Karyotypic changes in chromosome number and structure are drivers in the divergent evolution of diverse plant species and lineages. This study aimed to reveal the origins of the unique karyotype (2n = 12) and phylogenetic relationships of the genus Megadenia (Brassicaceae). A high-quality chromosome-scale genome was assembled for Megadenia pygmaea using Nanopore long reads and high-throughput chromosome conformation capture (Hi-C). The assembled genome is 215.2 Mb and is anchored on six pseudochromosomes. We annotated a total of 25,607 high-confidence protein-coding genes and corroborated the phylogenetic affinity of Megadenia with the Brassicaceae expanded lineage II, containing numerous agricultural crops. We dated the divergence of Megadenia from its closest relatives to 27.04 (19.11-36.60) million years ago. A reconstruction of the chromosomal composition of the species was performed based on the de novo assembled genome and comparative chromosome painting analysis. The karyotype structure of M. pygmaea is very similar to the previously inferred proto-Calepineae karyotype (PCK; n = 7) of the lineage II. However, an end-to-end translocation between two ancestral chromosomes reduced the chromosome number from n = 7 to n = 6 in Megadenia. Our reference genome provides fundamental information for karyotypic evolution and evolutionary study of this genus.

Central European Institute of Technology Masaryk University Brno Czech Republic

Key Laboratory of Bio Resource and Eco Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu China

State Key Laboratory of Grassland AgroEcosystem Institute of Innovation Ecology Lanzhou University Lanzhou China

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Arnegard, M. E., McGee, M. D., Matthews, B., Marchinko, K. B., Conte, G. L., Kabir, S. M.,Bedford, N., Bergek, S., Frank Chan, Y., Jones, F. C., Kingsley, D. M., Peichel, C. L., & Schluter, D. (2014). Genetics of ecological divergence during speciation. Nature, 511(7509), 307-311.

Artyukova, E. V., Kozyrenko, M. M., Boltenkov, E. V., & Gorovoy, P. G. (2014). One or three species in Megadenia (Brassicaceae): Insight from molecular studies. Genetica, 142(4), 337-350. https://doi.org/10.1007/s10709-014-9778-1

Bairoch, A., & Apweiler, R. (2000). The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Research, 28(1), 45-48. https://doi.org/10.1093/nar/28.1.45

Beilstein, M. A., Al-Shehbaz, I. A., Mathews, S., & Kellogg, E. A. (2008). Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: Tribes and trichomes revisited. American Journal of Botany, 95(10), 1307-1327.

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114-2120. https://doi.org/10.1093/bioinformatics/btu170

Cheng, F., Wu, J., & Wang, X. (2014). Genome triplication drove the diversification of Brassica plants. Horticulture Research, 1(1), 1-8. https://doi.org/10.1038/hortres.2014.24

Conesa, A., Götz, S., García-Gómez, J. M., Terol, J., Talón, M., & Robles, M. (2005). Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21(18), 3674-3676. https://doi.org/10.1093/bioinformatics/bti610

De Bie, T., Cristianini, N., Demuth, J. P., & Hahn, M. W. (2006). CAFE: A computational tool for the study of gene family evolution. Bioinformatics, 22(10), 1269-1271. https://doi.org/10.1093/bioinformatics/btl097

Dorofeyev, V. I. (2004). System of family Cruciferae B. Juss.(Brassicaceae Burnett). Turczaninowia, 7(3), 43-52.

Dudchenko, O., Batra, S. S., Omer, A. D., Nyquist, S. K., Hoeger, M., Durand, N. C., & Aiden, A. P. (2017). De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 356(6333), 92-95.

Dudchenko, O., Shamim, M. S., Batra, S., Durand, N. C., Musial, N. T., Mostofa, R., Stamenova, E. (2018). The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. Biorxiv, 254797.

Durand, N. C., Robinson, J. T., Shamim, M. S., Machol, I., Mesirov, J. P., Lander, E. S., & Aiden, E. L. (2016). Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Systems, 3(1), 99-101. https://doi.org/10.1016/j.cels.2015.07.012

Durand, N. C., Shamim, M. S., Machol, I., Rao, S. S. P., Huntley, M. H., Lander, E. S., & Aiden, E. L. (2016). Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Systems, 3(1), 95-98. https://doi.org/10.1016/j.cels.2016.07.002

Ellinghaus, D., Kurtz, S., & Willhoeft, U. (2008). LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics, 9(1), 18. https://doi.org/10.1186/1471-2105-9-18

Emms, D. M. (2018). STAG: Species Tree Inference from All Genes. BioRxiv, 267914.

