.
Michael, T.P. & VanBuren, R. (2020). Building near-complete plant genomes. Current Opinion in Plant Biology, 54, 26–33. Retrieved from https://doi.org/10.1016/j.pbi.2019.12.009
Nicholson, A.M., Olpe, C., Hoyle, A., Thorsen, A.S., Rus, T., Colombé, M., Brunton-Sim, R., Kemp, R., Marks, K., Quirke, P., Malhotra, S., Hoopen, R. ten, Ibrahim, A., Lindskog, C., Myers, M.B., Parsons, B., Tavaré, S., Wilkinson, M., Morrissey, E. & Winton, D.J. (2018). Fixation and spread of somatic mutations in adult human colonic epithelium. Cell Stem Cell, 22, 909–918.e8.
Orr, A.J., Padovan, A., Kainer, D., Külheim, C., Bromham, L., Bustos-Segura, C., Foley, W., Haff, T., Hsieh, J.F., Morales-Suarez, A., Cartwright, R.A. & Lanfear, R. (2019). A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant. bioRxiv.
Plomion, C., Aury, J.M., Amselem, J., Leroy, T., Murat, F., Duplessis, S., Faye, S., Francillonne, N., Labadie, K., Provost, G.L., Lesur, I., Bartholomé, J., Faivre-Rampant, P., Kohler, A., Leplé, J.C., Chantret, N., Chen, J., Diévart, A., Alaeitabar, T., Barbe, V., Belser, C., Bergès, H., Bodénès, C., Bogeat-Triboulot, M.B., Bouffaud, M.L., Brachi, B., Chancerel, E., Cohen, D., Couloux, A., Silva, C.D., Dossat, C., Ehrenmann, F., Gaspin, C., Grima-Pettenati, J., Guichoux, E., Hecker, A., Herrmann, S., Hugueney, P., Hummel, I., Klopp, C., Lalanne, C., Lascoux, M., Lasserre, E., Lemainque, A., Desprez-Loustau, M.L., Luyten, I., Madoui, M.A., Mangenot, S., Marchal, C., Maumus, F., Mercier, J., Michotey, C., Panaud, O., Picault, N., Rouhier, N., Rué, O., Rustenholz, C., Salin, F., Soler, M., Tarkka, M., Velt, A., Zanne, A.E., Martin, F., Wincker, P., Quesneville, H., Kremer, A. & Salse, J. (2018). Oak genome reveals facets of long lifespan. Nature Plants, 4, 440–452. Retrieved from http://dx.doi.org/10.1038/s41477-018-0172-3
Ramu, A., Noordam, M.J., Schwartz, R.S., Wuster, A., Hurles, M.E., Cartwright, R.A. & Conrad, D.F. (2013). DeNovoGear: De novo indel and point mutation discovery and phasing. Nature Methods, 10, 985–987. Retrieved from http://dx.doi.org/10.1038/nmeth.2611
Schmid-Siegert, E., Sarkar, N., Iseli, C., Calderon, S., Gouhier-Darimont, C., Chrast, J., Cattaneo, P., Schütz, F., Farinelli, L., Pagni, M., Schneider, M., Voumard, J., Jaboyedoff, M., Fankhauser, C., Hardtke, C.S., Keller, L., Pannell, J.R., Reymond, A., Robinson-Rechavi, M., Xenarios, I. & Reymond, P. (2017). Low number of fixed somatic mutations in a long-lived oak tree. Nature Plants, 3, 926–929. Retrieved from http://dx.doi.org/10.1038/s41477-017-0066-9