Emms, D. M., & Kelly, S. (2019). OrthoFinder: Phylogenetic orthology inference for comparative genomics. Genome Biology, 20(1). https://doi.org/10.1186/s13059-019-1832-y

Geiser, C., Mandáková, T., Arrigo, N., Lysak, M. A., & Parisod, C. (2016). Repeated whole-genome duplication, karyotype reshuffling, and biased retention of stress-responding genes in buckler mustard. The Plant Cell, 28(1), 17-27. https://doi.org/10.1105/tpc.15.00791

German, D. A., & Al-Shehbaz, I. A. (2008). Five additional tribes (Aphragmeae, Biscutelleae, Calepineae, Conringieae, and Erysimeae) in the Brassicaceae (Cruciferae). Harvard Papers in Botany, 13(1), 165-170. https://doi.org/10.3100/1043-4534(2008)13[165:FATABC]2.0.CO;2

Guo, X., Liu, J., Hao, G., Zhang, L., Mao, K., Wang, X., Zhang, D., Ma, T., Hu, Q., Al-Shehbaz, I. A., & Koch, M. A. (2017). Plastome phylogeny and early diversification of Brassicaceae. BMC Genomics, 18(1), 176. https://doi.org/10.1186/s12864-017-3555-3

Haas, B. J., Delcher, A. L., Mount, S. M., Wortman, J. R., Smith, R. K. Jr, Hannick, L. I., & Town, C. D. (2003). Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Research, 31(19), 5654-5666. https://doi.org/10.1093/nar/gkg770

Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., Couger, M. B., Eccles, D., Li, B. O., Lieber, M., MacManes, M. D., Ott, M., Orvis, J., Pochet, N., Strozzi, F., Weeks, N., Westerman, R., William, T., Dewey, C. N., … Regev, A. (2013). De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols, 8(8), 1494. https://doi.org/10.1038/nprot.2013.084

Haas, B. J., Salzberg, S. L., Zhu, W., Pertea, M., Allen, J. E., Orvis, J., White, O., Buell, C. R., & Wortman, J. R. (2008). Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology, 9(1), R7. https://doi.org/10.1186/gb-2008-9-1-r7

Hedges, S. B., Dudley, J., & Kumar, S. (2006). TimeTree: A public knowledge-base of divergence times among organisms. Bioinformatics, 22(23), 2971-2972. https://doi.org/10.1093/bioinformatics/btl505

Huang, C.-H., Sun, R., Hu, Y. I., Zeng, L., Zhang, N., Cai, L., Zhang, Q., Koch, M. A., Al-Shehbaz, I., Edger, P. P., Pires, J. C., Tan, D.-Y., Zhong, Y., & Ma, H. (2016). Resolution of brassicaceae phylogeny using nuclear genes uncovers nested radiations and supports convergent morphological evolution. Molecular Biology and Evolution, 33(2), 394-412. https://doi.org/10.1093/molbev/msv226

Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., & Tanabe, M. (2012). KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Research, 40(D1), D109-D114. https://doi.org/10.1093/nar/gkr988

Kang, M., Wu, H., Yang, Q., Huang, L. I., Hu, Q., Ma, T., Li, Z., & Liu, J. (2020). A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine. Horticulture Research, 7(1), 1-10. https://doi.org/10.1038/s41438-020-0240-5

Kang, Y. J., Kim, S. K., Kim, M. Y., Lestari, P., Kim, K. H., Ha, B.-K., Jun, T. H., Hwang, W. J., Lee, T., Lee, J., Shim, S., Yoon, M. Y., Jang, Y. E., Han, K. S., Taeprayoon, P., Yoon, N. A., Somta, P., Tanya, P., Kim, K. S., … Lee, S.-H. (2014). Genome sequence of mungbean and insights into evolution within Vigna species. Nature Communications, 5, 5443. https://doi.org/10.1038/ncomms6443

Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution, 30(4), 772-780. https://doi.org/10.1093/molbev/mst010

Kiefer, M., Schmickl, R., German, D. A., Mandáková, T., Lysak, M. A., Al-Shehbaz, I. A., Franzke, A., Mummenhoff, K., Stamatakis, A., & Koch, M. A. (2014). BrassiBase: Introduction to a novel knowledge database on Brassicaceae evolution. Plant and Cell Physiology, 55(1), e3. https://doi.org/10.1093/pcp/pct158

Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., & Phillippy, A. M. (2017). Canu: Scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research, 27(5), 722-736.

Lv, H., Fang, Z., Yang, L., Zhang, Y., & Wang, Y. (2020). An update on the arsenal: Mining resistance genes for disease management of Brassica crops in the genomic era. Horticulture Research, 7(1), 1-18.

Lysak, M. A. (2014). Live and let die: Centromere loss during evolution of plant chromosomes. New Phytologist, 203(4), 1082-1089.

Lysak, M. A., Mandáková, T., & Schranz, M. E. (2016). Comparative paleogenomics of crucifers: Ancestral genomic blocks revisited. Current Opinion in Plant Biology, 30, 108-115.

Majoros, W. H., Pertea, M., & Salzberg, S. L. (2004). TigrScan and GlimmerHMM: Two open source ab initio eukaryotic gene-finders. Bioinformatics, 20(16), 2878-2879.

Mandáková, T., Guo, X., Özüdoğru, B., Mummenhoff, K., & Lysak, M. A. (2018). Hybridization-facilitated genome merger and repeated chromosome fusion after 8 million years. Plant Journal, 96(4), 748-760.

Mandáková, T., & Lysak, M. A. (2008). Chromosomal phylogeny and karyotype evolution in x= 7 crucifer species (Brassicaceae). The Plant Cell, 20(10), 2559-2570.

Mandáková, T., & Lysak, M. A. (2016a). Painting of Arabidopsis chromosomes with chromosome-specific BAC clones. Current Protocols in Plant Biology, 1(2), 359-371.

Mandáková, T., & Lysak, M. A. (2016b). Chromosome preparation for cytogenetic analyses in Arabidopsis. Current Protocols in Plant BiologyPlant Biology, 1(1), 43-51.

Mandáková, T., & Lysak, M. A. (2018). Post-polyploid diploidization and diversification through dysploid changes. Current Opinion in Plant Biology, 42, 55-65.

Marçais, G., & Kingsford, C. (2011). A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics, 27(6), 764-770.

Nikolov, L. A., Shushkov, P., Nevado, B., Gan, X., Al-Shehbaz, I. A., Filatov, D., Bailey, C. D., & Tsiantis, M. (2019). Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity. New Phytologist, 222(3), 1638-1651. https://doi.org/10.1111/nph.15732

Ossowski, S., Schneeberger, K., Lucas-Lledó, J. I., Warthmann, N., Clark, R. M., Shaw, R. G., & Lynch, M. (2010). The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science, 327(5961), 92-94.

Ou, S., & Jiang, N. (2018). LTR_retriever: A highly accurate and sensitive program for identification of long terminal repeat retrotransposons. Plant Physiology, 176(2), 1410-1422. https://doi.org/10.1104/pp.17.01310

Price, M. N., Dehal, P. S., & Arkin, A. P. (2010). FastTree 2 - Approximately maximum-likelihood trees for large alignments. PLoS One, 5(3). https://doi.org/10.1371/journal.pone.0009490

Price, A. L., Jones, N. C., & Pevzner, P. A. (2005). De novo identification of repeat families in large genomes. Bioinformatics, 21, i351-i358.

Ranallo-Benavidez, T. R., Jaron, K. S., & Schatz, M. C. (2020). GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nature Communications, 11(1), 1-10.

Schranz, M. E., Lysak, M. A., & Mitchell-Olds, T. (2006). The ABC’s of comparative genomics in the Brassicaceae: Building blocks of crucifer genomes. Trends in Plant Science, 11(11), 535-542. https://doi.org/10.1016/j.tplants.2006.09.002

Slater, G. S. C., & Birney, E. (2005). Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics, 6.

Stanke, M., Steinkamp, R., Waack, S., & Morgenstern, B. (2004). AUGUSTUS: A web server for gene finding in eukaryotes. Nucleic Acids Research, 32(suppl_2), W309-W312. https://doi.org/10.1093/nar/gkh379

Stebbins, G. L. (1971). Chromosomal evolution in higher plants. Edward Arnold Ltd.

Sun, H., Ding, J., Piednoël, M., & Schneeberger, K. (2018). findGSE: Estimating genome size variation within human and Arabidopsis using k-mer frequencies. Bioinformatics, 34(4), 550-557. https://doi.org/10.1093/bioinformatics/btx637

Tarailo-Graovac, M., & Chen, N. (2009). Using RepeatMasker to identify repetitive elements in genomic sequences. Current Protocols in Bioinformatics, 25(1), 4-10. https://doi.org/10.1002/0471250953.bi0410s25

van Berkum, N. L., Lieberman-Aiden, E., Williams, L., Imakaev, M., Gnirke, A., Mirny, L. A., Dekker, J., & Lander, E. S. (2010). Hi-C: A method to study the three-dimensional architecture of genomes. Journal of Visualized Experiments, 39, 1-7. https://doi.org/10.3791/1869

Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J., Young, S. K., & Earl, A. M. (2014). Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One, 9(11). https://doi.org/10.1371/journal.pone.0112963

Wang, Y., Tang, H., DeBarry, J. D., Tan, X., Li, J., Wang, X., Lee, T.-H., Jin, H., Marler, B., Guo, H., Kissinger, J. C., & Paterson, A. H. (2012). MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research, 40(7), e49. https://doi.org/10.1093/nar/gkr1293

Xu, Z., & Wang, H. (2007). LTR_FINDER: An efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Research, 35(suppl_2), W265-W268. https://doi.org/10.1093/nar/gkm286

Zdobnov, E. M., & Apweiler, R. (2001). InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17(9), 847-848. https://doi.org/10.1093/bioinformatics/17.9.847

Zhang, L., Cai, X. U., Wu, J., Liu, M., Grob, S., Cheng, F., Liang, J., Cai, C., Liu, Z., Liu, B. O., Wang, F., Li, S., Liu, F., Li, X., Cheng, L., Yang, W., Li, M.-H., Grossniklaus, U., Zheng, H., & Wang, X. (2018). Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies. Horticulture Research, 5(1), 1-11. https://doi.org/10.1038/s41438-018-0071-9

Zhou, T. Y. (2001). Brassicaceae. Flora of China, 8, 1-193.

Celebrating Mendel, McClintock, and Darlington: On end-to-end chromosome fusions and nested chromosome fusions

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